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19 34 T cell receptor protein_type Hotspot autoimmune T cell receptor binding underlies pathogen and insulin peptide cross-reactivity TITLE |
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66 73 insulin chemical Hotspot autoimmune T cell receptor binding underlies pathogen and insulin peptide cross-reactivity TITLE |
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46 69 T cell antigen receptor complex_assembly However, the mechanisms that allow the clonal T cell antigen receptor (TCR) to functionally engage multiple peptide–major histocompatibility complexes (pMHC) are unclear. ABSTRACT |
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71 74 TCR complex_assembly However, the mechanisms that allow the clonal T cell antigen receptor (TCR) to functionally engage multiple peptide–major histocompatibility complexes (pMHC) are unclear. ABSTRACT |
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108 150 peptide–major histocompatibility complexes complex_assembly However, the mechanisms that allow the clonal T cell antigen receptor (TCR) to functionally engage multiple peptide–major histocompatibility complexes (pMHC) are unclear. ABSTRACT |
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152 156 pMHC complex_assembly However, the mechanisms that allow the clonal T cell antigen receptor (TCR) to functionally engage multiple peptide–major histocompatibility complexes (pMHC) are unclear. ABSTRACT |
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49 54 human species Here, we studied multiligand discrimination by a human, preproinsulin reactive, MHC class-I–restricted CD8+ T cell clone (1E6) that can recognize over 1 million different peptides. ABSTRACT |
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56 69 preproinsulin protein Here, we studied multiligand discrimination by a human, preproinsulin reactive, MHC class-I–restricted CD8+ T cell clone (1E6) that can recognize over 1 million different peptides. ABSTRACT |
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80 83 MHC complex_assembly Here, we studied multiligand discrimination by a human, preproinsulin reactive, MHC class-I–restricted CD8+ T cell clone (1E6) that can recognize over 1 million different peptides. ABSTRACT |
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29 39 structures evidence We generated high-resolution structures of the 1E6 TCR bound to 7 altered peptide ligands, including a pathogen-derived peptide that was an order of magnitude more potent than the natural self-peptide. ABSTRACT |
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47 54 1E6 TCR complex_assembly We generated high-resolution structures of the 1E6 TCR bound to 7 altered peptide ligands, including a pathogen-derived peptide that was an order of magnitude more potent than the natural self-peptide. ABSTRACT |
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55 63 bound to protein_state We generated high-resolution structures of the 1E6 TCR bound to 7 altered peptide ligands, including a pathogen-derived peptide that was an order of magnitude more potent than the natural self-peptide. ABSTRACT |
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66 89 altered peptide ligands chemical We generated high-resolution structures of the 1E6 TCR bound to 7 altered peptide ligands, including a pathogen-derived peptide that was an order of magnitude more potent than the natural self-peptide. ABSTRACT |
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20 30 structures evidence Evaluation of these structures demonstrated that binding was stabilized through a conserved lock-and-key–like minimal binding footprint that enables 1E6 TCR to tolerate vast numbers of substitutions outside of this so-called hotspot. ABSTRACT |
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149 156 1E6 TCR complex_assembly Evaluation of these structures demonstrated that binding was stabilized through a conserved lock-and-key–like minimal binding footprint that enables 1E6 TCR to tolerate vast numbers of substitutions outside of this so-called hotspot. ABSTRACT |
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30 37 1E6 TCR complex_assembly Highly potent antigens of the 1E6 TCR engaged with a strong antipathogen-like binding affinity |
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60 94 antipathogen-like binding affinity evidence Highly potent antigens of the 1E6 TCR engaged with a strong antipathogen-like binding affinity |
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150 174 major histocompatibility complex_assembly T cells perform an essential role in adaptive immunity by interrogating the host proteome for anomalies, classically by recognizing peptides bound in major histocompatibility (MHC) molecules at the cell surface. INTRO |
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176 179 MHC complex_assembly T cells perform an essential role in adaptive immunity by interrogating the host proteome for anomalies, classically by recognizing peptides bound in major histocompatibility (MHC) molecules at the cell surface. INTRO |
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64 79 highly variable protein_state Recent data supports the notion that, to perform this role, the highly variable αβ T cell antigen receptor (TCR) must be able to recognize thousands, if not millions, of different peptide ligands. INTRO |
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80 106 αβ T cell antigen receptor complex_assembly Recent data supports the notion that, to perform this role, the highly variable αβ T cell antigen receptor (TCR) must be able to recognize thousands, if not millions, of different peptide ligands. INTRO |
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108 111 TCR complex_assembly Recent data supports the notion that, to perform this role, the highly variable αβ T cell antigen receptor (TCR) must be able to recognize thousands, if not millions, of different peptide ligands. INTRO |
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69 73 TCRs complex_assembly This ability is required to enable the estimated 25 million distinct TCRs expressed in humans to provide effective immune coverage against all possible foreign peptide antigens. INTRO |
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87 93 humans species This ability is required to enable the estimated 25 million distinct TCRs expressed in humans to provide effective immune coverage against all possible foreign peptide antigens. INTRO |
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29 33 TCRs complex_assembly Several mechanisms, by which TCRs could bind to a large number of different peptide-MHC (pMHC), have been proposed. INTRO |
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76 87 peptide-MHC complex_assembly Several mechanisms, by which TCRs could bind to a large number of different peptide-MHC (pMHC), have been proposed. INTRO |
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89 93 pMHC complex_assembly Several mechanisms, by which TCRs could bind to a large number of different peptide-MHC (pMHC), have been proposed. INTRO |
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0 10 Structures evidence Structures of unligated and ligated TCRs have shown that the TCR complementarity determining region (CDR) loops can be flexible, perhaps enabling peptide binding using different loop conformations. INTRO |
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14 23 unligated protein_state Structures of unligated and ligated TCRs have shown that the TCR complementarity determining region (CDR) loops can be flexible, perhaps enabling peptide binding using different loop conformations. INTRO |
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28 35 ligated protein_state Structures of unligated and ligated TCRs have shown that the TCR complementarity determining region (CDR) loops can be flexible, perhaps enabling peptide binding using different loop conformations. INTRO |
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36 40 TCRs complex_assembly Structures of unligated and ligated TCRs have shown that the TCR complementarity determining region (CDR) loops can be flexible, perhaps enabling peptide binding using different loop conformations. INTRO |
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61 64 TCR complex_assembly Structures of unligated and ligated TCRs have shown that the TCR complementarity determining region (CDR) loops can be flexible, perhaps enabling peptide binding using different loop conformations. INTRO |
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65 99 complementarity determining region structure_element Structures of unligated and ligated TCRs have shown that the TCR complementarity determining region (CDR) loops can be flexible, perhaps enabling peptide binding using different loop conformations. INTRO |
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101 104 CDR structure_element Structures of unligated and ligated TCRs have shown that the TCR complementarity determining region (CDR) loops can be flexible, perhaps enabling peptide binding using different loop conformations. INTRO |
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106 111 loops structure_element Structures of unligated and ligated TCRs have shown that the TCR complementarity determining region (CDR) loops can be flexible, perhaps enabling peptide binding using different loop conformations. INTRO |
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178 182 loop structure_element Structures of unligated and ligated TCRs have shown that the TCR complementarity determining region (CDR) loops can be flexible, perhaps enabling peptide binding using different loop conformations. INTRO |
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5 8 MHC complex_assembly Both MHC and peptide have also been shown to undergo structural changes upon TCR binding, mediating an induced fit between the TCR and pMHC. INTRO |
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13 20 peptide chemical Both MHC and peptide have also been shown to undergo structural changes upon TCR binding, mediating an induced fit between the TCR and pMHC. INTRO |
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77 80 TCR complex_assembly Both MHC and peptide have also been shown to undergo structural changes upon TCR binding, mediating an induced fit between the TCR and pMHC. INTRO |
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127 130 TCR complex_assembly Both MHC and peptide have also been shown to undergo structural changes upon TCR binding, mediating an induced fit between the TCR and pMHC. INTRO |
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135 139 pMHC complex_assembly Both MHC and peptide have also been shown to undergo structural changes upon TCR binding, mediating an induced fit between the TCR and pMHC. INTRO |
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29 35 murine taxonomy_domain Other studies, mainly in the murine system, have demonstrated that the same TCR can interact with different pMHCs using a common or divergent modality. INTRO |
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76 79 TCR complex_assembly Other studies, mainly in the murine system, have demonstrated that the same TCR can interact with different pMHCs using a common or divergent modality. INTRO |
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108 113 pMHCs complex_assembly Other studies, mainly in the murine system, have demonstrated that the same TCR can interact with different pMHCs using a common or divergent modality. INTRO |
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24 30 murine taxonomy_domain Recent studies in model murine systems demonstrate that TCR cross-reactivity can be governed by recognition of a conserved region in the peptide that allows tolerance of peptide sequence variation outside of this hotspot. INTRO |
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56 59 TCR complex_assembly Recent studies in model murine systems demonstrate that TCR cross-reactivity can be governed by recognition of a conserved region in the peptide that allows tolerance of peptide sequence variation outside of this hotspot. INTRO |
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34 39 human species We recently reported that the 1E6 human CD8+ T cell clone — which mediates the destruction of β cells through the recognition of a major, HLA-A*0201–restricted, preproinsulin signal peptide (ALWGPDPAAA15–24) — can recognize upwards of 1 million different peptides. INTRO |
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138 148 HLA-A*0201 protein We recently reported that the 1E6 human CD8+ T cell clone — which mediates the destruction of β cells through the recognition of a major, HLA-A*0201–restricted, preproinsulin signal peptide (ALWGPDPAAA15–24) — can recognize upwards of 1 million different peptides. INTRO |
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161 174 preproinsulin protein We recently reported that the 1E6 human CD8+ T cell clone — which mediates the destruction of β cells through the recognition of a major, HLA-A*0201–restricted, preproinsulin signal peptide (ALWGPDPAAA15–24) — can recognize upwards of 1 million different peptides. INTRO |
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175 189 signal peptide structure_element We recently reported that the 1E6 human CD8+ T cell clone — which mediates the destruction of β cells through the recognition of a major, HLA-A*0201–restricted, preproinsulin signal peptide (ALWGPDPAAA15–24) — can recognize upwards of 1 million different peptides. INTRO |
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191 206 ALWGPDPAAA15–24 chemical We recently reported that the 1E6 human CD8+ T cell clone — which mediates the destruction of β cells through the recognition of a major, HLA-A*0201–restricted, preproinsulin signal peptide (ALWGPDPAAA15–24) — can recognize upwards of 1 million different peptides. INTRO |
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28 49 HLA-A*0201–ALWGPDPAAA complex_assembly CD8+ T cells that recognize HLA-A*0201–ALWGPDPAAA have been shown to populate insulitic lesions in patients with type 1 diabetes (T1D). INTRO |
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25 28 TCR complex_assembly We demonstrated that the TCR from the 1E6 T cell clone bound to HLA-A*0201–ALWGPDPAAA using a limited footprint and very weak binding affinity. INTRO |
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55 63 bound to protein_state We demonstrated that the TCR from the 1E6 T cell clone bound to HLA-A*0201–ALWGPDPAAA using a limited footprint and very weak binding affinity. INTRO |
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64 85 HLA-A*0201–ALWGPDPAAA complex_assembly We demonstrated that the TCR from the 1E6 T cell clone bound to HLA-A*0201–ALWGPDPAAA using a limited footprint and very weak binding affinity. INTRO |
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126 142 binding affinity evidence We demonstrated that the TCR from the 1E6 T cell clone bound to HLA-A*0201–ALWGPDPAAA using a limited footprint and very weak binding affinity. INTRO |
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86 91 human species This first experimental evidence of a high level of CD8+ T cell cross-reactivity in a human autoimmune disease system hinted toward molecular mimicry by a more potent pathogenic peptide as a potential mechanism leading to β cell destruction. INTRO |
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9 15 solved experimental_method Here, we solved the structure of the 1E6 TCR with 7 altered peptide ligands (APLs) determined by our previously published combinatorial peptide library (CPL) screening, 2 of which mapped within human pathogens. INTRO |
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20 29 structure evidence Here, we solved the structure of the 1E6 TCR with 7 altered peptide ligands (APLs) determined by our previously published combinatorial peptide library (CPL) screening, 2 of which mapped within human pathogens. INTRO |
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37 44 1E6 TCR complex_assembly Here, we solved the structure of the 1E6 TCR with 7 altered peptide ligands (APLs) determined by our previously published combinatorial peptide library (CPL) screening, 2 of which mapped within human pathogens. INTRO |
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52 75 altered peptide ligands chemical Here, we solved the structure of the 1E6 TCR with 7 altered peptide ligands (APLs) determined by our previously published combinatorial peptide library (CPL) screening, 2 of which mapped within human pathogens. INTRO |
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77 81 APLs chemical Here, we solved the structure of the 1E6 TCR with 7 altered peptide ligands (APLs) determined by our previously published combinatorial peptide library (CPL) screening, 2 of which mapped within human pathogens. INTRO |
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122 167 combinatorial peptide library (CPL) screening experimental_method Here, we solved the structure of the 1E6 TCR with 7 altered peptide ligands (APLs) determined by our previously published combinatorial peptide library (CPL) screening, 2 of which mapped within human pathogens. INTRO |
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194 199 human species Here, we solved the structure of the 1E6 TCR with 7 altered peptide ligands (APLs) determined by our previously published combinatorial peptide library (CPL) screening, 2 of which mapped within human pathogens. INTRO |
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6 10 APLs chemical These APLs differed from the natural preproinsulin peptide by up to 7 of 10 residues. INTRO |
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37 50 preproinsulin protein These APLs differed from the natural preproinsulin peptide by up to 7 of 10 residues. INTRO |
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8 14 solved experimental_method We also solved the structure of each unligated APL to investigate whether structural changes occurred before or after binding — which, combined with an in-depth cellular and biophysical analysis of the 1E6 interaction with each APL, demonstrated the molecular mechanism mediating the high level of cross-reactivity exhibited by this preproinsulin-reactive human CD8+ T cell clone. INTRO |
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19 28 structure evidence We also solved the structure of each unligated APL to investigate whether structural changes occurred before or after binding — which, combined with an in-depth cellular and biophysical analysis of the 1E6 interaction with each APL, demonstrated the molecular mechanism mediating the high level of cross-reactivity exhibited by this preproinsulin-reactive human CD8+ T cell clone. INTRO |
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37 46 unligated protein_state We also solved the structure of each unligated APL to investigate whether structural changes occurred before or after binding — which, combined with an in-depth cellular and biophysical analysis of the 1E6 interaction with each APL, demonstrated the molecular mechanism mediating the high level of cross-reactivity exhibited by this preproinsulin-reactive human CD8+ T cell clone. INTRO |
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47 50 APL chemical We also solved the structure of each unligated APL to investigate whether structural changes occurred before or after binding — which, combined with an in-depth cellular and biophysical analysis of the 1E6 interaction with each APL, demonstrated the molecular mechanism mediating the high level of cross-reactivity exhibited by this preproinsulin-reactive human CD8+ T cell clone. INTRO |
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161 194 cellular and biophysical analysis experimental_method We also solved the structure of each unligated APL to investigate whether structural changes occurred before or after binding — which, combined with an in-depth cellular and biophysical analysis of the 1E6 interaction with each APL, demonstrated the molecular mechanism mediating the high level of cross-reactivity exhibited by this preproinsulin-reactive human CD8+ T cell clone. INTRO |
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228 231 APL chemical We also solved the structure of each unligated APL to investigate whether structural changes occurred before or after binding — which, combined with an in-depth cellular and biophysical analysis of the 1E6 interaction with each APL, demonstrated the molecular mechanism mediating the high level of cross-reactivity exhibited by this preproinsulin-reactive human CD8+ T cell clone. INTRO |
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333 346 preproinsulin protein We also solved the structure of each unligated APL to investigate whether structural changes occurred before or after binding — which, combined with an in-depth cellular and biophysical analysis of the 1E6 interaction with each APL, demonstrated the molecular mechanism mediating the high level of cross-reactivity exhibited by this preproinsulin-reactive human CD8+ T cell clone. INTRO |
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356 361 human species We also solved the structure of each unligated APL to investigate whether structural changes occurred before or after binding — which, combined with an in-depth cellular and biophysical analysis of the 1E6 interaction with each APL, demonstrated the molecular mechanism mediating the high level of cross-reactivity exhibited by this preproinsulin-reactive human CD8+ T cell clone. INTRO |
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32 36 APLs chemical The 1E6 T cell clone recognizes APLs across a large dynamic range. RESULTS |
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166 179 preproinsulin protein We have previously demonstrated that the 1E6 T cell clone can recognize over 1 million different peptides with a potency comparable with, or better than, the cognate preproinsulin peptide ALWGPDPAAA. RESULTS |
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188 198 ALWGPDPAAA chemical We have previously demonstrated that the 1E6 T cell clone can recognize over 1 million different peptides with a potency comparable with, or better than, the cognate preproinsulin peptide ALWGPDPAAA. RESULTS |
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57 61 APLs chemical From this large functional scan, we selected 7 different APLs that activated the 1E6 T cell clone across a wide (4-log) functional range (Table 1). RESULTS |
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23 33 MVWGPDPLYV chemical Two of these peptides, MVWGPDPLYV and RQFGPDWIVA (bold text signifies amino acids that are different from the index preproinsulin–derived sequence), are contained within the proteomes of the human pathogens Bacteroides fragilis/thetaiotaomicron and Clostridium asparagiforme, respectively. RESULTS |
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38 48 RQFGPDWIVA chemical Two of these peptides, MVWGPDPLYV and RQFGPDWIVA (bold text signifies amino acids that are different from the index preproinsulin–derived sequence), are contained within the proteomes of the human pathogens Bacteroides fragilis/thetaiotaomicron and Clostridium asparagiforme, respectively. RESULTS |
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116 129 preproinsulin protein Two of these peptides, MVWGPDPLYV and RQFGPDWIVA (bold text signifies amino acids that are different from the index preproinsulin–derived sequence), are contained within the proteomes of the human pathogens Bacteroides fragilis/thetaiotaomicron and Clostridium asparagiforme, respectively. RESULTS |
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191 196 human species Two of these peptides, MVWGPDPLYV and RQFGPDWIVA (bold text signifies amino acids that are different from the index preproinsulin–derived sequence), are contained within the proteomes of the human pathogens Bacteroides fragilis/thetaiotaomicron and Clostridium asparagiforme, respectively. RESULTS |
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207 244 Bacteroides fragilis/thetaiotaomicron species Two of these peptides, MVWGPDPLYV and RQFGPDWIVA (bold text signifies amino acids that are different from the index preproinsulin–derived sequence), are contained within the proteomes of the human pathogens Bacteroides fragilis/thetaiotaomicron and Clostridium asparagiforme, respectively. RESULTS |
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249 274 Clostridium asparagiforme species Two of these peptides, MVWGPDPLYV and RQFGPDWIVA (bold text signifies amino acids that are different from the index preproinsulin–derived sequence), are contained within the proteomes of the human pathogens Bacteroides fragilis/thetaiotaomicron and Clostridium asparagiforme, respectively. RESULTS |
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0 30 Competitive functional testing experimental_method Competitive functional testing revealed that the preproinsulin-derived sequence ALWGPDPAAA was one of the least potent targets for 1E6, with only the MVWGPDPLYV and YLGGPDFPTI demonstrating a similar low-activity profile in MIP-1β secretion and target killing assays (Figure 1, A and B). RESULTS |
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49 62 preproinsulin protein Competitive functional testing revealed that the preproinsulin-derived sequence ALWGPDPAAA was one of the least potent targets for 1E6, with only the MVWGPDPLYV and YLGGPDFPTI demonstrating a similar low-activity profile in MIP-1β secretion and target killing assays (Figure 1, A and B). RESULTS |
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80 90 ALWGPDPAAA chemical Competitive functional testing revealed that the preproinsulin-derived sequence ALWGPDPAAA was one of the least potent targets for 1E6, with only the MVWGPDPLYV and YLGGPDFPTI demonstrating a similar low-activity profile in MIP-1β secretion and target killing assays (Figure 1, A and B). RESULTS |
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150 160 MVWGPDPLYV chemical Competitive functional testing revealed that the preproinsulin-derived sequence ALWGPDPAAA was one of the least potent targets for 1E6, with only the MVWGPDPLYV and YLGGPDFPTI demonstrating a similar low-activity profile in MIP-1β secretion and target killing assays (Figure 1, A and B). RESULTS |
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165 175 YLGGPDFPTI chemical Competitive functional testing revealed that the preproinsulin-derived sequence ALWGPDPAAA was one of the least potent targets for 1E6, with only the MVWGPDPLYV and YLGGPDFPTI demonstrating a similar low-activity profile in MIP-1β secretion and target killing assays (Figure 1, A and B). RESULTS |
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224 230 MIP-1β protein Competitive functional testing revealed that the preproinsulin-derived sequence ALWGPDPAAA was one of the least potent targets for 1E6, with only the MVWGPDPLYV and YLGGPDFPTI demonstrating a similar low-activity profile in MIP-1β secretion and target killing assays (Figure 1, A and B). RESULTS |
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4 14 RQFGPDWIVA chemical The RQFGPDWIVA sequence (present in C. asparagiforme) activated the 1E6 T cell with around 1 log–greater potency compared with ALWGPDPAAA. RESULTS |
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36 52 C. asparagiforme species The RQFGPDWIVA sequence (present in C. asparagiforme) activated the 1E6 T cell with around 1 log–greater potency compared with ALWGPDPAAA. RESULTS |
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127 137 ALWGPDPAAA chemical The RQFGPDWIVA sequence (present in C. asparagiforme) activated the 1E6 T cell with around 1 log–greater potency compared with ALWGPDPAAA. RESULTS |
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38 48 RQFGPDFPTI chemical At the other end of the spectrum, the RQFGPDFPTI peptide stimulated MIP-1β release and killing by 1E6 at an exogenous peptide concentration 2–3 logs lower compared with ALWGPDPAAA. RESULTS |
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68 74 MIP-1β protein At the other end of the spectrum, the RQFGPDFPTI peptide stimulated MIP-1β release and killing by 1E6 at an exogenous peptide concentration 2–3 logs lower compared with ALWGPDPAAA. RESULTS |
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169 179 ALWGPDPAAA chemical At the other end of the spectrum, the RQFGPDFPTI peptide stimulated MIP-1β release and killing by 1E6 at an exogenous peptide concentration 2–3 logs lower compared with ALWGPDPAAA. RESULTS |
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55 59 pMHC complex_assembly The pattern of peptide potency was closely mirrored by pMHC tetramer staining experiments (Figure 1C and plots shown in Supplemental Figure 1 |
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60 77 tetramer staining experimental_method The pattern of peptide potency was closely mirrored by pMHC tetramer staining experiments (Figure 1C and plots shown in Supplemental Figure 1 |
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10 23 A2-RQFGPDFPTI chemical Here, the A2-RQFGPDFPTI tetramer stained 1E6 with the greatest MFI, gradually decreasing to the weakest tetramers: A2-MVWGPDPLYV and -YLGGPDFPTI. RESULTS |
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24 32 tetramer oligomeric_state Here, the A2-RQFGPDFPTI tetramer stained 1E6 with the greatest MFI, gradually decreasing to the weakest tetramers: A2-MVWGPDPLYV and -YLGGPDFPTI. RESULTS |
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104 113 tetramers oligomeric_state Here, the A2-RQFGPDFPTI tetramer stained 1E6 with the greatest MFI, gradually decreasing to the weakest tetramers: A2-MVWGPDPLYV and -YLGGPDFPTI. RESULTS |
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115 128 A2-MVWGPDPLYV chemical Here, the A2-RQFGPDFPTI tetramer stained 1E6 with the greatest MFI, gradually decreasing to the weakest tetramers: A2-MVWGPDPLYV and -YLGGPDFPTI. RESULTS |
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134 144 YLGGPDFPTI chemical Here, the A2-RQFGPDFPTI tetramer stained 1E6 with the greatest MFI, gradually decreasing to the weakest tetramers: A2-MVWGPDPLYV and -YLGGPDFPTI. RESULTS |
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55 67 thermal melt experimental_method To parallel the functional analysis, we also performed thermal melt (Tm) experiments using synchrotron radiation circular dichroism (SRCD) to investigate the stability of each APL (Figure 1D). RESULTS |
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69 71 Tm evidence To parallel the functional analysis, we also performed thermal melt (Tm) experiments using synchrotron radiation circular dichroism (SRCD) to investigate the stability of each APL (Figure 1D). RESULTS |
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91 131 synchrotron radiation circular dichroism experimental_method To parallel the functional analysis, we also performed thermal melt (Tm) experiments using synchrotron radiation circular dichroism (SRCD) to investigate the stability of each APL (Figure 1D). RESULTS |
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133 137 SRCD experimental_method To parallel the functional analysis, we also performed thermal melt (Tm) experiments using synchrotron radiation circular dichroism (SRCD) to investigate the stability of each APL (Figure 1D). RESULTS |
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176 179 APL chemical To parallel the functional analysis, we also performed thermal melt (Tm) experiments using synchrotron radiation circular dichroism (SRCD) to investigate the stability of each APL (Figure 1D). RESULTS |
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13 15 Tm evidence The range of Tm was between 49.4°C (RQFGPDWIVA) and 60.3°C (YQFGPDFPIA), with an average approximately 55°C, similar to our previous findings. RESULTS |
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36 46 RQFGPDWIVA chemical The range of Tm was between 49.4°C (RQFGPDWIVA) and 60.3°C (YQFGPDFPIA), with an average approximately 55°C, similar to our previous findings. RESULTS |
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60 70 YQFGPDFPIA chemical The range of Tm was between 49.4°C (RQFGPDWIVA) and 60.3°C (YQFGPDFPIA), with an average approximately 55°C, similar to our previous findings. RESULTS |
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74 91 tetramer staining experimental_method This pattern of stability did not correlate with the T cell activation or tetramer staining experiments, indicating that peptide binding to the MHC do not explain ligand potency. RESULTS |
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144 147 MHC complex_assembly This pattern of stability did not correlate with the T cell activation or tetramer staining experiments, indicating that peptide binding to the MHC do not explain ligand potency. RESULTS |
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4 11 1E6 TCR complex_assembly The 1E6 TCR can bind peptides with strong antipathogen-like affinities. RESULTS |
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65 69 TCRs complex_assembly We, and others, have previously demonstrated that antipathogenic TCRs tend to bind with stronger affinity compared with self-reactive TCRs, likely a consequence of the deletion of T cells with high-affinity self-reactive TCR during thymic selection. RESULTS |
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97 105 affinity evidence We, and others, have previously demonstrated that antipathogenic TCRs tend to bind with stronger affinity compared with self-reactive TCRs, likely a consequence of the deletion of T cells with high-affinity self-reactive TCR during thymic selection. RESULTS |
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134 138 TCRs complex_assembly We, and others, have previously demonstrated that antipathogenic TCRs tend to bind with stronger affinity compared with self-reactive TCRs, likely a consequence of the deletion of T cells with high-affinity self-reactive TCR during thymic selection. RESULTS |
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198 206 affinity evidence We, and others, have previously demonstrated that antipathogenic TCRs tend to bind with stronger affinity compared with self-reactive TCRs, likely a consequence of the deletion of T cells with high-affinity self-reactive TCR during thymic selection. RESULTS |
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221 224 TCR complex_assembly We, and others, have previously demonstrated that antipathogenic TCRs tend to bind with stronger affinity compared with self-reactive TCRs, likely a consequence of the deletion of T cells with high-affinity self-reactive TCR during thymic selection. RESULTS |
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35 42 1E6 TCR complex_assembly In accordance with this trend, the 1E6 TCR bound the natural preproinsulin peptide, ALWGPDPAAA, with the weakest affinity currently published for a human CD8+ T cell–derived TCR with a biologically relevant ligand (KD > 200 μM |
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43 48 bound protein_state In accordance with this trend, the 1E6 TCR bound the natural preproinsulin peptide, ALWGPDPAAA, with the weakest affinity currently published for a human CD8+ T cell–derived TCR with a biologically relevant ligand (KD > 200 μM |
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61 74 preproinsulin protein In accordance with this trend, the 1E6 TCR bound the natural preproinsulin peptide, ALWGPDPAAA, with the weakest affinity currently published for a human CD8+ T cell–derived TCR with a biologically relevant ligand (KD > 200 μM |
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84 94 ALWGPDPAAA chemical In accordance with this trend, the 1E6 TCR bound the natural preproinsulin peptide, ALWGPDPAAA, with the weakest affinity currently published for a human CD8+ T cell–derived TCR with a biologically relevant ligand (KD > 200 μM |
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113 121 affinity evidence In accordance with this trend, the 1E6 TCR bound the natural preproinsulin peptide, ALWGPDPAAA, with the weakest affinity currently published for a human CD8+ T cell–derived TCR with a biologically relevant ligand (KD > 200 μM |
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148 153 human species In accordance with this trend, the 1E6 TCR bound the natural preproinsulin peptide, ALWGPDPAAA, with the weakest affinity currently published for a human CD8+ T cell–derived TCR with a biologically relevant ligand (KD > 200 μM |
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174 177 TCR complex_assembly In accordance with this trend, the 1E6 TCR bound the natural preproinsulin peptide, ALWGPDPAAA, with the weakest affinity currently published for a human CD8+ T cell–derived TCR with a biologically relevant ligand (KD > 200 μM |
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215 217 KD evidence In accordance with this trend, the 1E6 TCR bound the natural preproinsulin peptide, ALWGPDPAAA, with the weakest affinity currently published for a human CD8+ T cell–derived TCR with a biologically relevant ligand (KD > 200 μM |
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228 230 KD evidence In accordance with this trend, the 1E6 TCR bound the natural preproinsulin peptide, ALWGPDPAAA, with the weakest affinity currently published for a human CD8+ T cell–derived TCR with a biologically relevant ligand (KD > 200 μM |
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232 260 equilibrium binding constant evidence In accordance with this trend, the 1E6 TCR bound the natural preproinsulin peptide, ALWGPDPAAA, with the weakest affinity currently published for a human CD8+ T cell–derived TCR with a biologically relevant ligand (KD > 200 μM |
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0 25 Surface plasmon resonance experimental_method Surface plasmon resonance (SPR) analysis of the 1E6 TCR–pMHC interaction for all 7 APLs (Figure 2, A–H) demonstrated that stronger binding affinity (represented as ΔG°, kcal/mol) correlated well with the EC50 values (peptide concentration required to reach half-maximal 1E6 T cell killing) for each ligand, demonstrated by a Pearson’s correlation analysis value of 0.8 (P = 0.01) (Figure 2I). RESULTS |
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27 30 SPR experimental_method Surface plasmon resonance (SPR) analysis of the 1E6 TCR–pMHC interaction for all 7 APLs (Figure 2, A–H) demonstrated that stronger binding affinity (represented as ΔG°, kcal/mol) correlated well with the EC50 values (peptide concentration required to reach half-maximal 1E6 T cell killing) for each ligand, demonstrated by a Pearson’s correlation analysis value of 0.8 (P = 0.01) (Figure 2I). RESULTS |
|
48 55 1E6 TCR complex_assembly Surface plasmon resonance (SPR) analysis of the 1E6 TCR–pMHC interaction for all 7 APLs (Figure 2, A–H) demonstrated that stronger binding affinity (represented as ΔG°, kcal/mol) correlated well with the EC50 values (peptide concentration required to reach half-maximal 1E6 T cell killing) for each ligand, demonstrated by a Pearson’s correlation analysis value of 0.8 (P = 0.01) (Figure 2I). RESULTS |
|
56 60 pMHC complex_assembly Surface plasmon resonance (SPR) analysis of the 1E6 TCR–pMHC interaction for all 7 APLs (Figure 2, A–H) demonstrated that stronger binding affinity (represented as ΔG°, kcal/mol) correlated well with the EC50 values (peptide concentration required to reach half-maximal 1E6 T cell killing) for each ligand, demonstrated by a Pearson’s correlation analysis value of 0.8 (P = 0.01) (Figure 2I). RESULTS |
|
83 87 APLs chemical Surface plasmon resonance (SPR) analysis of the 1E6 TCR–pMHC interaction for all 7 APLs (Figure 2, A–H) demonstrated that stronger binding affinity (represented as ΔG°, kcal/mol) correlated well with the EC50 values (peptide concentration required to reach half-maximal 1E6 T cell killing) for each ligand, demonstrated by a Pearson’s correlation analysis value of 0.8 (P = 0.01) (Figure 2I). RESULTS |
|
131 147 binding affinity evidence Surface plasmon resonance (SPR) analysis of the 1E6 TCR–pMHC interaction for all 7 APLs (Figure 2, A–H) demonstrated that stronger binding affinity (represented as ΔG°, kcal/mol) correlated well with the EC50 values (peptide concentration required to reach half-maximal 1E6 T cell killing) for each ligand, demonstrated by a Pearson’s correlation analysis value of 0.8 (P = 0.01) (Figure 2I). RESULTS |
|
164 167 ΔG° evidence Surface plasmon resonance (SPR) analysis of the 1E6 TCR–pMHC interaction for all 7 APLs (Figure 2, A–H) demonstrated that stronger binding affinity (represented as ΔG°, kcal/mol) correlated well with the EC50 values (peptide concentration required to reach half-maximal 1E6 T cell killing) for each ligand, demonstrated by a Pearson’s correlation analysis value of 0.8 (P = 0.01) (Figure 2I). RESULTS |
|
204 208 EC50 evidence Surface plasmon resonance (SPR) analysis of the 1E6 TCR–pMHC interaction for all 7 APLs (Figure 2, A–H) demonstrated that stronger binding affinity (represented as ΔG°, kcal/mol) correlated well with the EC50 values (peptide concentration required to reach half-maximal 1E6 T cell killing) for each ligand, demonstrated by a Pearson’s correlation analysis value of 0.8 (P = 0.01) (Figure 2I). RESULTS |
|
325 355 Pearson’s correlation analysis experimental_method Surface plasmon resonance (SPR) analysis of the 1E6 TCR–pMHC interaction for all 7 APLs (Figure 2, A–H) demonstrated that stronger binding affinity (represented as ΔG°, kcal/mol) correlated well with the EC50 values (peptide concentration required to reach half-maximal 1E6 T cell killing) for each ligand, demonstrated by a Pearson’s correlation analysis value of 0.8 (P = 0.01) (Figure 2I). RESULTS |
|
121 131 affinities evidence It should be noted that this correlation, although consistent with the T cell killing experiments, uses only approximate affinities calculated for the 2 weakest ligands. RESULTS |
|
75 95 TCR binding affinity evidence First, the 1E6 T cell could still functionally respond to peptide when the TCR binding affinity was extremely weak, e.g., the 1E6 TCR binding affinity for the A2-MVWGPDPLYV peptide was KD = ~600 μM. Second, the 1E6 TCR bound to A2-RQFGPDFPTI with KD = 0.5 μM, equivalent to the binding affinity of the very strongest antipathogen TCRs. RESULTS |
|
126 150 1E6 TCR binding affinity evidence First, the 1E6 T cell could still functionally respond to peptide when the TCR binding affinity was extremely weak, e.g., the 1E6 TCR binding affinity for the A2-MVWGPDPLYV peptide was KD = ~600 μM. Second, the 1E6 TCR bound to A2-RQFGPDFPTI with KD = 0.5 μM, equivalent to the binding affinity of the very strongest antipathogen TCRs. RESULTS |
|
159 172 A2-MVWGPDPLYV chemical First, the 1E6 T cell could still functionally respond to peptide when the TCR binding affinity was extremely weak, e.g., the 1E6 TCR binding affinity for the A2-MVWGPDPLYV peptide was KD = ~600 μM. Second, the 1E6 TCR bound to A2-RQFGPDFPTI with KD = 0.5 μM, equivalent to the binding affinity of the very strongest antipathogen TCRs. RESULTS |
|
185 187 KD evidence First, the 1E6 T cell could still functionally respond to peptide when the TCR binding affinity was extremely weak, e.g., the 1E6 TCR binding affinity for the A2-MVWGPDPLYV peptide was KD = ~600 μM. Second, the 1E6 TCR bound to A2-RQFGPDFPTI with KD = 0.5 μM, equivalent to the binding affinity of the very strongest antipathogen TCRs. RESULTS |
|
211 218 1E6 TCR complex_assembly First, the 1E6 T cell could still functionally respond to peptide when the TCR binding affinity was extremely weak, e.g., the 1E6 TCR binding affinity for the A2-MVWGPDPLYV peptide was KD = ~600 μM. Second, the 1E6 TCR bound to A2-RQFGPDFPTI with KD = 0.5 μM, equivalent to the binding affinity of the very strongest antipathogen TCRs. RESULTS |
|
219 227 bound to protein_state First, the 1E6 T cell could still functionally respond to peptide when the TCR binding affinity was extremely weak, e.g., the 1E6 TCR binding affinity for the A2-MVWGPDPLYV peptide was KD = ~600 μM. Second, the 1E6 TCR bound to A2-RQFGPDFPTI with KD = 0.5 μM, equivalent to the binding affinity of the very strongest antipathogen TCRs. RESULTS |
|
228 241 A2-RQFGPDFPTI chemical First, the 1E6 T cell could still functionally respond to peptide when the TCR binding affinity was extremely weak, e.g., the 1E6 TCR binding affinity for the A2-MVWGPDPLYV peptide was KD = ~600 μM. Second, the 1E6 TCR bound to A2-RQFGPDFPTI with KD = 0.5 μM, equivalent to the binding affinity of the very strongest antipathogen TCRs. RESULTS |
|
247 249 KD evidence First, the 1E6 T cell could still functionally respond to peptide when the TCR binding affinity was extremely weak, e.g., the 1E6 TCR binding affinity for the A2-MVWGPDPLYV peptide was KD = ~600 μM. Second, the 1E6 TCR bound to A2-RQFGPDFPTI with KD = 0.5 μM, equivalent to the binding affinity of the very strongest antipathogen TCRs. RESULTS |
|
278 294 binding affinity evidence First, the 1E6 T cell could still functionally respond to peptide when the TCR binding affinity was extremely weak, e.g., the 1E6 TCR binding affinity for the A2-MVWGPDPLYV peptide was KD = ~600 μM. Second, the 1E6 TCR bound to A2-RQFGPDFPTI with KD = 0.5 μM, equivalent to the binding affinity of the very strongest antipathogen TCRs. RESULTS |
|
330 334 TCRs complex_assembly First, the 1E6 T cell could still functionally respond to peptide when the TCR binding affinity was extremely weak, e.g., the 1E6 TCR binding affinity for the A2-MVWGPDPLYV peptide was KD = ~600 μM. Second, the 1E6 TCR bound to A2-RQFGPDFPTI with KD = 0.5 μM, equivalent to the binding affinity of the very strongest antipathogen TCRs. RESULTS |
|
11 18 1E6 TCR complex_assembly Third, the 1E6 TCR bound to A2-RQFGPDWIVA peptide, within the C. asparagiforme proteome, with approximately 4-fold stronger affinity than A2-ALWGPDPAAA, demonstrating the potential for a pathogen-derived antigen to initiate a response to the self-derived sequence. RESULTS |
|
19 27 bound to protein_state Third, the 1E6 TCR bound to A2-RQFGPDWIVA peptide, within the C. asparagiforme proteome, with approximately 4-fold stronger affinity than A2-ALWGPDPAAA, demonstrating the potential for a pathogen-derived antigen to initiate a response to the self-derived sequence. RESULTS |
|
28 41 A2-RQFGPDWIVA chemical Third, the 1E6 TCR bound to A2-RQFGPDWIVA peptide, within the C. asparagiforme proteome, with approximately 4-fold stronger affinity than A2-ALWGPDPAAA, demonstrating the potential for a pathogen-derived antigen to initiate a response to the self-derived sequence. RESULTS |
|
62 78 C. asparagiforme species Third, the 1E6 TCR bound to A2-RQFGPDWIVA peptide, within the C. asparagiforme proteome, with approximately 4-fold stronger affinity than A2-ALWGPDPAAA, demonstrating the potential for a pathogen-derived antigen to initiate a response to the self-derived sequence. RESULTS |
|
124 132 affinity evidence Third, the 1E6 TCR bound to A2-RQFGPDWIVA peptide, within the C. asparagiforme proteome, with approximately 4-fold stronger affinity than A2-ALWGPDPAAA, demonstrating the potential for a pathogen-derived antigen to initiate a response to the self-derived sequence. RESULTS |
|
138 151 A2-ALWGPDPAAA chemical Third, the 1E6 TCR bound to A2-RQFGPDWIVA peptide, within the C. asparagiforme proteome, with approximately 4-fold stronger affinity than A2-ALWGPDPAAA, demonstrating the potential for a pathogen-derived antigen to initiate a response to the self-derived sequence. RESULTS |
|
53 71 binding affinities evidence Finally, these data demonstrate the largest range of binding affinities reported for a natural, endogenous human TCR of more than 3 logs of magnitude (A2-MVWGPDPLYV vs. A2-RQFGPDFPTI). RESULTS |
|
96 106 endogenous protein_state Finally, these data demonstrate the largest range of binding affinities reported for a natural, endogenous human TCR of more than 3 logs of magnitude (A2-MVWGPDPLYV vs. A2-RQFGPDFPTI). RESULTS |
|
107 112 human species Finally, these data demonstrate the largest range of binding affinities reported for a natural, endogenous human TCR of more than 3 logs of magnitude (A2-MVWGPDPLYV vs. A2-RQFGPDFPTI). RESULTS |
|
113 116 TCR complex_assembly Finally, these data demonstrate the largest range of binding affinities reported for a natural, endogenous human TCR of more than 3 logs of magnitude (A2-MVWGPDPLYV vs. A2-RQFGPDFPTI). RESULTS |
|
151 164 A2-MVWGPDPLYV chemical Finally, these data demonstrate the largest range of binding affinities reported for a natural, endogenous human TCR of more than 3 logs of magnitude (A2-MVWGPDPLYV vs. A2-RQFGPDFPTI). RESULTS |
|
169 182 A2-RQFGPDFPTI chemical Finally, these data demonstrate the largest range of binding affinities reported for a natural, endogenous human TCR of more than 3 logs of magnitude (A2-MVWGPDPLYV vs. A2-RQFGPDFPTI). RESULTS |
|
15 23 affinity evidence To confirm the affinity spread detected by SPR, and to evaluate whether experiments performed using soluble molecules were biologically relevant to events at the T cell surface, we determined the effective 2D affinity of each APL using an adhesion frequency assay in which a human rbc coated in pMHC acted as an adhesion sensor. RESULTS |
|
43 46 SPR experimental_method To confirm the affinity spread detected by SPR, and to evaluate whether experiments performed using soluble molecules were biologically relevant to events at the T cell surface, we determined the effective 2D affinity of each APL using an adhesion frequency assay in which a human rbc coated in pMHC acted as an adhesion sensor. RESULTS |
|
206 217 2D affinity evidence To confirm the affinity spread detected by SPR, and to evaluate whether experiments performed using soluble molecules were biologically relevant to events at the T cell surface, we determined the effective 2D affinity of each APL using an adhesion frequency assay in which a human rbc coated in pMHC acted as an adhesion sensor. RESULTS |
|
226 229 APL chemical To confirm the affinity spread detected by SPR, and to evaluate whether experiments performed using soluble molecules were biologically relevant to events at the T cell surface, we determined the effective 2D affinity of each APL using an adhesion frequency assay in which a human rbc coated in pMHC acted as an adhesion sensor. RESULTS |
|
239 263 adhesion frequency assay experimental_method To confirm the affinity spread detected by SPR, and to evaluate whether experiments performed using soluble molecules were biologically relevant to events at the T cell surface, we determined the effective 2D affinity of each APL using an adhesion frequency assay in which a human rbc coated in pMHC acted as an adhesion sensor. RESULTS |
|
275 280 human species To confirm the affinity spread detected by SPR, and to evaluate whether experiments performed using soluble molecules were biologically relevant to events at the T cell surface, we determined the effective 2D affinity of each APL using an adhesion frequency assay in which a human rbc coated in pMHC acted as an adhesion sensor. RESULTS |
|
295 299 pMHC complex_assembly To confirm the affinity spread detected by SPR, and to evaluate whether experiments performed using soluble molecules were biologically relevant to events at the T cell surface, we determined the effective 2D affinity of each APL using an adhesion frequency assay in which a human rbc coated in pMHC acted as an adhesion sensor. RESULTS |
|
18 21 SPR experimental_method In agreement with SPR experiments, the range of 2D affinities we detected differed by around 3 logs, with the A2-MVWGPDPLYV generating the weakest 2D affinity (2.6 × 10–5 AcKa μm4) and A2-RQFGPDFPTI the strongest (4.5 × 10–2 AcKa μm4) (Figure 2J). RESULTS |
|
48 61 2D affinities evidence In agreement with SPR experiments, the range of 2D affinities we detected differed by around 3 logs, with the A2-MVWGPDPLYV generating the weakest 2D affinity (2.6 × 10–5 AcKa μm4) and A2-RQFGPDFPTI the strongest (4.5 × 10–2 AcKa μm4) (Figure 2J). RESULTS |
|
110 123 A2-MVWGPDPLYV chemical In agreement with SPR experiments, the range of 2D affinities we detected differed by around 3 logs, with the A2-MVWGPDPLYV generating the weakest 2D affinity (2.6 × 10–5 AcKa μm4) and A2-RQFGPDFPTI the strongest (4.5 × 10–2 AcKa μm4) (Figure 2J). RESULTS |
|
147 158 2D affinity evidence In agreement with SPR experiments, the range of 2D affinities we detected differed by around 3 logs, with the A2-MVWGPDPLYV generating the weakest 2D affinity (2.6 × 10–5 AcKa μm4) and A2-RQFGPDFPTI the strongest (4.5 × 10–2 AcKa μm4) (Figure 2J). RESULTS |
|
171 175 AcKa evidence In agreement with SPR experiments, the range of 2D affinities we detected differed by around 3 logs, with the A2-MVWGPDPLYV generating the weakest 2D affinity (2.6 × 10–5 AcKa μm4) and A2-RQFGPDFPTI the strongest (4.5 × 10–2 AcKa μm4) (Figure 2J). RESULTS |
|
185 198 A2-RQFGPDFPTI chemical In agreement with SPR experiments, the range of 2D affinities we detected differed by around 3 logs, with the A2-MVWGPDPLYV generating the weakest 2D affinity (2.6 × 10–5 AcKa μm4) and A2-RQFGPDFPTI the strongest (4.5 × 10–2 AcKa μm4) (Figure 2J). RESULTS |
|
225 229 AcKa evidence In agreement with SPR experiments, the range of 2D affinities we detected differed by around 3 logs, with the A2-MVWGPDPLYV generating the weakest 2D affinity (2.6 × 10–5 AcKa μm4) and A2-RQFGPDFPTI the strongest (4.5 × 10–2 AcKa μm4) (Figure 2J). RESULTS |
|
12 23 3D affinity evidence As with the 3D affinity measurements, the 2D affinity measurements correlated well with the EC50 values for each ligand (Figure 2K) demonstrating a strong correlation (Pearson’s correlation = 0.8, P = 0.01) between T cell antigen sensitivity and TCR binding affinity. RESULTS |
|
42 53 2D affinity evidence As with the 3D affinity measurements, the 2D affinity measurements correlated well with the EC50 values for each ligand (Figure 2K) demonstrating a strong correlation (Pearson’s correlation = 0.8, P = 0.01) between T cell antigen sensitivity and TCR binding affinity. RESULTS |
|
92 96 EC50 evidence As with the 3D affinity measurements, the 2D affinity measurements correlated well with the EC50 values for each ligand (Figure 2K) demonstrating a strong correlation (Pearson’s correlation = 0.8, P = 0.01) between T cell antigen sensitivity and TCR binding affinity. RESULTS |
|
168 189 Pearson’s correlation evidence As with the 3D affinity measurements, the 2D affinity measurements correlated well with the EC50 values for each ligand (Figure 2K) demonstrating a strong correlation (Pearson’s correlation = 0.8, P = 0.01) between T cell antigen sensitivity and TCR binding affinity. RESULTS |
|
197 198 P evidence As with the 3D affinity measurements, the 2D affinity measurements correlated well with the EC50 values for each ligand (Figure 2K) demonstrating a strong correlation (Pearson’s correlation = 0.8, P = 0.01) between T cell antigen sensitivity and TCR binding affinity. RESULTS |
|
246 266 TCR binding affinity evidence As with the 3D affinity measurements, the 2D affinity measurements correlated well with the EC50 values for each ligand (Figure 2K) demonstrating a strong correlation (Pearson’s correlation = 0.8, P = 0.01) between T cell antigen sensitivity and TCR binding affinity. RESULTS |
|
62 73 3D affinity evidence Of note, these data demonstrate a close agreement between the 3D affinity values generated using SPR and 2D affinity values generated using adhesion frequency assays. RESULTS |
|
97 100 SPR experimental_method Of note, these data demonstrate a close agreement between the 3D affinity values generated using SPR and 2D affinity values generated using adhesion frequency assays. RESULTS |
|
105 116 2D affinity evidence Of note, these data demonstrate a close agreement between the 3D affinity values generated using SPR and 2D affinity values generated using adhesion frequency assays. RESULTS |
|
4 11 1E6 TCR complex_assembly The 1E6 TCR uses a consensus binding mode to engage multiple APLs. RESULTS |
|
61 65 APLs chemical The 1E6 TCR uses a consensus binding mode to engage multiple APLs. RESULTS |
|
13 22 structure evidence Our previous structure of the 1E6-A2-ALWGPDPAAA complex demonstrated a limited binding footprint between the TCR and pMHC. RESULTS |
|
30 47 1E6-A2-ALWGPDPAAA complex_assembly Our previous structure of the 1E6-A2-ALWGPDPAAA complex demonstrated a limited binding footprint between the TCR and pMHC. RESULTS |
|
79 96 binding footprint site Our previous structure of the 1E6-A2-ALWGPDPAAA complex demonstrated a limited binding footprint between the TCR and pMHC. RESULTS |
|
109 112 TCR complex_assembly Our previous structure of the 1E6-A2-ALWGPDPAAA complex demonstrated a limited binding footprint between the TCR and pMHC. RESULTS |
|
117 121 pMHC complex_assembly Our previous structure of the 1E6-A2-ALWGPDPAAA complex demonstrated a limited binding footprint between the TCR and pMHC. RESULTS |
|
87 103 binding affinity evidence The low number of contacts between the 2 molecules most likely contributed to the weak binding affinity of the interaction. RESULTS |
|
47 54 1E6 TCR complex_assembly In order to examine the mechanism by which the 1E6 TCR engaged a wide range of peptides with divergent binding affinities, we solved the structure of the 1E6 TCR in complex with all 7 APLs used in Figure 2. RESULTS |
|
103 121 binding affinities evidence In order to examine the mechanism by which the 1E6 TCR engaged a wide range of peptides with divergent binding affinities, we solved the structure of the 1E6 TCR in complex with all 7 APLs used in Figure 2. RESULTS |
|
126 132 solved experimental_method In order to examine the mechanism by which the 1E6 TCR engaged a wide range of peptides with divergent binding affinities, we solved the structure of the 1E6 TCR in complex with all 7 APLs used in Figure 2. RESULTS |
|
137 146 structure evidence In order to examine the mechanism by which the 1E6 TCR engaged a wide range of peptides with divergent binding affinities, we solved the structure of the 1E6 TCR in complex with all 7 APLs used in Figure 2. RESULTS |
|
154 161 1E6 TCR complex_assembly In order to examine the mechanism by which the 1E6 TCR engaged a wide range of peptides with divergent binding affinities, we solved the structure of the 1E6 TCR in complex with all 7 APLs used in Figure 2. RESULTS |
|
162 177 in complex with protein_state In order to examine the mechanism by which the 1E6 TCR engaged a wide range of peptides with divergent binding affinities, we solved the structure of the 1E6 TCR in complex with all 7 APLs used in Figure 2. RESULTS |
|
184 188 APLs chemical In order to examine the mechanism by which the 1E6 TCR engaged a wide range of peptides with divergent binding affinities, we solved the structure of the 1E6 TCR in complex with all 7 APLs used in Figure 2. RESULTS |
|
4 14 structures evidence All structures were solved in space group P1 to 2–3 Å resolution with crystallographic Rwork/Rfree ratios within accepted limits as shown in the theoretically expected distribution (ref. and Supplemental Table 1). RESULTS |
|
20 26 solved experimental_method All structures were solved in space group P1 to 2–3 Å resolution with crystallographic Rwork/Rfree ratios within accepted limits as shown in the theoretically expected distribution (ref. and Supplemental Table 1). RESULTS |
|
87 105 Rwork/Rfree ratios evidence All structures were solved in space group P1 to 2–3 Å resolution with crystallographic Rwork/Rfree ratios within accepted limits as shown in the theoretically expected distribution (ref. and Supplemental Table 1). RESULTS |
|
4 11 1E6 TCR complex_assembly The 1E6 TCR used a very similar overall binding modality to engage all of the APLs, with root mean square deviation ranging between 0.81 and 1.12 Å2 (compared with 1E6-A2-ALWGPDPAAA). RESULTS |
|
78 82 APLs chemical The 1E6 TCR used a very similar overall binding modality to engage all of the APLs, with root mean square deviation ranging between 0.81 and 1.12 Å2 (compared with 1E6-A2-ALWGPDPAAA). RESULTS |
|
89 115 root mean square deviation evidence The 1E6 TCR used a very similar overall binding modality to engage all of the APLs, with root mean square deviation ranging between 0.81 and 1.12 Å2 (compared with 1E6-A2-ALWGPDPAAA). RESULTS |
|
164 181 1E6-A2-ALWGPDPAAA complex_assembly The 1E6 TCR used a very similar overall binding modality to engage all of the APLs, with root mean square deviation ranging between 0.81 and 1.12 Å2 (compared with 1E6-A2-ALWGPDPAAA). RESULTS |
|
96 116 TCR binding affinity evidence The relatively broad range of buried surface areas (1,670–1,920 Å2) did not correlate well with TCR binding affinity (Pearson’s correlation = 0.45, P = 0.2). RESULTS |
|
118 139 Pearson’s correlation evidence The relatively broad range of buried surface areas (1,670–1,920 Å2) did not correlate well with TCR binding affinity (Pearson’s correlation = 0.45, P = 0.2). RESULTS |
|
148 149 P evidence The relatively broad range of buried surface areas (1,670–1,920 Å2) did not correlate well with TCR binding affinity (Pearson’s correlation = 0.45, P = 0.2). RESULTS |
|
4 34 surface complementarity values evidence The surface complementarity values (0.52–0.7) correlated slightly with affinity (Pearson’s correlation = 0.7, P = 0.05) but could not explain all differences in binding (Figure 3A and Table 2). RESULTS |
|
71 79 affinity evidence The surface complementarity values (0.52–0.7) correlated slightly with affinity (Pearson’s correlation = 0.7, P = 0.05) but could not explain all differences in binding (Figure 3A and Table 2). RESULTS |
|
81 102 Pearson’s correlation evidence The surface complementarity values (0.52–0.7) correlated slightly with affinity (Pearson’s correlation = 0.7, P = 0.05) but could not explain all differences in binding (Figure 3A and Table 2). RESULTS |
|
110 111 P evidence The surface complementarity values (0.52–0.7) correlated slightly with affinity (Pearson’s correlation = 0.7, P = 0.05) but could not explain all differences in binding (Figure 3A and Table 2). RESULTS |
|
4 7 TCR complex_assembly The TCR CDR loops were in a very similar position in all complexes, apart from some slight deviations in the TCR β-chain (Figure 3B) |
|
8 17 CDR loops structure_element The TCR CDR loops were in a very similar position in all complexes, apart from some slight deviations in the TCR β-chain (Figure 3B) |
|
109 112 TCR complex_assembly The TCR CDR loops were in a very similar position in all complexes, apart from some slight deviations in the TCR β-chain (Figure 3B) |
|
113 120 β-chain structure_element The TCR CDR loops were in a very similar position in all complexes, apart from some slight deviations in the TCR β-chain (Figure 3B) |
|
263 266 TCR complex_assembly The TCR CDR loops were in a very similar position in all complexes, apart from some slight deviations in the TCR β-chain (Figure 3B) |
|
13 20 1E6 TCR complex_assembly Overall, the 1E6 TCR used a canonical binding mode to engage each APL with the TCR α-chain positioned over the MHC class I (MHCI) α2-helix and the TCR β-chain over the MHCI α-1 helix, straddling the peptide cargo. RESULTS |
|
66 69 APL chemical Overall, the 1E6 TCR used a canonical binding mode to engage each APL with the TCR α-chain positioned over the MHC class I (MHCI) α2-helix and the TCR β-chain over the MHCI α-1 helix, straddling the peptide cargo. RESULTS |
|
79 82 TCR complex_assembly Overall, the 1E6 TCR used a canonical binding mode to engage each APL with the TCR α-chain positioned over the MHC class I (MHCI) α2-helix and the TCR β-chain over the MHCI α-1 helix, straddling the peptide cargo. RESULTS |
|
83 90 α-chain structure_element Overall, the 1E6 TCR used a canonical binding mode to engage each APL with the TCR α-chain positioned over the MHC class I (MHCI) α2-helix and the TCR β-chain over the MHCI α-1 helix, straddling the peptide cargo. RESULTS |
|
111 122 MHC class I complex_assembly Overall, the 1E6 TCR used a canonical binding mode to engage each APL with the TCR α-chain positioned over the MHC class I (MHCI) α2-helix and the TCR β-chain over the MHCI α-1 helix, straddling the peptide cargo. RESULTS |
|
124 128 MHCI complex_assembly Overall, the 1E6 TCR used a canonical binding mode to engage each APL with the TCR α-chain positioned over the MHC class I (MHCI) α2-helix and the TCR β-chain over the MHCI α-1 helix, straddling the peptide cargo. RESULTS |
|
130 138 α2-helix structure_element Overall, the 1E6 TCR used a canonical binding mode to engage each APL with the TCR α-chain positioned over the MHC class I (MHCI) α2-helix and the TCR β-chain over the MHCI α-1 helix, straddling the peptide cargo. RESULTS |
|
147 150 TCR complex_assembly Overall, the 1E6 TCR used a canonical binding mode to engage each APL with the TCR α-chain positioned over the MHC class I (MHCI) α2-helix and the TCR β-chain over the MHCI α-1 helix, straddling the peptide cargo. RESULTS |
|
151 158 β-chain structure_element Overall, the 1E6 TCR used a canonical binding mode to engage each APL with the TCR α-chain positioned over the MHC class I (MHCI) α2-helix and the TCR β-chain over the MHCI α-1 helix, straddling the peptide cargo. RESULTS |
|
168 172 MHCI complex_assembly Overall, the 1E6 TCR used a canonical binding mode to engage each APL with the TCR α-chain positioned over the MHC class I (MHCI) α2-helix and the TCR β-chain over the MHCI α-1 helix, straddling the peptide cargo. RESULTS |
|
173 182 α-1 helix structure_element Overall, the 1E6 TCR used a canonical binding mode to engage each APL with the TCR α-chain positioned over the MHC class I (MHCI) α2-helix and the TCR β-chain over the MHCI α-1 helix, straddling the peptide cargo. RESULTS |
|
46 56 interfaces site However, subtle differences in the respective interfaces were apparent (discussed below) and resulted in altered binding affinities of the respective complexes. RESULTS |
|
113 131 binding affinities evidence However, subtle differences in the respective interfaces were apparent (discussed below) and resulted in altered binding affinities of the respective complexes. RESULTS |
|
25 32 1E6 TCR complex_assembly Interactions between the 1E6 TCR and different APLs are focused around a conserved GPD peptide motif. RESULTS |
|
47 51 APLs chemical Interactions between the 1E6 TCR and different APLs are focused around a conserved GPD peptide motif. RESULTS |
|
73 82 conserved protein_state Interactions between the 1E6 TCR and different APLs are focused around a conserved GPD peptide motif. RESULTS |
|
83 100 GPD peptide motif structure_element Interactions between the 1E6 TCR and different APLs are focused around a conserved GPD peptide motif. RESULTS |
|
30 45 atomic analysis experimental_method We next performed an in-depth atomic analysis of the contacts between the 1E6 TCR and each APL to determine the structural basis for the altered T cell peptide sensitivities and TCR binding affinities (Table 2). RESULTS |
|
74 81 1E6 TCR complex_assembly We next performed an in-depth atomic analysis of the contacts between the 1E6 TCR and each APL to determine the structural basis for the altered T cell peptide sensitivities and TCR binding affinities (Table 2). RESULTS |
|
91 94 APL chemical We next performed an in-depth atomic analysis of the contacts between the 1E6 TCR and each APL to determine the structural basis for the altered T cell peptide sensitivities and TCR binding affinities (Table 2). RESULTS |
|
178 200 TCR binding affinities evidence We next performed an in-depth atomic analysis of the contacts between the 1E6 TCR and each APL to determine the structural basis for the altered T cell peptide sensitivities and TCR binding affinities (Table 2). RESULTS |
|
40 47 1E6 TCR complex_assembly Concomitant with our global analysis of 1E6 TCR binding to the APLs, we observed a common interaction element, consistent with our previous findings, that utilized TCR residues Tyr97α and Trp97β, forming an aromatic cap over a central GPD motif that was present in all of the APLs (Figure 4). RESULTS |
|
63 67 APLs chemical Concomitant with our global analysis of 1E6 TCR binding to the APLs, we observed a common interaction element, consistent with our previous findings, that utilized TCR residues Tyr97α and Trp97β, forming an aromatic cap over a central GPD motif that was present in all of the APLs (Figure 4). RESULTS |
|
164 167 TCR complex_assembly Concomitant with our global analysis of 1E6 TCR binding to the APLs, we observed a common interaction element, consistent with our previous findings, that utilized TCR residues Tyr97α and Trp97β, forming an aromatic cap over a central GPD motif that was present in all of the APLs (Figure 4). RESULTS |
|
177 183 Tyr97α residue_name_number Concomitant with our global analysis of 1E6 TCR binding to the APLs, we observed a common interaction element, consistent with our previous findings, that utilized TCR residues Tyr97α and Trp97β, forming an aromatic cap over a central GPD motif that was present in all of the APLs (Figure 4). RESULTS |
|
188 194 Trp97β residue_name_number Concomitant with our global analysis of 1E6 TCR binding to the APLs, we observed a common interaction element, consistent with our previous findings, that utilized TCR residues Tyr97α and Trp97β, forming an aromatic cap over a central GPD motif that was present in all of the APLs (Figure 4). RESULTS |
|
207 219 aromatic cap structure_element Concomitant with our global analysis of 1E6 TCR binding to the APLs, we observed a common interaction element, consistent with our previous findings, that utilized TCR residues Tyr97α and Trp97β, forming an aromatic cap over a central GPD motif that was present in all of the APLs (Figure 4). RESULTS |
|
235 244 GPD motif structure_element Concomitant with our global analysis of 1E6 TCR binding to the APLs, we observed a common interaction element, consistent with our previous findings, that utilized TCR residues Tyr97α and Trp97β, forming an aromatic cap over a central GPD motif that was present in all of the APLs (Figure 4). RESULTS |
|
276 280 APLs chemical Concomitant with our global analysis of 1E6 TCR binding to the APLs, we observed a common interaction element, consistent with our previous findings, that utilized TCR residues Tyr97α and Trp97β, forming an aromatic cap over a central GPD motif that was present in all of the APLs (Figure 4). RESULTS |
|
29 32 TCR complex_assembly Interactions between these 2 TCR and 3 peptide residues accounted for 41%–50% of the total contacts across all complexes (Table 2), demonstrating the conserved peptide centric binding mode utilized by the 1E6 TCR. RESULTS |
|
150 159 conserved protein_state Interactions between these 2 TCR and 3 peptide residues accounted for 41%–50% of the total contacts across all complexes (Table 2), demonstrating the conserved peptide centric binding mode utilized by the 1E6 TCR. RESULTS |
|
205 212 1E6 TCR complex_assembly Interactions between these 2 TCR and 3 peptide residues accounted for 41%–50% of the total contacts across all complexes (Table 2), demonstrating the conserved peptide centric binding mode utilized by the 1E6 TCR. RESULTS |
|
84 92 TCR-pMHC complex_assembly This fixed anchoring between the 2 molecules was important for stabilization of the TCR-pMHC complex, as — although other peptides without the ‘GDP’ motif were tested and shown to activate the 1E6 T cell clone — we were unable to measure robust affinities using SPR (data not shown). RESULTS |
|
143 154 ‘GDP’ motif structure_element This fixed anchoring between the 2 molecules was important for stabilization of the TCR-pMHC complex, as — although other peptides without the ‘GDP’ motif were tested and shown to activate the 1E6 T cell clone — we were unable to measure robust affinities using SPR (data not shown). RESULTS |
|
245 255 affinities evidence This fixed anchoring between the 2 molecules was important for stabilization of the TCR-pMHC complex, as — although other peptides without the ‘GDP’ motif were tested and shown to activate the 1E6 T cell clone — we were unable to measure robust affinities using SPR (data not shown). RESULTS |
|
262 265 SPR experimental_method This fixed anchoring between the 2 molecules was important for stabilization of the TCR-pMHC complex, as — although other peptides without the ‘GDP’ motif were tested and shown to activate the 1E6 T cell clone — we were unable to measure robust affinities using SPR (data not shown). RESULTS |
|
41 50 conserved protein_state These data support the requirement for a conserved interaction between the 1E6 TCR and the GPD motif, as we observed in our previously published 1E6-A2-ALWGPDPAAA structure. RESULTS |
|
75 82 1E6 TCR complex_assembly These data support the requirement for a conserved interaction between the 1E6 TCR and the GPD motif, as we observed in our previously published 1E6-A2-ALWGPDPAAA structure. RESULTS |
|
91 100 GPD motif structure_element These data support the requirement for a conserved interaction between the 1E6 TCR and the GPD motif, as we observed in our previously published 1E6-A2-ALWGPDPAAA structure. RESULTS |
|
145 162 1E6-A2-ALWGPDPAAA complex_assembly These data support the requirement for a conserved interaction between the 1E6 TCR and the GPD motif, as we observed in our previously published 1E6-A2-ALWGPDPAAA structure. RESULTS |
|
163 172 structure evidence These data support the requirement for a conserved interaction between the 1E6 TCR and the GPD motif, as we observed in our previously published 1E6-A2-ALWGPDPAAA structure. RESULTS |
|
33 42 conserved protein_state Focused hotspot binding around a conserved GPD motif enables the 1E6 TCR to tolerate peptide degeneracy. RESULTS |
|
43 52 GPD motif structure_element Focused hotspot binding around a conserved GPD motif enables the 1E6 TCR to tolerate peptide degeneracy. RESULTS |
|
65 72 1E6 TCR complex_assembly Focused hotspot binding around a conserved GPD motif enables the 1E6 TCR to tolerate peptide degeneracy. RESULTS |
|
13 20 1E6 TCR complex_assembly Although the 1E6 TCR formed a similar overall interaction with each APL, the stabilization between the TCR and the GPD motif enabled fine differences in the contact network with both the peptide and MHC surface that allowed discrimination between each ligand (Figure 5). RESULTS |
|
68 71 APL chemical Although the 1E6 TCR formed a similar overall interaction with each APL, the stabilization between the TCR and the GPD motif enabled fine differences in the contact network with both the peptide and MHC surface that allowed discrimination between each ligand (Figure 5). RESULTS |
|
103 106 TCR complex_assembly Although the 1E6 TCR formed a similar overall interaction with each APL, the stabilization between the TCR and the GPD motif enabled fine differences in the contact network with both the peptide and MHC surface that allowed discrimination between each ligand (Figure 5). RESULTS |
|
115 124 GPD motif structure_element Although the 1E6 TCR formed a similar overall interaction with each APL, the stabilization between the TCR and the GPD motif enabled fine differences in the contact network with both the peptide and MHC surface that allowed discrimination between each ligand (Figure 5). RESULTS |
|
157 172 contact network site Although the 1E6 TCR formed a similar overall interaction with each APL, the stabilization between the TCR and the GPD motif enabled fine differences in the contact network with both the peptide and MHC surface that allowed discrimination between each ligand (Figure 5). RESULTS |
|
187 194 peptide chemical Although the 1E6 TCR formed a similar overall interaction with each APL, the stabilization between the TCR and the GPD motif enabled fine differences in the contact network with both the peptide and MHC surface that allowed discrimination between each ligand (Figure 5). RESULTS |
|
199 210 MHC surface site Although the 1E6 TCR formed a similar overall interaction with each APL, the stabilization between the TCR and the GPD motif enabled fine differences in the contact network with both the peptide and MHC surface that allowed discrimination between each ligand (Figure 5). RESULTS |
|
17 24 1E6 TCR complex_assembly For example, the 1E6 TCR made only 47 peptide contacts with A2-MVWGPDPLYV (KD = ~600 μM) compared with 63 and 57 contacts with A2-YQFGPDFPIA (KD = 7.4 μM) and A2-RQFGPDFPTI (KD = 0.5 μM), respectively. RESULTS |
|
60 73 A2-MVWGPDPLYV chemical For example, the 1E6 TCR made only 47 peptide contacts with A2-MVWGPDPLYV (KD = ~600 μM) compared with 63 and 57 contacts with A2-YQFGPDFPIA (KD = 7.4 μM) and A2-RQFGPDFPTI (KD = 0.5 μM), respectively. RESULTS |
|
75 77 KD evidence For example, the 1E6 TCR made only 47 peptide contacts with A2-MVWGPDPLYV (KD = ~600 μM) compared with 63 and 57 contacts with A2-YQFGPDFPIA (KD = 7.4 μM) and A2-RQFGPDFPTI (KD = 0.5 μM), respectively. RESULTS |
|
127 140 A2-YQFGPDFPIA chemical For example, the 1E6 TCR made only 47 peptide contacts with A2-MVWGPDPLYV (KD = ~600 μM) compared with 63 and 57 contacts with A2-YQFGPDFPIA (KD = 7.4 μM) and A2-RQFGPDFPTI (KD = 0.5 μM), respectively. RESULTS |
|
142 144 KD evidence For example, the 1E6 TCR made only 47 peptide contacts with A2-MVWGPDPLYV (KD = ~600 μM) compared with 63 and 57 contacts with A2-YQFGPDFPIA (KD = 7.4 μM) and A2-RQFGPDFPTI (KD = 0.5 μM), respectively. RESULTS |
|
159 172 A2-RQFGPDFPTI chemical For example, the 1E6 TCR made only 47 peptide contacts with A2-MVWGPDPLYV (KD = ~600 μM) compared with 63 and 57 contacts with A2-YQFGPDFPIA (KD = 7.4 μM) and A2-RQFGPDFPTI (KD = 0.5 μM), respectively. RESULTS |
|
174 176 KD evidence For example, the 1E6 TCR made only 47 peptide contacts with A2-MVWGPDPLYV (KD = ~600 μM) compared with 63 and 57 contacts with A2-YQFGPDFPIA (KD = 7.4 μM) and A2-RQFGPDFPTI (KD = 0.5 μM), respectively. RESULTS |
|
64 84 TCR binding affinity evidence Although the number of peptide contacts was a good predictor of TCR binding affinity for some of the APLs, for others, the correlation was poor (Pearson’s correlation = 0.045, P = 0.92), possibly because of different resolutions for each complex structure. RESULTS |
|
101 105 APLs chemical Although the number of peptide contacts was a good predictor of TCR binding affinity for some of the APLs, for others, the correlation was poor (Pearson’s correlation = 0.045, P = 0.92), possibly because of different resolutions for each complex structure. RESULTS |
|
145 166 Pearson’s correlation evidence Although the number of peptide contacts was a good predictor of TCR binding affinity for some of the APLs, for others, the correlation was poor (Pearson’s correlation = 0.045, P = 0.92), possibly because of different resolutions for each complex structure. RESULTS |
|
246 255 structure evidence Although the number of peptide contacts was a good predictor of TCR binding affinity for some of the APLs, for others, the correlation was poor (Pearson’s correlation = 0.045, P = 0.92), possibly because of different resolutions for each complex structure. RESULTS |
|
17 24 1E6 TCR complex_assembly For example, the 1E6 TCR made 64 peptide contacts with A2-YLGGPDFPTI (KD = ~400 μM) compared with 43 contacts with A2-RQWGPDPAAV (KD = 7.8 μM). RESULTS |
|
55 68 A2-YLGGPDFPTI chemical For example, the 1E6 TCR made 64 peptide contacts with A2-YLGGPDFPTI (KD = ~400 μM) compared with 43 contacts with A2-RQWGPDPAAV (KD = 7.8 μM). RESULTS |
|
70 72 KD evidence For example, the 1E6 TCR made 64 peptide contacts with A2-YLGGPDFPTI (KD = ~400 μM) compared with 43 contacts with A2-RQWGPDPAAV (KD = 7.8 μM). RESULTS |
|
115 128 A2-RQWGPDPAAV chemical For example, the 1E6 TCR made 64 peptide contacts with A2-YLGGPDFPTI (KD = ~400 μM) compared with 43 contacts with A2-RQWGPDPAAV (KD = 7.8 μM). RESULTS |
|
130 132 KD evidence For example, the 1E6 TCR made 64 peptide contacts with A2-YLGGPDFPTI (KD = ~400 μM) compared with 43 contacts with A2-RQWGPDPAAV (KD = 7.8 μM). RESULTS |
|
97 98 1 residue_number The most important peptide modification in terms of generating new contacts was peptide position 1. RESULTS |
|
53 56 Arg residue_name The stronger ligands all encoded larger side chains (Arg or Tyr) at peptide position 1 (Figure 5, E–H), enabling interactions with 1E6 that were not present in the weaker APLs that lacked large side chains in this position (Figure 5, A, C, and D). RESULTS |
|
60 63 Tyr residue_name The stronger ligands all encoded larger side chains (Arg or Tyr) at peptide position 1 (Figure 5, E–H), enabling interactions with 1E6 that were not present in the weaker APLs that lacked large side chains in this position (Figure 5, A, C, and D). RESULTS |
|
85 86 1 residue_number The stronger ligands all encoded larger side chains (Arg or Tyr) at peptide position 1 (Figure 5, E–H), enabling interactions with 1E6 that were not present in the weaker APLs that lacked large side chains in this position (Figure 5, A, C, and D). RESULTS |
|
171 175 APLs chemical The stronger ligands all encoded larger side chains (Arg or Tyr) at peptide position 1 (Figure 5, E–H), enabling interactions with 1E6 that were not present in the weaker APLs that lacked large side chains in this position (Figure 5, A, C, and D). RESULTS |
|
34 41 1E6 TCR complex_assembly We have previously shown that the 1E6 TCR uses a rigid lock-and-key mechanism during binding to A2-ALWGPDPAAA. RESULTS |
|
96 109 A2-ALWGPDPAAA chemical We have previously shown that the 1E6 TCR uses a rigid lock-and-key mechanism during binding to A2-ALWGPDPAAA. RESULTS |
|
33 42 unligated protein_state These data demonstrated that the unligated structure of the 1E6 TCR was virtually identical to its ligated counterparts. RESULTS |
|
43 52 structure evidence These data demonstrated that the unligated structure of the 1E6 TCR was virtually identical to its ligated counterparts. RESULTS |
|
60 67 1E6 TCR complex_assembly These data demonstrated that the unligated structure of the 1E6 TCR was virtually identical to its ligated counterparts. RESULTS |
|
99 106 ligated protein_state These data demonstrated that the unligated structure of the 1E6 TCR was virtually identical to its ligated counterparts. RESULTS |
|
41 45 APLs chemical In order to determine whether any of the APLs required an induced fit mechanism during binding that could explain the difference in free binding energy (ΔG) between each complex (Table 2), we solved the unligated structures of all 7 APLs (the A2-ALWGPDPAAA structure has been previously published and was used in this comparison, ref.) (Figure 6 and Supplemental Table 2). RESULTS |
|
132 151 free binding energy evidence In order to determine whether any of the APLs required an induced fit mechanism during binding that could explain the difference in free binding energy (ΔG) between each complex (Table 2), we solved the unligated structures of all 7 APLs (the A2-ALWGPDPAAA structure has been previously published and was used in this comparison, ref.) (Figure 6 and Supplemental Table 2). RESULTS |
|
153 155 ΔG evidence In order to determine whether any of the APLs required an induced fit mechanism during binding that could explain the difference in free binding energy (ΔG) between each complex (Table 2), we solved the unligated structures of all 7 APLs (the A2-ALWGPDPAAA structure has been previously published and was used in this comparison, ref.) (Figure 6 and Supplemental Table 2). RESULTS |
|
192 198 solved experimental_method In order to determine whether any of the APLs required an induced fit mechanism during binding that could explain the difference in free binding energy (ΔG) between each complex (Table 2), we solved the unligated structures of all 7 APLs (the A2-ALWGPDPAAA structure has been previously published and was used in this comparison, ref.) (Figure 6 and Supplemental Table 2). RESULTS |
|
203 212 unligated protein_state In order to determine whether any of the APLs required an induced fit mechanism during binding that could explain the difference in free binding energy (ΔG) between each complex (Table 2), we solved the unligated structures of all 7 APLs (the A2-ALWGPDPAAA structure has been previously published and was used in this comparison, ref.) (Figure 6 and Supplemental Table 2). RESULTS |
|
213 223 structures evidence In order to determine whether any of the APLs required an induced fit mechanism during binding that could explain the difference in free binding energy (ΔG) between each complex (Table 2), we solved the unligated structures of all 7 APLs (the A2-ALWGPDPAAA structure has been previously published and was used in this comparison, ref.) (Figure 6 and Supplemental Table 2). RESULTS |
|
233 237 APLs chemical In order to determine whether any of the APLs required an induced fit mechanism during binding that could explain the difference in free binding energy (ΔG) between each complex (Table 2), we solved the unligated structures of all 7 APLs (the A2-ALWGPDPAAA structure has been previously published and was used in this comparison, ref.) (Figure 6 and Supplemental Table 2). RESULTS |
|
243 256 A2-ALWGPDPAAA chemical In order to determine whether any of the APLs required an induced fit mechanism during binding that could explain the difference in free binding energy (ΔG) between each complex (Table 2), we solved the unligated structures of all 7 APLs (the A2-ALWGPDPAAA structure has been previously published and was used in this comparison, ref.) (Figure 6 and Supplemental Table 2). RESULTS |
|
257 266 structure evidence In order to determine whether any of the APLs required an induced fit mechanism during binding that could explain the difference in free binding energy (ΔG) between each complex (Table 2), we solved the unligated structures of all 7 APLs (the A2-ALWGPDPAAA structure has been previously published and was used in this comparison, ref.) (Figure 6 and Supplemental Table 2). RESULTS |
|
4 13 unligated protein_state The unligated A2-MVWGPDPLYV (KD = ~600 μM) structure revealed that the side chain Tyr9 swung around 8 Å in the complex structure, subsequently making contacts with TCR residues Asp30β and Asn51β (Figure 6A and Figure 5A, respectively). RESULTS |
|
14 27 A2-MVWGPDPLYV chemical The unligated A2-MVWGPDPLYV (KD = ~600 μM) structure revealed that the side chain Tyr9 swung around 8 Å in the complex structure, subsequently making contacts with TCR residues Asp30β and Asn51β (Figure 6A and Figure 5A, respectively). RESULTS |
|
29 31 KD evidence The unligated A2-MVWGPDPLYV (KD = ~600 μM) structure revealed that the side chain Tyr9 swung around 8 Å in the complex structure, subsequently making contacts with TCR residues Asp30β and Asn51β (Figure 6A and Figure 5A, respectively). RESULTS |
|
43 52 structure evidence The unligated A2-MVWGPDPLYV (KD = ~600 μM) structure revealed that the side chain Tyr9 swung around 8 Å in the complex structure, subsequently making contacts with TCR residues Asp30β and Asn51β (Figure 6A and Figure 5A, respectively). RESULTS |
|
82 86 Tyr9 residue_name_number The unligated A2-MVWGPDPLYV (KD = ~600 μM) structure revealed that the side chain Tyr9 swung around 8 Å in the complex structure, subsequently making contacts with TCR residues Asp30β and Asn51β (Figure 6A and Figure 5A, respectively). RESULTS |
|
119 128 structure evidence The unligated A2-MVWGPDPLYV (KD = ~600 μM) structure revealed that the side chain Tyr9 swung around 8 Å in the complex structure, subsequently making contacts with TCR residues Asp30β and Asn51β (Figure 6A and Figure 5A, respectively). RESULTS |
|
164 167 TCR complex_assembly The unligated A2-MVWGPDPLYV (KD = ~600 μM) structure revealed that the side chain Tyr9 swung around 8 Å in the complex structure, subsequently making contacts with TCR residues Asp30β and Asn51β (Figure 6A and Figure 5A, respectively). RESULTS |
|
177 183 Asp30β residue_name_number The unligated A2-MVWGPDPLYV (KD = ~600 μM) structure revealed that the side chain Tyr9 swung around 8 Å in the complex structure, subsequently making contacts with TCR residues Asp30β and Asn51β (Figure 6A and Figure 5A, respectively). RESULTS |
|
188 194 Asn51β residue_name_number The unligated A2-MVWGPDPLYV (KD = ~600 μM) structure revealed that the side chain Tyr9 swung around 8 Å in the complex structure, subsequently making contacts with TCR residues Asp30β and Asn51β (Figure 6A and Figure 5A, respectively). RESULTS |
|
75 95 TCR binding affinity evidence This movement could result in an entropic penalty contributing to the weak TCR binding affinity we observed for this ligand. RESULTS |
|
84 88 Asp6 residue_name_number Additional small movements in the Cα backbone of the peptide around peptide residue Asp6 were apparent in the A2-YLGGPDFPTI (KD = ~400 μM), A2-ALWGPDPAAA (KD = ~208 μM), and A2-RQFGPDWIVA (KD = 44.4 μM) structures (Figure 6, B, C, and E). RESULTS |
|
110 123 A2-YLGGPDFPTI chemical Additional small movements in the Cα backbone of the peptide around peptide residue Asp6 were apparent in the A2-YLGGPDFPTI (KD = ~400 μM), A2-ALWGPDPAAA (KD = ~208 μM), and A2-RQFGPDWIVA (KD = 44.4 μM) structures (Figure 6, B, C, and E). RESULTS |
|
125 127 KD evidence Additional small movements in the Cα backbone of the peptide around peptide residue Asp6 were apparent in the A2-YLGGPDFPTI (KD = ~400 μM), A2-ALWGPDPAAA (KD = ~208 μM), and A2-RQFGPDWIVA (KD = 44.4 μM) structures (Figure 6, B, C, and E). RESULTS |
|
140 153 A2-ALWGPDPAAA chemical Additional small movements in the Cα backbone of the peptide around peptide residue Asp6 were apparent in the A2-YLGGPDFPTI (KD = ~400 μM), A2-ALWGPDPAAA (KD = ~208 μM), and A2-RQFGPDWIVA (KD = 44.4 μM) structures (Figure 6, B, C, and E). RESULTS |
|
155 157 KD evidence Additional small movements in the Cα backbone of the peptide around peptide residue Asp6 were apparent in the A2-YLGGPDFPTI (KD = ~400 μM), A2-ALWGPDPAAA (KD = ~208 μM), and A2-RQFGPDWIVA (KD = 44.4 μM) structures (Figure 6, B, C, and E). RESULTS |
|
174 187 A2-RQFGPDWIVA chemical Additional small movements in the Cα backbone of the peptide around peptide residue Asp6 were apparent in the A2-YLGGPDFPTI (KD = ~400 μM), A2-ALWGPDPAAA (KD = ~208 μM), and A2-RQFGPDWIVA (KD = 44.4 μM) structures (Figure 6, B, C, and E). RESULTS |
|
189 191 KD evidence Additional small movements in the Cα backbone of the peptide around peptide residue Asp6 were apparent in the A2-YLGGPDFPTI (KD = ~400 μM), A2-ALWGPDPAAA (KD = ~208 μM), and A2-RQFGPDWIVA (KD = 44.4 μM) structures (Figure 6, B, C, and E). RESULTS |
|
203 213 structures evidence Additional small movements in the Cα backbone of the peptide around peptide residue Asp6 were apparent in the A2-YLGGPDFPTI (KD = ~400 μM), A2-ALWGPDPAAA (KD = ~208 μM), and A2-RQFGPDWIVA (KD = 44.4 μM) structures (Figure 6, B, C, and E). RESULTS |
|
4 13 unligated protein_state The unligated structures of A2-AQWGPDAAA, A2-RQWGPDPAAV, A2-YQFGPDFPIA, and A2-RQFGPDFPTI were virtually identical when in complex with 1E6 (Figure 6, D and F–H). RESULTS |
|
14 24 structures evidence The unligated structures of A2-AQWGPDAAA, A2-RQWGPDPAAV, A2-YQFGPDFPIA, and A2-RQFGPDFPTI were virtually identical when in complex with 1E6 (Figure 6, D and F–H). RESULTS |
|
28 40 A2-AQWGPDAAA chemical The unligated structures of A2-AQWGPDAAA, A2-RQWGPDPAAV, A2-YQFGPDFPIA, and A2-RQFGPDFPTI were virtually identical when in complex with 1E6 (Figure 6, D and F–H). RESULTS |
|
42 55 A2-RQWGPDPAAV chemical The unligated structures of A2-AQWGPDAAA, A2-RQWGPDPAAV, A2-YQFGPDFPIA, and A2-RQFGPDFPTI were virtually identical when in complex with 1E6 (Figure 6, D and F–H). RESULTS |
|
57 70 A2-YQFGPDFPIA chemical The unligated structures of A2-AQWGPDAAA, A2-RQWGPDPAAV, A2-YQFGPDFPIA, and A2-RQFGPDFPTI were virtually identical when in complex with 1E6 (Figure 6, D and F–H). RESULTS |
|
76 89 A2-RQFGPDFPTI chemical The unligated structures of A2-AQWGPDAAA, A2-RQWGPDPAAV, A2-YQFGPDFPIA, and A2-RQFGPDFPTI were virtually identical when in complex with 1E6 (Figure 6, D and F–H). RESULTS |
|
120 135 in complex with protein_state The unligated structures of A2-AQWGPDAAA, A2-RQWGPDPAAV, A2-YQFGPDFPIA, and A2-RQFGPDFPTI were virtually identical when in complex with 1E6 (Figure 6, D and F–H). RESULTS |
|
23 35 A2-AQWGPDAAA chemical Apart from the case of A2-AQWGPDAAA (KD = 61.9 μM), these observations support the conclusion that the higher-affinity ligands required less conformational melding during binding, which could be energetically beneficial (lower entopic cost) during ligation with the 1E6 TCR. RESULTS |
|
37 39 KD evidence Apart from the case of A2-AQWGPDAAA (KD = 61.9 μM), these observations support the conclusion that the higher-affinity ligands required less conformational melding during binding, which could be energetically beneficial (lower entopic cost) during ligation with the 1E6 TCR. RESULTS |
|
110 118 affinity evidence Apart from the case of A2-AQWGPDAAA (KD = 61.9 μM), these observations support the conclusion that the higher-affinity ligands required less conformational melding during binding, which could be energetically beneficial (lower entopic cost) during ligation with the 1E6 TCR. RESULTS |
|
266 273 1E6 TCR complex_assembly Apart from the case of A2-AQWGPDAAA (KD = 61.9 μM), these observations support the conclusion that the higher-affinity ligands required less conformational melding during binding, which could be energetically beneficial (lower entopic cost) during ligation with the 1E6 TCR. RESULTS |
|
56 63 1E6 TCR complex_assembly Peptide modifications alter the interaction between the 1E6 TCR and the MHC surface. RESULTS |
|
72 83 MHC surface site Peptide modifications alter the interaction between the 1E6 TCR and the MHC surface. RESULTS |
|
35 38 TCR complex_assembly In addition to changes between the TCR and peptide component, we also observed that different APLs had different knock-on effects between the TCR and MHC. RESULTS |
|
94 98 APLs chemical In addition to changes between the TCR and peptide component, we also observed that different APLs had different knock-on effects between the TCR and MHC. RESULTS |
|
142 145 TCR complex_assembly In addition to changes between the TCR and peptide component, we also observed that different APLs had different knock-on effects between the TCR and MHC. RESULTS |
|
150 153 MHC complex_assembly In addition to changes between the TCR and peptide component, we also observed that different APLs had different knock-on effects between the TCR and MHC. RESULTS |
|
0 3 MHC complex_assembly MHC residue Arg65 that forms part of the MHC restriction triad (Arg65, Ala69, and Gln155) played a central role in TCR-MHC contacts, with Gln155 playing a less important role and Ala69 playing no role in binding at the interface (Figure 7). RESULTS |
|
12 17 Arg65 residue_name_number MHC residue Arg65 that forms part of the MHC restriction triad (Arg65, Ala69, and Gln155) played a central role in TCR-MHC contacts, with Gln155 playing a less important role and Ala69 playing no role in binding at the interface (Figure 7). RESULTS |
|
41 62 MHC restriction triad site MHC residue Arg65 that forms part of the MHC restriction triad (Arg65, Ala69, and Gln155) played a central role in TCR-MHC contacts, with Gln155 playing a less important role and Ala69 playing no role in binding at the interface (Figure 7). RESULTS |
|
64 69 Arg65 residue_name_number MHC residue Arg65 that forms part of the MHC restriction triad (Arg65, Ala69, and Gln155) played a central role in TCR-MHC contacts, with Gln155 playing a less important role and Ala69 playing no role in binding at the interface (Figure 7). RESULTS |
|
71 76 Ala69 residue_name_number MHC residue Arg65 that forms part of the MHC restriction triad (Arg65, Ala69, and Gln155) played a central role in TCR-MHC contacts, with Gln155 playing a less important role and Ala69 playing no role in binding at the interface (Figure 7). RESULTS |
|
82 88 Gln155 residue_name_number MHC residue Arg65 that forms part of the MHC restriction triad (Arg65, Ala69, and Gln155) played a central role in TCR-MHC contacts, with Gln155 playing a less important role and Ala69 playing no role in binding at the interface (Figure 7). RESULTS |
|
115 118 TCR complex_assembly MHC residue Arg65 that forms part of the MHC restriction triad (Arg65, Ala69, and Gln155) played a central role in TCR-MHC contacts, with Gln155 playing a less important role and Ala69 playing no role in binding at the interface (Figure 7). RESULTS |
|
119 122 MHC complex_assembly MHC residue Arg65 that forms part of the MHC restriction triad (Arg65, Ala69, and Gln155) played a central role in TCR-MHC contacts, with Gln155 playing a less important role and Ala69 playing no role in binding at the interface (Figure 7). RESULTS |
|
138 144 Gln155 residue_name_number MHC residue Arg65 that forms part of the MHC restriction triad (Arg65, Ala69, and Gln155) played a central role in TCR-MHC contacts, with Gln155 playing a less important role and Ala69 playing no role in binding at the interface (Figure 7). RESULTS |
|
179 184 Ala69 residue_name_number MHC residue Arg65 that forms part of the MHC restriction triad (Arg65, Ala69, and Gln155) played a central role in TCR-MHC contacts, with Gln155 playing a less important role and Ala69 playing no role in binding at the interface (Figure 7). RESULTS |
|
219 228 interface site MHC residue Arg65 that forms part of the MHC restriction triad (Arg65, Ala69, and Gln155) played a central role in TCR-MHC contacts, with Gln155 playing a less important role and Ala69 playing no role in binding at the interface (Figure 7). RESULTS |
|
22 30 affinity evidence Generally, the weaker-affinity APLs made fewer contacts with the MHC surface (27–29 interactions) compared with the stronger-affinity APLs (29–35 contacts), consistent with a better Pearson’s correlation value (0.55) compared with TCR-peptide interactions versus affinity (0.045). RESULTS |
|
31 35 APLs chemical Generally, the weaker-affinity APLs made fewer contacts with the MHC surface (27–29 interactions) compared with the stronger-affinity APLs (29–35 contacts), consistent with a better Pearson’s correlation value (0.55) compared with TCR-peptide interactions versus affinity (0.045). RESULTS |
|
65 68 MHC complex_assembly Generally, the weaker-affinity APLs made fewer contacts with the MHC surface (27–29 interactions) compared with the stronger-affinity APLs (29–35 contacts), consistent with a better Pearson’s correlation value (0.55) compared with TCR-peptide interactions versus affinity (0.045). RESULTS |
|
125 133 affinity evidence Generally, the weaker-affinity APLs made fewer contacts with the MHC surface (27–29 interactions) compared with the stronger-affinity APLs (29–35 contacts), consistent with a better Pearson’s correlation value (0.55) compared with TCR-peptide interactions versus affinity (0.045). RESULTS |
|
134 138 APLs chemical Generally, the weaker-affinity APLs made fewer contacts with the MHC surface (27–29 interactions) compared with the stronger-affinity APLs (29–35 contacts), consistent with a better Pearson’s correlation value (0.55) compared with TCR-peptide interactions versus affinity (0.045). RESULTS |
|
182 209 Pearson’s correlation value evidence Generally, the weaker-affinity APLs made fewer contacts with the MHC surface (27–29 interactions) compared with the stronger-affinity APLs (29–35 contacts), consistent with a better Pearson’s correlation value (0.55) compared with TCR-peptide interactions versus affinity (0.045). RESULTS |
|
231 234 TCR complex_assembly Generally, the weaker-affinity APLs made fewer contacts with the MHC surface (27–29 interactions) compared with the stronger-affinity APLs (29–35 contacts), consistent with a better Pearson’s correlation value (0.55) compared with TCR-peptide interactions versus affinity (0.045). RESULTS |
|
263 271 affinity evidence Generally, the weaker-affinity APLs made fewer contacts with the MHC surface (27–29 interactions) compared with the stronger-affinity APLs (29–35 contacts), consistent with a better Pearson’s correlation value (0.55) compared with TCR-peptide interactions versus affinity (0.045). RESULTS |
|
41 44 TCR complex_assembly For instance, contacts were made between TCR residue Val53β and MHC residue Gln72 in all APLs except for in the weakest affinity ligand pair, 1E6-A2-MVWGPDPLYV, in which a subtle change in TCR conformation — probably mediated by different peptide contacts — abrogated this interaction (Figure 7A). RESULTS |
|
53 59 Val53β residue_name_number For instance, contacts were made between TCR residue Val53β and MHC residue Gln72 in all APLs except for in the weakest affinity ligand pair, 1E6-A2-MVWGPDPLYV, in which a subtle change in TCR conformation — probably mediated by different peptide contacts — abrogated this interaction (Figure 7A). RESULTS |
|
64 67 MHC complex_assembly For instance, contacts were made between TCR residue Val53β and MHC residue Gln72 in all APLs except for in the weakest affinity ligand pair, 1E6-A2-MVWGPDPLYV, in which a subtle change in TCR conformation — probably mediated by different peptide contacts — abrogated this interaction (Figure 7A). RESULTS |
|
76 81 Gln72 residue_name_number For instance, contacts were made between TCR residue Val53β and MHC residue Gln72 in all APLs except for in the weakest affinity ligand pair, 1E6-A2-MVWGPDPLYV, in which a subtle change in TCR conformation — probably mediated by different peptide contacts — abrogated this interaction (Figure 7A). RESULTS |
|
89 93 APLs chemical For instance, contacts were made between TCR residue Val53β and MHC residue Gln72 in all APLs except for in the weakest affinity ligand pair, 1E6-A2-MVWGPDPLYV, in which a subtle change in TCR conformation — probably mediated by different peptide contacts — abrogated this interaction (Figure 7A). RESULTS |
|
120 128 affinity evidence For instance, contacts were made between TCR residue Val53β and MHC residue Gln72 in all APLs except for in the weakest affinity ligand pair, 1E6-A2-MVWGPDPLYV, in which a subtle change in TCR conformation — probably mediated by different peptide contacts — abrogated this interaction (Figure 7A). RESULTS |
|
142 159 1E6-A2-MVWGPDPLYV complex_assembly For instance, contacts were made between TCR residue Val53β and MHC residue Gln72 in all APLs except for in the weakest affinity ligand pair, 1E6-A2-MVWGPDPLYV, in which a subtle change in TCR conformation — probably mediated by different peptide contacts — abrogated this interaction (Figure 7A). RESULTS |
|
189 192 TCR complex_assembly For instance, contacts were made between TCR residue Val53β and MHC residue Gln72 in all APLs except for in the weakest affinity ligand pair, 1E6-A2-MVWGPDPLYV, in which a subtle change in TCR conformation — probably mediated by different peptide contacts — abrogated this interaction (Figure 7A). RESULTS |
|
50 57 entropy evidence An energetic switch from unfavorable to favorable entropy (order-to-disorder) correlates with antigen potency. RESULTS |
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20 35 contact network site Our analysis of the contact network provided some clues that could explain the different antigen potencies and binding affinities between the 1E6 TCR and the different APLs. RESULTS |
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111 129 binding affinities evidence Our analysis of the contact network provided some clues that could explain the different antigen potencies and binding affinities between the 1E6 TCR and the different APLs. RESULTS |
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142 149 1E6 TCR complex_assembly Our analysis of the contact network provided some clues that could explain the different antigen potencies and binding affinities between the 1E6 TCR and the different APLs. RESULTS |
|
168 172 APLs chemical Our analysis of the contact network provided some clues that could explain the different antigen potencies and binding affinities between the 1E6 TCR and the different APLs. RESULTS |
|
17 24 1E6 TCR complex_assembly For example, the 1E6 TCR bound to A2-RQWGPDPAAV with the third strongest affinity (KD = 7.8 μM) but made fewer contacts than with A2-ALWGPDPAAA (KD = ~208 μM) (Table 2). RESULTS |
|
25 33 bound to protein_state For example, the 1E6 TCR bound to A2-RQWGPDPAAV with the third strongest affinity (KD = 7.8 μM) but made fewer contacts than with A2-ALWGPDPAAA (KD = ~208 μM) (Table 2). RESULTS |
|
34 47 A2-RQWGPDPAAV chemical For example, the 1E6 TCR bound to A2-RQWGPDPAAV with the third strongest affinity (KD = 7.8 μM) but made fewer contacts than with A2-ALWGPDPAAA (KD = ~208 μM) (Table 2). RESULTS |
|
73 81 affinity evidence For example, the 1E6 TCR bound to A2-RQWGPDPAAV with the third strongest affinity (KD = 7.8 μM) but made fewer contacts than with A2-ALWGPDPAAA (KD = ~208 μM) (Table 2). RESULTS |
|
83 85 KD evidence For example, the 1E6 TCR bound to A2-RQWGPDPAAV with the third strongest affinity (KD = 7.8 μM) but made fewer contacts than with A2-ALWGPDPAAA (KD = ~208 μM) (Table 2). RESULTS |
|
130 143 A2-ALWGPDPAAA chemical For example, the 1E6 TCR bound to A2-RQWGPDPAAV with the third strongest affinity (KD = 7.8 μM) but made fewer contacts than with A2-ALWGPDPAAA (KD = ~208 μM) (Table 2). RESULTS |
|
145 147 KD evidence For example, the 1E6 TCR bound to A2-RQWGPDPAAV with the third strongest affinity (KD = 7.8 μM) but made fewer contacts than with A2-ALWGPDPAAA (KD = ~208 μM) (Table 2). RESULTS |
|
31 53 thermodynamic analysis experimental_method Thus, we performed an in-depth thermodynamic analysis of 6 of the ligands under investigation (Figure 8 and Supplemental Table 3). RESULTS |
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9 25 binding affinity evidence The weak binding affinity between 1E6 and A2-MVWGPDPLYV and A2-YLGGPDFPTI generated thermodynamic data that were not robust enough to gain insight into the enthalpic (ΔH°) and entropic (TΔS°) changes that contributed to the different binding affinities/potencies for each APL. RESULTS |
|
42 55 A2-MVWGPDPLYV chemical The weak binding affinity between 1E6 and A2-MVWGPDPLYV and A2-YLGGPDFPTI generated thermodynamic data that were not robust enough to gain insight into the enthalpic (ΔH°) and entropic (TΔS°) changes that contributed to the different binding affinities/potencies for each APL. RESULTS |
|
60 73 A2-YLGGPDFPTI chemical The weak binding affinity between 1E6 and A2-MVWGPDPLYV and A2-YLGGPDFPTI generated thermodynamic data that were not robust enough to gain insight into the enthalpic (ΔH°) and entropic (TΔS°) changes that contributed to the different binding affinities/potencies for each APL. RESULTS |
|
156 165 enthalpic evidence The weak binding affinity between 1E6 and A2-MVWGPDPLYV and A2-YLGGPDFPTI generated thermodynamic data that were not robust enough to gain insight into the enthalpic (ΔH°) and entropic (TΔS°) changes that contributed to the different binding affinities/potencies for each APL. RESULTS |
|
167 170 ΔH° evidence The weak binding affinity between 1E6 and A2-MVWGPDPLYV and A2-YLGGPDFPTI generated thermodynamic data that were not robust enough to gain insight into the enthalpic (ΔH°) and entropic (TΔS°) changes that contributed to the different binding affinities/potencies for each APL. RESULTS |
|
176 184 entropic evidence The weak binding affinity between 1E6 and A2-MVWGPDPLYV and A2-YLGGPDFPTI generated thermodynamic data that were not robust enough to gain insight into the enthalpic (ΔH°) and entropic (TΔS°) changes that contributed to the different binding affinities/potencies for each APL. RESULTS |
|
186 190 TΔS° evidence The weak binding affinity between 1E6 and A2-MVWGPDPLYV and A2-YLGGPDFPTI generated thermodynamic data that were not robust enough to gain insight into the enthalpic (ΔH°) and entropic (TΔS°) changes that contributed to the different binding affinities/potencies for each APL. RESULTS |
|
234 252 binding affinities evidence The weak binding affinity between 1E6 and A2-MVWGPDPLYV and A2-YLGGPDFPTI generated thermodynamic data that were not robust enough to gain insight into the enthalpic (ΔH°) and entropic (TΔS°) changes that contributed to the different binding affinities/potencies for each APL. RESULTS |
|
272 275 APL chemical The weak binding affinity between 1E6 and A2-MVWGPDPLYV and A2-YLGGPDFPTI generated thermodynamic data that were not robust enough to gain insight into the enthalpic (ΔH°) and entropic (TΔS°) changes that contributed to the different binding affinities/potencies for each APL. RESULTS |
|
12 33 free binding energies evidence The overall free binding energies (ΔG°) were between –4.4 and –8.6 kcal/mol, reflecting the wide range of TCR binding affinities we observed for the different APLs. RESULTS |
|
35 38 ΔG° evidence The overall free binding energies (ΔG°) were between –4.4 and –8.6 kcal/mol, reflecting the wide range of TCR binding affinities we observed for the different APLs. RESULTS |
|
106 128 TCR binding affinities evidence The overall free binding energies (ΔG°) were between –4.4 and –8.6 kcal/mol, reflecting the wide range of TCR binding affinities we observed for the different APLs. RESULTS |
|
159 163 APLs chemical The overall free binding energies (ΔG°) were between –4.4 and –8.6 kcal/mol, reflecting the wide range of TCR binding affinities we observed for the different APLs. RESULTS |
|
77 85 affinity evidence The enthalpic contribution in each complex did not follow a clear trend with affinity, with all but the 1E6-A2-RQFGPDFPTI interaction (ΔH° = 6.3 kcal/mol) generating an energetically favorable enthalpy value (ΔH° = –3.7 to –11.4 kcal/mol) |
|
104 121 1E6-A2-RQFGPDFPTI complex_assembly The enthalpic contribution in each complex did not follow a clear trend with affinity, with all but the 1E6-A2-RQFGPDFPTI interaction (ΔH° = 6.3 kcal/mol) generating an energetically favorable enthalpy value (ΔH° = –3.7 to –11.4 kcal/mol) |
|
135 138 ΔH° evidence The enthalpic contribution in each complex did not follow a clear trend with affinity, with all but the 1E6-A2-RQFGPDFPTI interaction (ΔH° = 6.3 kcal/mol) generating an energetically favorable enthalpy value (ΔH° = –3.7 to –11.4 kcal/mol) |
|
193 201 enthalpy evidence The enthalpic contribution in each complex did not follow a clear trend with affinity, with all but the 1E6-A2-RQFGPDFPTI interaction (ΔH° = 6.3 kcal/mol) generating an energetically favorable enthalpy value (ΔH° = –3.7 to –11.4 kcal/mol) |
|
209 212 ΔH° evidence The enthalpic contribution in each complex did not follow a clear trend with affinity, with all but the 1E6-A2-RQFGPDFPTI interaction (ΔH° = 6.3 kcal/mol) generating an energetically favorable enthalpy value (ΔH° = –3.7 to –11.4 kcal/mol) |
|
37 44 entropy evidence However, there was a clear switch in entropy between the weaker-affinity and stronger-affinity ligands, indicated by a strong Pearson’s correlation value between entropy and affinity (Pearson’s correlation value 0.93, P =0.007). RESULTS |
|
64 72 affinity evidence However, there was a clear switch in entropy between the weaker-affinity and stronger-affinity ligands, indicated by a strong Pearson’s correlation value between entropy and affinity (Pearson’s correlation value 0.93, P =0.007). RESULTS |
|
86 94 affinity evidence However, there was a clear switch in entropy between the weaker-affinity and stronger-affinity ligands, indicated by a strong Pearson’s correlation value between entropy and affinity (Pearson’s correlation value 0.93, P =0.007). RESULTS |
|
126 153 Pearson’s correlation value evidence However, there was a clear switch in entropy between the weaker-affinity and stronger-affinity ligands, indicated by a strong Pearson’s correlation value between entropy and affinity (Pearson’s correlation value 0.93, P =0.007). RESULTS |
|
162 169 entropy evidence However, there was a clear switch in entropy between the weaker-affinity and stronger-affinity ligands, indicated by a strong Pearson’s correlation value between entropy and affinity (Pearson’s correlation value 0.93, P =0.007). RESULTS |
|
174 182 affinity evidence However, there was a clear switch in entropy between the weaker-affinity and stronger-affinity ligands, indicated by a strong Pearson’s correlation value between entropy and affinity (Pearson’s correlation value 0.93, P =0.007). RESULTS |
|
184 211 Pearson’s correlation value evidence However, there was a clear switch in entropy between the weaker-affinity and stronger-affinity ligands, indicated by a strong Pearson’s correlation value between entropy and affinity (Pearson’s correlation value 0.93, P =0.007). RESULTS |
|
218 219 P evidence However, there was a clear switch in entropy between the weaker-affinity and stronger-affinity ligands, indicated by a strong Pearson’s correlation value between entropy and affinity (Pearson’s correlation value 0.93, P =0.007). RESULTS |
|
18 31 A2-ALWGPDPAAA chemical For instance, the A2-ALWGPDPAAA, A2-AQWGPDAAA, and A2-RQFGPDWIVA (KD = ~208 μM, KD = 61.9 μM, and KD = 44.4 μM, respectively) were all entropically unfavorable (TΔS° = –2.9 to –5.6 kcal/mol), indicating a net change from disorder to order. RESULTS |
|
33 45 A2-AQWGPDAAA chemical For instance, the A2-ALWGPDPAAA, A2-AQWGPDAAA, and A2-RQFGPDWIVA (KD = ~208 μM, KD = 61.9 μM, and KD = 44.4 μM, respectively) were all entropically unfavorable (TΔS° = –2.9 to –5.6 kcal/mol), indicating a net change from disorder to order. RESULTS |
|
51 64 A2-RQFGPDWIVA chemical For instance, the A2-ALWGPDPAAA, A2-AQWGPDAAA, and A2-RQFGPDWIVA (KD = ~208 μM, KD = 61.9 μM, and KD = 44.4 μM, respectively) were all entropically unfavorable (TΔS° = –2.9 to –5.6 kcal/mol), indicating a net change from disorder to order. RESULTS |
|
66 68 KD evidence For instance, the A2-ALWGPDPAAA, A2-AQWGPDAAA, and A2-RQFGPDWIVA (KD = ~208 μM, KD = 61.9 μM, and KD = 44.4 μM, respectively) were all entropically unfavorable (TΔS° = –2.9 to –5.6 kcal/mol), indicating a net change from disorder to order. RESULTS |
|
80 82 KD evidence For instance, the A2-ALWGPDPAAA, A2-AQWGPDAAA, and A2-RQFGPDWIVA (KD = ~208 μM, KD = 61.9 μM, and KD = 44.4 μM, respectively) were all entropically unfavorable (TΔS° = –2.9 to –5.6 kcal/mol), indicating a net change from disorder to order. RESULTS |
|
98 100 KD evidence For instance, the A2-ALWGPDPAAA, A2-AQWGPDAAA, and A2-RQFGPDWIVA (KD = ~208 μM, KD = 61.9 μM, and KD = 44.4 μM, respectively) were all entropically unfavorable (TΔS° = –2.9 to –5.6 kcal/mol), indicating a net change from disorder to order. RESULTS |
|
161 165 TΔS° evidence For instance, the A2-ALWGPDPAAA, A2-AQWGPDAAA, and A2-RQFGPDWIVA (KD = ~208 μM, KD = 61.9 μM, and KD = 44.4 μM, respectively) were all entropically unfavorable (TΔS° = –2.9 to –5.6 kcal/mol), indicating a net change from disorder to order. RESULTS |
|
25 33 affinity evidence Conversely, the stronger-affinity ligands A2-RQWGPDPAAV (KD = 7.8 μM), A2-YQFGPDFPIA (KD = 7.4 μM), and A2-RQFGPDFPTI (KD = 0.5 μM) exhibited favorable entropy (TΔS° = 2.2 to 14.9 kcal/mol), indicating an order-to-disorder change during binding, possibly through the expulsion of ordered water molecules. RESULTS |
|
42 55 A2-RQWGPDPAAV chemical Conversely, the stronger-affinity ligands A2-RQWGPDPAAV (KD = 7.8 μM), A2-YQFGPDFPIA (KD = 7.4 μM), and A2-RQFGPDFPTI (KD = 0.5 μM) exhibited favorable entropy (TΔS° = 2.2 to 14.9 kcal/mol), indicating an order-to-disorder change during binding, possibly through the expulsion of ordered water molecules. RESULTS |
|
57 59 KD evidence Conversely, the stronger-affinity ligands A2-RQWGPDPAAV (KD = 7.8 μM), A2-YQFGPDFPIA (KD = 7.4 μM), and A2-RQFGPDFPTI (KD = 0.5 μM) exhibited favorable entropy (TΔS° = 2.2 to 14.9 kcal/mol), indicating an order-to-disorder change during binding, possibly through the expulsion of ordered water molecules. RESULTS |
|
71 84 A2-YQFGPDFPIA chemical Conversely, the stronger-affinity ligands A2-RQWGPDPAAV (KD = 7.8 μM), A2-YQFGPDFPIA (KD = 7.4 μM), and A2-RQFGPDFPTI (KD = 0.5 μM) exhibited favorable entropy (TΔS° = 2.2 to 14.9 kcal/mol), indicating an order-to-disorder change during binding, possibly through the expulsion of ordered water molecules. RESULTS |
|
86 88 KD evidence Conversely, the stronger-affinity ligands A2-RQWGPDPAAV (KD = 7.8 μM), A2-YQFGPDFPIA (KD = 7.4 μM), and A2-RQFGPDFPTI (KD = 0.5 μM) exhibited favorable entropy (TΔS° = 2.2 to 14.9 kcal/mol), indicating an order-to-disorder change during binding, possibly through the expulsion of ordered water molecules. RESULTS |
|
104 117 A2-RQFGPDFPTI chemical Conversely, the stronger-affinity ligands A2-RQWGPDPAAV (KD = 7.8 μM), A2-YQFGPDFPIA (KD = 7.4 μM), and A2-RQFGPDFPTI (KD = 0.5 μM) exhibited favorable entropy (TΔS° = 2.2 to 14.9 kcal/mol), indicating an order-to-disorder change during binding, possibly through the expulsion of ordered water molecules. RESULTS |
|
119 121 KD evidence Conversely, the stronger-affinity ligands A2-RQWGPDPAAV (KD = 7.8 μM), A2-YQFGPDFPIA (KD = 7.4 μM), and A2-RQFGPDFPTI (KD = 0.5 μM) exhibited favorable entropy (TΔS° = 2.2 to 14.9 kcal/mol), indicating an order-to-disorder change during binding, possibly through the expulsion of ordered water molecules. RESULTS |
|
152 159 entropy evidence Conversely, the stronger-affinity ligands A2-RQWGPDPAAV (KD = 7.8 μM), A2-YQFGPDFPIA (KD = 7.4 μM), and A2-RQFGPDFPTI (KD = 0.5 μM) exhibited favorable entropy (TΔS° = 2.2 to 14.9 kcal/mol), indicating an order-to-disorder change during binding, possibly through the expulsion of ordered water molecules. RESULTS |
|
161 165 TΔS° evidence Conversely, the stronger-affinity ligands A2-RQWGPDPAAV (KD = 7.8 μM), A2-YQFGPDFPIA (KD = 7.4 μM), and A2-RQFGPDFPTI (KD = 0.5 μM) exhibited favorable entropy (TΔS° = 2.2 to 14.9 kcal/mol), indicating an order-to-disorder change during binding, possibly through the expulsion of ordered water molecules. RESULTS |
|
35 44 unligated protein_state Furthermore, the structures of the unligated pMHCs demonstrated that, for these stronger-affinity ligands, there was less conformational difference between the TCR ligated pMHCs compared with the weaker-affinity ligands (Figure 6). RESULTS |
|
45 50 pMHCs complex_assembly Furthermore, the structures of the unligated pMHCs demonstrated that, for these stronger-affinity ligands, there was less conformational difference between the TCR ligated pMHCs compared with the weaker-affinity ligands (Figure 6). RESULTS |
|
89 97 affinity evidence Furthermore, the structures of the unligated pMHCs demonstrated that, for these stronger-affinity ligands, there was less conformational difference between the TCR ligated pMHCs compared with the weaker-affinity ligands (Figure 6). RESULTS |
|
160 163 TCR complex_assembly Furthermore, the structures of the unligated pMHCs demonstrated that, for these stronger-affinity ligands, there was less conformational difference between the TCR ligated pMHCs compared with the weaker-affinity ligands (Figure 6). RESULTS |
|
164 171 ligated protein_state Furthermore, the structures of the unligated pMHCs demonstrated that, for these stronger-affinity ligands, there was less conformational difference between the TCR ligated pMHCs compared with the weaker-affinity ligands (Figure 6). RESULTS |
|
172 177 pMHCs complex_assembly Furthermore, the structures of the unligated pMHCs demonstrated that, for these stronger-affinity ligands, there was less conformational difference between the TCR ligated pMHCs compared with the weaker-affinity ligands (Figure 6). RESULTS |
|
203 211 affinity evidence Furthermore, the structures of the unligated pMHCs demonstrated that, for these stronger-affinity ligands, there was less conformational difference between the TCR ligated pMHCs compared with the weaker-affinity ligands (Figure 6). RESULTS |
|
92 100 affinity evidence The potential requirement for a larger degree of induced fit during binding to these weaker-affinity ligands is consistent with the larger entropic penalties observed for these interactions. RESULTS |
|
23 30 1E6 TCR complex_assembly Potential epitopes for 1E6 TCR occur commonly in the viral proteome. RESULTS |
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53 58 viral taxonomy_domain Potential epitopes for 1E6 TCR occur commonly in the viral proteome. RESULTS |
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56 64 peptides chemical We searched a database of over 1,924,572 unique decamer peptides from the proteome of viral pathogens that are known, or strongly suspected, to infect humans. RESULTS |
|
86 91 viral taxonomy_domain We searched a database of over 1,924,572 unique decamer peptides from the proteome of viral pathogens that are known, or strongly suspected, to infect humans. RESULTS |
|
151 157 humans species We searched a database of over 1,924,572 unique decamer peptides from the proteome of viral pathogens that are known, or strongly suspected, to infect humans. RESULTS |
|
65 75 xxxGPDxxxx structure_element Three hundred forty-two of these decamers conformed to the motif xxxGPDxxxx. RESULTS |
|
42 52 xOxGPDxxxO structure_element Of these, 53 peptides contained the motif xOxGPDxxxO, where O is one of the hydrophobic amino acid residues A,V, I, L, M, Y, F, and W that might allow binding to HLA-A*0201 (Supplemental Table 4). RESULTS |
|
108 109 A residue_name Of these, 53 peptides contained the motif xOxGPDxxxO, where O is one of the hydrophobic amino acid residues A,V, I, L, M, Y, F, and W that might allow binding to HLA-A*0201 (Supplemental Table 4). RESULTS |
|
110 111 V residue_name Of these, 53 peptides contained the motif xOxGPDxxxO, where O is one of the hydrophobic amino acid residues A,V, I, L, M, Y, F, and W that might allow binding to HLA-A*0201 (Supplemental Table 4). RESULTS |
|
113 114 I residue_name Of these, 53 peptides contained the motif xOxGPDxxxO, where O is one of the hydrophobic amino acid residues A,V, I, L, M, Y, F, and W that might allow binding to HLA-A*0201 (Supplemental Table 4). RESULTS |
|
116 117 L residue_name Of these, 53 peptides contained the motif xOxGPDxxxO, where O is one of the hydrophobic amino acid residues A,V, I, L, M, Y, F, and W that might allow binding to HLA-A*0201 (Supplemental Table 4). RESULTS |
|
119 120 M residue_name Of these, 53 peptides contained the motif xOxGPDxxxO, where O is one of the hydrophobic amino acid residues A,V, I, L, M, Y, F, and W that might allow binding to HLA-A*0201 (Supplemental Table 4). RESULTS |
|
122 123 Y residue_name Of these, 53 peptides contained the motif xOxGPDxxxO, where O is one of the hydrophobic amino acid residues A,V, I, L, M, Y, F, and W that might allow binding to HLA-A*0201 (Supplemental Table 4). RESULTS |
|
125 126 F residue_name Of these, 53 peptides contained the motif xOxGPDxxxO, where O is one of the hydrophobic amino acid residues A,V, I, L, M, Y, F, and W that might allow binding to HLA-A*0201 (Supplemental Table 4). RESULTS |
|
132 133 W residue_name Of these, 53 peptides contained the motif xOxGPDxxxO, where O is one of the hydrophobic amino acid residues A,V, I, L, M, Y, F, and W that might allow binding to HLA-A*0201 (Supplemental Table 4). RESULTS |
|
162 172 HLA-A*0201 protein Of these, 53 peptides contained the motif xOxGPDxxxO, where O is one of the hydrophobic amino acid residues A,V, I, L, M, Y, F, and W that might allow binding to HLA-A*0201 (Supplemental Table 4). RESULTS |
|
104 114 MVWGPDPLYV chemical Thus, there are many pathogen-encoded peptides that could act as agonists for the 1E6 T cell beyond the MVWGPDPLYV and RQFGPDWIVA sequences studied here. RESULTS |
|
119 129 RQFGPDWIVA chemical Thus, there are many pathogen-encoded peptides that could act as agonists for the 1E6 T cell beyond the MVWGPDPLYV and RQFGPDWIVA sequences studied here. RESULTS |
|
61 70 bacterial taxonomy_domain Extension of these analyses to include the larger genomes of bacterial pathogens would be expected to considerably increase these numbers. RESULTS |
|
4 20 binding affinity evidence The binding affinity of the 1E6 TCR interaction with A2-RQFGPDWIVA is considerably higher than with the disease-implicated A2-ALWGPDPAAA sequence (KD = 44.4 μM and KD > 200 μM, respectively), highlighting how a pathogen-derived sequence might be capable of priming a 1E6-like T cell. RESULTS |
|
28 35 1E6 TCR complex_assembly The binding affinity of the 1E6 TCR interaction with A2-RQFGPDWIVA is considerably higher than with the disease-implicated A2-ALWGPDPAAA sequence (KD = 44.4 μM and KD > 200 μM, respectively), highlighting how a pathogen-derived sequence might be capable of priming a 1E6-like T cell. RESULTS |
|
53 66 A2-RQFGPDWIVA chemical The binding affinity of the 1E6 TCR interaction with A2-RQFGPDWIVA is considerably higher than with the disease-implicated A2-ALWGPDPAAA sequence (KD = 44.4 μM and KD > 200 μM, respectively), highlighting how a pathogen-derived sequence might be capable of priming a 1E6-like T cell. RESULTS |
|
123 136 A2-ALWGPDPAAA chemical The binding affinity of the 1E6 TCR interaction with A2-RQFGPDWIVA is considerably higher than with the disease-implicated A2-ALWGPDPAAA sequence (KD = 44.4 μM and KD > 200 μM, respectively), highlighting how a pathogen-derived sequence might be capable of priming a 1E6-like T cell. RESULTS |
|
147 149 KD evidence The binding affinity of the 1E6 TCR interaction with A2-RQFGPDWIVA is considerably higher than with the disease-implicated A2-ALWGPDPAAA sequence (KD = 44.4 μM and KD > 200 μM, respectively), highlighting how a pathogen-derived sequence might be capable of priming a 1E6-like T cell. RESULTS |
|
164 166 KD evidence The binding affinity of the 1E6 TCR interaction with A2-RQFGPDWIVA is considerably higher than with the disease-implicated A2-ALWGPDPAAA sequence (KD = 44.4 μM and KD > 200 μM, respectively), highlighting how a pathogen-derived sequence might be capable of priming a 1E6-like T cell. RESULTS |
|
91 94 TCR complex_assembly T cell antigen discrimination is governed by an interaction between the clonally expressed TCR and pMHC, mediated by the chemical characteristics of the interacting molecules. DISCUSS |
|
99 103 pMHC complex_assembly T cell antigen discrimination is governed by an interaction between the clonally expressed TCR and pMHC, mediated by the chemical characteristics of the interacting molecules. DISCUSS |
|
34 37 TCR complex_assembly It has recently become clear that TCR cross-reactivity with large numbers of different pMHC ligands is essential to plug holes in T cell immune coverage that pathogens could exploit. DISCUSS |
|
87 91 pMHC complex_assembly It has recently become clear that TCR cross-reactivity with large numbers of different pMHC ligands is essential to plug holes in T cell immune coverage that pathogens could exploit. DISCUSS |
|
19 28 interface site Flexibility at the interface between the TCR and pMHC, demonstrated in various studies, has been suggested as a mechanism mediating T cell cross-reactivity with multiple distinct epitopes. DISCUSS |
|
41 44 TCR complex_assembly Flexibility at the interface between the TCR and pMHC, demonstrated in various studies, has been suggested as a mechanism mediating T cell cross-reactivity with multiple distinct epitopes. DISCUSS |
|
49 53 pMHC complex_assembly Flexibility at the interface between the TCR and pMHC, demonstrated in various studies, has been suggested as a mechanism mediating T cell cross-reactivity with multiple distinct epitopes. DISCUSS |
|
38 47 CDR loops structure_element This notion is attractive because the CDR loops, which form the TCR antigen-binding site, are usually the most flexible part of the TCR and have the ability to mold around differently shaped ligands. DISCUSS |
|
64 88 TCR antigen-binding site site This notion is attractive because the CDR loops, which form the TCR antigen-binding site, are usually the most flexible part of the TCR and have the ability to mold around differently shaped ligands. DISCUSS |
|
132 135 TCR complex_assembly This notion is attractive because the CDR loops, which form the TCR antigen-binding site, are usually the most flexible part of the TCR and have the ability to mold around differently shaped ligands. DISCUSS |
|
109 112 TCR complex_assembly Focused binding around a minimal peptide motif has also been implicated as an alternative mechanism enabling TCR cross-reactivity. DISCUSS |
|
69 81 alloreactive protein_state Notably among these studies, Garcia and colleagues recently used the alloreactive murine TCR-MHC pair of the 42F3 TCR and H2-Ld to demonstrate recognition of a large number of different peptides via conserved hotspot contacts with prominent up-facing peptide residues. DISCUSS |
|
82 88 murine taxonomy_domain Notably among these studies, Garcia and colleagues recently used the alloreactive murine TCR-MHC pair of the 42F3 TCR and H2-Ld to demonstrate recognition of a large number of different peptides via conserved hotspot contacts with prominent up-facing peptide residues. DISCUSS |
|
89 92 TCR complex_assembly Notably among these studies, Garcia and colleagues recently used the alloreactive murine TCR-MHC pair of the 42F3 TCR and H2-Ld to demonstrate recognition of a large number of different peptides via conserved hotspot contacts with prominent up-facing peptide residues. DISCUSS |
|
93 96 MHC complex_assembly Notably among these studies, Garcia and colleagues recently used the alloreactive murine TCR-MHC pair of the 42F3 TCR and H2-Ld to demonstrate recognition of a large number of different peptides via conserved hotspot contacts with prominent up-facing peptide residues. DISCUSS |
|
109 113 42F3 protein Notably among these studies, Garcia and colleagues recently used the alloreactive murine TCR-MHC pair of the 42F3 TCR and H2-Ld to demonstrate recognition of a large number of different peptides via conserved hotspot contacts with prominent up-facing peptide residues. DISCUSS |
|
114 117 TCR complex_assembly Notably among these studies, Garcia and colleagues recently used the alloreactive murine TCR-MHC pair of the 42F3 TCR and H2-Ld to demonstrate recognition of a large number of different peptides via conserved hotspot contacts with prominent up-facing peptide residues. DISCUSS |
|
122 127 H2-Ld protein Notably among these studies, Garcia and colleagues recently used the alloreactive murine TCR-MHC pair of the 42F3 TCR and H2-Ld to demonstrate recognition of a large number of different peptides via conserved hotspot contacts with prominent up-facing peptide residues. DISCUSS |
|
199 208 conserved protein_state Notably among these studies, Garcia and colleagues recently used the alloreactive murine TCR-MHC pair of the 42F3 TCR and H2-Ld to demonstrate recognition of a large number of different peptides via conserved hotspot contacts with prominent up-facing peptide residues. DISCUSS |
|
209 216 hotspot site Notably among these studies, Garcia and colleagues recently used the alloreactive murine TCR-MHC pair of the 42F3 TCR and H2-Ld to demonstrate recognition of a large number of different peptides via conserved hotspot contacts with prominent up-facing peptide residues. DISCUSS |
|
52 57 MHCII protein_type Sethi and colleagues recently demonstrated that the MHCII-restricted Hy.1B11 TCR, which was isolated from a patient with multiple sclerosis, could anchor into a deep pocket formed from peptide residues 2, 3, and 5 (from MBP85–99 bound to HLA-DQ1). DISCUSS |
|
69 76 Hy.1B11 protein Sethi and colleagues recently demonstrated that the MHCII-restricted Hy.1B11 TCR, which was isolated from a patient with multiple sclerosis, could anchor into a deep pocket formed from peptide residues 2, 3, and 5 (from MBP85–99 bound to HLA-DQ1). DISCUSS |
|
77 80 TCR complex_assembly Sethi and colleagues recently demonstrated that the MHCII-restricted Hy.1B11 TCR, which was isolated from a patient with multiple sclerosis, could anchor into a deep pocket formed from peptide residues 2, 3, and 5 (from MBP85–99 bound to HLA-DQ1). DISCUSS |
|
161 172 deep pocket site Sethi and colleagues recently demonstrated that the MHCII-restricted Hy.1B11 TCR, which was isolated from a patient with multiple sclerosis, could anchor into a deep pocket formed from peptide residues 2, 3, and 5 (from MBP85–99 bound to HLA-DQ1). DISCUSS |
|
202 203 2 residue_number Sethi and colleagues recently demonstrated that the MHCII-restricted Hy.1B11 TCR, which was isolated from a patient with multiple sclerosis, could anchor into a deep pocket formed from peptide residues 2, 3, and 5 (from MBP85–99 bound to HLA-DQ1). DISCUSS |
|
205 206 3 residue_number Sethi and colleagues recently demonstrated that the MHCII-restricted Hy.1B11 TCR, which was isolated from a patient with multiple sclerosis, could anchor into a deep pocket formed from peptide residues 2, 3, and 5 (from MBP85–99 bound to HLA-DQ1). DISCUSS |
|
212 213 5 residue_number Sethi and colleagues recently demonstrated that the MHCII-restricted Hy.1B11 TCR, which was isolated from a patient with multiple sclerosis, could anchor into a deep pocket formed from peptide residues 2, 3, and 5 (from MBP85–99 bound to HLA-DQ1). DISCUSS |
|
220 228 MBP85–99 protein Sethi and colleagues recently demonstrated that the MHCII-restricted Hy.1B11 TCR, which was isolated from a patient with multiple sclerosis, could anchor into a deep pocket formed from peptide residues 2, 3, and 5 (from MBP85–99 bound to HLA-DQ1). DISCUSS |
|
229 237 bound to protein_state Sethi and colleagues recently demonstrated that the MHCII-restricted Hy.1B11 TCR, which was isolated from a patient with multiple sclerosis, could anchor into a deep pocket formed from peptide residues 2, 3, and 5 (from MBP85–99 bound to HLA-DQ1). DISCUSS |
|
238 245 HLA-DQ1 protein Sethi and colleagues recently demonstrated that the MHCII-restricted Hy.1B11 TCR, which was isolated from a patient with multiple sclerosis, could anchor into a deep pocket formed from peptide residues 2, 3, and 5 (from MBP85–99 bound to HLA-DQ1). DISCUSS |
|
15 24 conserved protein_state This motif was conserved in at least 2 potential foreign peptides, originating from Herpes simplex virus and Pseudomonas aeruginosa, enabling TCR recognition of foreign epitopes. DISCUSS |
|
84 104 Herpes simplex virus species This motif was conserved in at least 2 potential foreign peptides, originating from Herpes simplex virus and Pseudomonas aeruginosa, enabling TCR recognition of foreign epitopes. DISCUSS |
|
109 131 Pseudomonas aeruginosa species This motif was conserved in at least 2 potential foreign peptides, originating from Herpes simplex virus and Pseudomonas aeruginosa, enabling TCR recognition of foreign epitopes. DISCUSS |
|
142 145 TCR complex_assembly This motif was conserved in at least 2 potential foreign peptides, originating from Herpes simplex virus and Pseudomonas aeruginosa, enabling TCR recognition of foreign epitopes. DISCUSS |
|
43 48 human species First, we currently know nothing about how human MHCI–restricted TCRs mediate cross-reactivity in the context of a clinically relevant model of autoimmunity, thought to be a major pathway of disease initiation in several autoimmune diseases. DISCUSS |
|
49 53 MHCI complex_assembly First, we currently know nothing about how human MHCI–restricted TCRs mediate cross-reactivity in the context of a clinically relevant model of autoimmunity, thought to be a major pathway of disease initiation in several autoimmune diseases. DISCUSS |
|
65 69 TCRs complex_assembly First, we currently know nothing about how human MHCI–restricted TCRs mediate cross-reactivity in the context of a clinically relevant model of autoimmunity, thought to be a major pathway of disease initiation in several autoimmune diseases. DISCUSS |
|
84 87 TCR complex_assembly Second, molecular studies have not yet revealed a broad set of rules that determine TCR cross-reactivity because, with the exception of the allo–TCR-MHC pair of the 42F3 TCR and H2-Ld that did not encounter each other during T cell development, studies have been limited to structures of a TCR with only 2 or 3 different ligands. DISCUSS |
|
140 144 allo protein_state Second, molecular studies have not yet revealed a broad set of rules that determine TCR cross-reactivity because, with the exception of the allo–TCR-MHC pair of the 42F3 TCR and H2-Ld that did not encounter each other during T cell development, studies have been limited to structures of a TCR with only 2 or 3 different ligands. DISCUSS |
|
145 152 TCR-MHC complex_assembly Second, molecular studies have not yet revealed a broad set of rules that determine TCR cross-reactivity because, with the exception of the allo–TCR-MHC pair of the 42F3 TCR and H2-Ld that did not encounter each other during T cell development, studies have been limited to structures of a TCR with only 2 or 3 different ligands. DISCUSS |
|
165 169 42F3 protein Second, molecular studies have not yet revealed a broad set of rules that determine TCR cross-reactivity because, with the exception of the allo–TCR-MHC pair of the 42F3 TCR and H2-Ld that did not encounter each other during T cell development, studies have been limited to structures of a TCR with only 2 or 3 different ligands. DISCUSS |
|
170 173 TCR complex_assembly Second, molecular studies have not yet revealed a broad set of rules that determine TCR cross-reactivity because, with the exception of the allo–TCR-MHC pair of the 42F3 TCR and H2-Ld that did not encounter each other during T cell development, studies have been limited to structures of a TCR with only 2 or 3 different ligands. DISCUSS |
|
178 183 H2-Ld protein Second, molecular studies have not yet revealed a broad set of rules that determine TCR cross-reactivity because, with the exception of the allo–TCR-MHC pair of the 42F3 TCR and H2-Ld that did not encounter each other during T cell development, studies have been limited to structures of a TCR with only 2 or 3 different ligands. DISCUSS |
|
274 284 structures evidence Second, molecular studies have not yet revealed a broad set of rules that determine TCR cross-reactivity because, with the exception of the allo–TCR-MHC pair of the 42F3 TCR and H2-Ld that did not encounter each other during T cell development, studies have been limited to structures of a TCR with only 2 or 3 different ligands. DISCUSS |
|
290 293 TCR complex_assembly Second, molecular studies have not yet revealed a broad set of rules that determine TCR cross-reactivity because, with the exception of the allo–TCR-MHC pair of the 42F3 TCR and H2-Ld that did not encounter each other during T cell development, studies have been limited to structures of a TCR with only 2 or 3 different ligands. DISCUSS |
|
46 50 MHCI complex_assembly Here, we investigated a highly cross-reactive MHCI-restricted TCR isolated from a patient with T1D that recognizes an HLA-A*0201–restricted preproinsulin signal peptide (ALWGPDPAAA15–24). DISCUSS |
|
62 65 TCR complex_assembly Here, we investigated a highly cross-reactive MHCI-restricted TCR isolated from a patient with T1D that recognizes an HLA-A*0201–restricted preproinsulin signal peptide (ALWGPDPAAA15–24). DISCUSS |
|
118 128 HLA-A*0201 protein Here, we investigated a highly cross-reactive MHCI-restricted TCR isolated from a patient with T1D that recognizes an HLA-A*0201–restricted preproinsulin signal peptide (ALWGPDPAAA15–24). DISCUSS |
|
140 153 preproinsulin protein Here, we investigated a highly cross-reactive MHCI-restricted TCR isolated from a patient with T1D that recognizes an HLA-A*0201–restricted preproinsulin signal peptide (ALWGPDPAAA15–24). DISCUSS |
|
154 168 signal peptide structure_element Here, we investigated a highly cross-reactive MHCI-restricted TCR isolated from a patient with T1D that recognizes an HLA-A*0201–restricted preproinsulin signal peptide (ALWGPDPAAA15–24). DISCUSS |
|
170 185 ALWGPDPAAA15–24 chemical Here, we investigated a highly cross-reactive MHCI-restricted TCR isolated from a patient with T1D that recognizes an HLA-A*0201–restricted preproinsulin signal peptide (ALWGPDPAAA15–24). DISCUSS |
|
0 5 Human species Human CD8+ T cell clones expressing TCRs with this specificity mediate the destruction of β cells, have been found in islets early in infection, and are proposed to be a major driver of disease. DISCUSS |
|
36 40 TCRs complex_assembly Human CD8+ T cell clones expressing TCRs with this specificity mediate the destruction of β cells, have been found in islets early in infection, and are proposed to be a major driver of disease. DISCUSS |
|
3 9 solved experimental_method We solved the structure of the 1E6 TCR with 7 APLs to enable a comprehensive analysis of the molecular basis of TCR degeneracy. DISCUSS |
|
14 23 structure evidence We solved the structure of the 1E6 TCR with 7 APLs to enable a comprehensive analysis of the molecular basis of TCR degeneracy. DISCUSS |
|
31 38 1E6 TCR complex_assembly We solved the structure of the 1E6 TCR with 7 APLs to enable a comprehensive analysis of the molecular basis of TCR degeneracy. DISCUSS |
|
46 50 APLs chemical We solved the structure of the 1E6 TCR with 7 APLs to enable a comprehensive analysis of the molecular basis of TCR degeneracy. DISCUSS |
|
112 115 TCR complex_assembly We solved the structure of the 1E6 TCR with 7 APLs to enable a comprehensive analysis of the molecular basis of TCR degeneracy. DISCUSS |
|
68 82 binding energy evidence Overall, the difference in antigen potency correlated well with the binding energy (ΔG° kcal/mol) of the 1E6 TCR for the different epitopes, which ranged from values of ΔG° = ~–4.4 to –8.6 kcal/mol (calculated from 3D affinity data) or 2D affinity values of AcKa = 2.5 × 10–5 to 4.4 × 10–2 μm4. DISCUSS |
|
84 87 ΔG° evidence Overall, the difference in antigen potency correlated well with the binding energy (ΔG° kcal/mol) of the 1E6 TCR for the different epitopes, which ranged from values of ΔG° = ~–4.4 to –8.6 kcal/mol (calculated from 3D affinity data) or 2D affinity values of AcKa = 2.5 × 10–5 to 4.4 × 10–2 μm4. DISCUSS |
|
105 112 1E6 TCR complex_assembly Overall, the difference in antigen potency correlated well with the binding energy (ΔG° kcal/mol) of the 1E6 TCR for the different epitopes, which ranged from values of ΔG° = ~–4.4 to –8.6 kcal/mol (calculated from 3D affinity data) or 2D affinity values of AcKa = 2.5 × 10–5 to 4.4 × 10–2 μm4. DISCUSS |
|
169 172 ΔG° evidence Overall, the difference in antigen potency correlated well with the binding energy (ΔG° kcal/mol) of the 1E6 TCR for the different epitopes, which ranged from values of ΔG° = ~–4.4 to –8.6 kcal/mol (calculated from 3D affinity data) or 2D affinity values of AcKa = 2.5 × 10–5 to 4.4 × 10–2 μm4. DISCUSS |
|
215 226 3D affinity evidence Overall, the difference in antigen potency correlated well with the binding energy (ΔG° kcal/mol) of the 1E6 TCR for the different epitopes, which ranged from values of ΔG° = ~–4.4 to –8.6 kcal/mol (calculated from 3D affinity data) or 2D affinity values of AcKa = 2.5 × 10–5 to 4.4 × 10–2 μm4. DISCUSS |
|
236 247 2D affinity evidence Overall, the difference in antigen potency correlated well with the binding energy (ΔG° kcal/mol) of the 1E6 TCR for the different epitopes, which ranged from values of ΔG° = ~–4.4 to –8.6 kcal/mol (calculated from 3D affinity data) or 2D affinity values of AcKa = 2.5 × 10–5 to 4.4 × 10–2 μm4. DISCUSS |
|
258 262 AcKa evidence Overall, the difference in antigen potency correlated well with the binding energy (ΔG° kcal/mol) of the 1E6 TCR for the different epitopes, which ranged from values of ΔG° = ~–4.4 to –8.6 kcal/mol (calculated from 3D affinity data) or 2D affinity values of AcKa = 2.5 × 10–5 to 4.4 × 10–2 μm4. DISCUSS |
|
126 149 TCR 3D binding affinity evidence The weaker end of this spectrum extends our understanding of the limits in which T cells can functionally operate in terms of TCR 3D binding affinity and is in line with the types of very low affinity, yet fully functional self-reactive CD8+ T cells we have observed in tumor-infiltrating lymphocytes. DISCUSS |
|
192 200 affinity evidence The weaker end of this spectrum extends our understanding of the limits in which T cells can functionally operate in terms of TCR 3D binding affinity and is in line with the types of very low affinity, yet fully functional self-reactive CD8+ T cells we have observed in tumor-infiltrating lymphocytes. DISCUSS |
|
33 37 TCRs complex_assembly Previous studies of autoreactive TCRs have shown that their binding mode is generally atypical, either due to an unusual binding manner, weak TCR binding affinity, an unstable pMHC, or a combination of these factors. DISCUSS |
|
142 162 TCR binding affinity evidence Previous studies of autoreactive TCRs have shown that their binding mode is generally atypical, either due to an unusual binding manner, weak TCR binding affinity, an unstable pMHC, or a combination of these factors. DISCUSS |
|
167 175 unstable protein_state Previous studies of autoreactive TCRs have shown that their binding mode is generally atypical, either due to an unusual binding manner, weak TCR binding affinity, an unstable pMHC, or a combination of these factors. DISCUSS |
|
176 180 pMHC complex_assembly Previous studies of autoreactive TCRs have shown that their binding mode is generally atypical, either due to an unusual binding manner, weak TCR binding affinity, an unstable pMHC, or a combination of these factors. DISCUSS |
|
55 58 TCR complex_assembly Our data demonstrate the potential for an autoreactive TCR to bind with a conventional binding mode to a stable pMHC with antipathogen-like affinity (KD = 0.5 μM) depending on the peptide sequence. DISCUSS |
|
105 111 stable protein_state Our data demonstrate the potential for an autoreactive TCR to bind with a conventional binding mode to a stable pMHC with antipathogen-like affinity (KD = 0.5 μM) depending on the peptide sequence. DISCUSS |
|
112 116 pMHC complex_assembly Our data demonstrate the potential for an autoreactive TCR to bind with a conventional binding mode to a stable pMHC with antipathogen-like affinity (KD = 0.5 μM) depending on the peptide sequence. DISCUSS |
|
140 148 affinity evidence Our data demonstrate the potential for an autoreactive TCR to bind with a conventional binding mode to a stable pMHC with antipathogen-like affinity (KD = 0.5 μM) depending on the peptide sequence. DISCUSS |
|
150 152 KD evidence Our data demonstrate the potential for an autoreactive TCR to bind with a conventional binding mode to a stable pMHC with antipathogen-like affinity (KD = 0.5 μM) depending on the peptide sequence. DISCUSS |
|
4 23 structural analysis experimental_method Our structural analysis revealed that the 1E6 TCR bound with a conserved conformation across all APLs investigated. DISCUSS |
|
42 49 1E6 TCR complex_assembly Our structural analysis revealed that the 1E6 TCR bound with a conserved conformation across all APLs investigated. DISCUSS |
|
50 55 bound protein_state Our structural analysis revealed that the 1E6 TCR bound with a conserved conformation across all APLs investigated. DISCUSS |
|
63 85 conserved conformation protein_state Our structural analysis revealed that the 1E6 TCR bound with a conserved conformation across all APLs investigated. DISCUSS |
|
97 101 APLs chemical Our structural analysis revealed that the 1E6 TCR bound with a conserved conformation across all APLs investigated. DISCUSS |
|
73 76 TCR complex_assembly This binding orientation was mediated through a focused interaction with TCR residues Tyr97α and Trp97β that formed an aromatic cap over a central ‘GDP’ motif that was common to all APLs. DISCUSS |
|
86 92 Tyr97α residue_name_number This binding orientation was mediated through a focused interaction with TCR residues Tyr97α and Trp97β that formed an aromatic cap over a central ‘GDP’ motif that was common to all APLs. DISCUSS |
|
97 103 Trp97β residue_name_number This binding orientation was mediated through a focused interaction with TCR residues Tyr97α and Trp97β that formed an aromatic cap over a central ‘GDP’ motif that was common to all APLs. DISCUSS |
|
119 131 aromatic cap structure_element This binding orientation was mediated through a focused interaction with TCR residues Tyr97α and Trp97β that formed an aromatic cap over a central ‘GDP’ motif that was common to all APLs. DISCUSS |
|
147 158 ‘GDP’ motif structure_element This binding orientation was mediated through a focused interaction with TCR residues Tyr97α and Trp97β that formed an aromatic cap over a central ‘GDP’ motif that was common to all APLs. DISCUSS |
|
182 186 APLs chemical This binding orientation was mediated through a focused interaction with TCR residues Tyr97α and Trp97β that formed an aromatic cap over a central ‘GDP’ motif that was common to all APLs. DISCUSS |
|
54 63 GPD motif structure_element We have previously demonstrated the importance of the GPD motif using a peptide library scan, as well as a CPL scan approach. DISCUSS |
|
72 92 peptide library scan experimental_method We have previously demonstrated the importance of the GPD motif using a peptide library scan, as well as a CPL scan approach. DISCUSS |
|
107 115 CPL scan experimental_method We have previously demonstrated the importance of the GPD motif using a peptide library scan, as well as a CPL scan approach. DISCUSS |
|
71 77 lacked protein_state Although the 1E6 T cell was able to activate weakly with peptides that lacked this motif, we were unable to robustly measure binding affinities or generate complex structures with these ligands, highlighting the central role of this interaction during 1E6 T cell antigen recognition. DISCUSS |
|
125 143 binding affinities evidence Although the 1E6 T cell was able to activate weakly with peptides that lacked this motif, we were unable to robustly measure binding affinities or generate complex structures with these ligands, highlighting the central role of this interaction during 1E6 T cell antigen recognition. DISCUSS |
|
164 174 structures evidence Although the 1E6 T cell was able to activate weakly with peptides that lacked this motif, we were unable to robustly measure binding affinities or generate complex structures with these ligands, highlighting the central role of this interaction during 1E6 T cell antigen recognition. DISCUSS |
|
178 181 TCR complex_assembly This hotspot binding, defined as a localized cluster of interactions that dominate binding energy during protein-protein interactions, has been previously shown to contribute to TCR recognition of MHC as a mechanism that tunes T cell cross-reactivity by providing fixed anchor points that enable TCRs to tolerate a variable peptide cargo. DISCUSS |
|
197 200 MHC complex_assembly This hotspot binding, defined as a localized cluster of interactions that dominate binding energy during protein-protein interactions, has been previously shown to contribute to TCR recognition of MHC as a mechanism that tunes T cell cross-reactivity by providing fixed anchor points that enable TCRs to tolerate a variable peptide cargo. DISCUSS |
|
296 300 TCRs complex_assembly This hotspot binding, defined as a localized cluster of interactions that dominate binding energy during protein-protein interactions, has been previously shown to contribute to TCR recognition of MHC as a mechanism that tunes T cell cross-reactivity by providing fixed anchor points that enable TCRs to tolerate a variable peptide cargo. DISCUSS |
|
40 43 TCR complex_assembly Alternatively, interactions between the TCR and peptide have been shown to dominate the energetic landscape during ligand engagement, ensuring that T cells retain peptide specificity. DISCUSS |
|
38 45 1E6 TCR complex_assembly The binding mechanism utilized by the 1E6 TCR during pMHC recognition is consistent with both of these models. DISCUSS |
|
53 57 pMHC complex_assembly The binding mechanism utilized by the 1E6 TCR during pMHC recognition is consistent with both of these models. DISCUSS |
|
103 112 GPD motif structure_element Ligand engagement is dominated by peptide interactions, but hotspot-like interactions with the central GPD motif enable the 1E6 TCR to tolerate peptide residues that vary outside of this region, explaining how T cells expressing this TCR may cross-react with a large number of different peptides. DISCUSS |
|
124 131 1E6 TCR complex_assembly Ligand engagement is dominated by peptide interactions, but hotspot-like interactions with the central GPD motif enable the 1E6 TCR to tolerate peptide residues that vary outside of this region, explaining how T cells expressing this TCR may cross-react with a large number of different peptides. DISCUSS |
|
234 237 TCR complex_assembly Ligand engagement is dominated by peptide interactions, but hotspot-like interactions with the central GPD motif enable the 1E6 TCR to tolerate peptide residues that vary outside of this region, explaining how T cells expressing this TCR may cross-react with a large number of different peptides. DISCUSS |
|
70 77 Hy.1B11 protein These findings are also analogous to the observed binding mode of the Hy.1B11 TCR, in which one aromatic residue of the TCR CDR3α loop anchored into a pocket created by a conserved peptide motif. DISCUSS |
|
78 81 TCR complex_assembly These findings are also analogous to the observed binding mode of the Hy.1B11 TCR, in which one aromatic residue of the TCR CDR3α loop anchored into a pocket created by a conserved peptide motif. DISCUSS |
|
120 123 TCR complex_assembly These findings are also analogous to the observed binding mode of the Hy.1B11 TCR, in which one aromatic residue of the TCR CDR3α loop anchored into a pocket created by a conserved peptide motif. DISCUSS |
|
124 134 CDR3α loop structure_element These findings are also analogous to the observed binding mode of the Hy.1B11 TCR, in which one aromatic residue of the TCR CDR3α loop anchored into a pocket created by a conserved peptide motif. DISCUSS |
|
59 62 TCR complex_assembly In both of these examples, self-recognition is mediated by TCR residues with aromatic side chains. DISCUSS |
|
84 94 CDR2 loops structure_element Combined with evidence demonstrating that aromatic side chains are conserved in the CDR2 loops of TCRs from many species, we speculate that these aromatic residues could impart a level of “stickiness” to TCRs, which might be enriched in an autoimmune setting when the TCR often binds in a nonoptimal fashion. DISCUSS |
|
98 102 TCRs complex_assembly Combined with evidence demonstrating that aromatic side chains are conserved in the CDR2 loops of TCRs from many species, we speculate that these aromatic residues could impart a level of “stickiness” to TCRs, which might be enriched in an autoimmune setting when the TCR often binds in a nonoptimal fashion. DISCUSS |
|
204 208 TCRs complex_assembly Combined with evidence demonstrating that aromatic side chains are conserved in the CDR2 loops of TCRs from many species, we speculate that these aromatic residues could impart a level of “stickiness” to TCRs, which might be enriched in an autoimmune setting when the TCR often binds in a nonoptimal fashion. DISCUSS |
|
268 271 TCR complex_assembly Combined with evidence demonstrating that aromatic side chains are conserved in the CDR2 loops of TCRs from many species, we speculate that these aromatic residues could impart a level of “stickiness” to TCRs, which might be enriched in an autoimmune setting when the TCR often binds in a nonoptimal fashion. DISCUSS |
|
54 77 surface complementarity evidence Despite some weak statistical correlation between the surface complementarity (SC) and affinity, closer inspection of the interface revealed no obvious structural signature that could definitively explain the differences in antigen potency and TCR binding strength between the different ligands. DISCUSS |
|
79 81 SC evidence Despite some weak statistical correlation between the surface complementarity (SC) and affinity, closer inspection of the interface revealed no obvious structural signature that could definitively explain the differences in antigen potency and TCR binding strength between the different ligands. DISCUSS |
|
87 95 affinity evidence Despite some weak statistical correlation between the surface complementarity (SC) and affinity, closer inspection of the interface revealed no obvious structural signature that could definitively explain the differences in antigen potency and TCR binding strength between the different ligands. DISCUSS |
|
122 131 interface site Despite some weak statistical correlation between the surface complementarity (SC) and affinity, closer inspection of the interface revealed no obvious structural signature that could definitively explain the differences in antigen potency and TCR binding strength between the different ligands. DISCUSS |
|
224 239 antigen potency evidence Despite some weak statistical correlation between the surface complementarity (SC) and affinity, closer inspection of the interface revealed no obvious structural signature that could definitively explain the differences in antigen potency and TCR binding strength between the different ligands. DISCUSS |
|
244 264 TCR binding strength evidence Despite some weak statistical correlation between the surface complementarity (SC) and affinity, closer inspection of the interface revealed no obvious structural signature that could definitively explain the differences in antigen potency and TCR binding strength between the different ligands. DISCUSS |
|
102 123 central peptide bulge structure_element However, similar to our findings in other systems, modifications to residues outside of the canonical central peptide bulge were important for generating new interactions. DISCUSS |
|
69 72 Arg residue_name For example, all of the stronger ligands encoded larger side chains (Arg or Tyr) at peptide position 1 that enabled new interactions with 1E6 not present with the Ala at this position in the natural preproinsulin peptide. DISCUSS |
|
76 79 Tyr residue_name For example, all of the stronger ligands encoded larger side chains (Arg or Tyr) at peptide position 1 that enabled new interactions with 1E6 not present with the Ala at this position in the natural preproinsulin peptide. DISCUSS |
|
101 102 1 residue_number For example, all of the stronger ligands encoded larger side chains (Arg or Tyr) at peptide position 1 that enabled new interactions with 1E6 not present with the Ala at this position in the natural preproinsulin peptide. DISCUSS |
|
163 166 Ala residue_name For example, all of the stronger ligands encoded larger side chains (Arg or Tyr) at peptide position 1 that enabled new interactions with 1E6 not present with the Ala at this position in the natural preproinsulin peptide. DISCUSS |
|
199 212 preproinsulin protein For example, all of the stronger ligands encoded larger side chains (Arg or Tyr) at peptide position 1 that enabled new interactions with 1E6 not present with the Ala at this position in the natural preproinsulin peptide. DISCUSS |
|
213 220 peptide chemical For example, all of the stronger ligands encoded larger side chains (Arg or Tyr) at peptide position 1 that enabled new interactions with 1E6 not present with the Ala at this position in the natural preproinsulin peptide. DISCUSS |
|
69 83 anchor residue structure_element These data also explain our previous findings that alteration of the anchor residue at peptide position 2 (Leu-Gln) has a direct effect on 1E6 TCR binding affinity because our structural analysis demonstrated that 1E6 made 3 additional bonds with A2-AQWGPDPAAA compared with A2-ALWGPDPAAA, consistent with the >3-fold stronger binding affinity. DISCUSS |
|
104 105 2 residue_number These data also explain our previous findings that alteration of the anchor residue at peptide position 2 (Leu-Gln) has a direct effect on 1E6 TCR binding affinity because our structural analysis demonstrated that 1E6 made 3 additional bonds with A2-AQWGPDPAAA compared with A2-ALWGPDPAAA, consistent with the >3-fold stronger binding affinity. DISCUSS |
|
107 114 Leu-Gln mutant These data also explain our previous findings that alteration of the anchor residue at peptide position 2 (Leu-Gln) has a direct effect on 1E6 TCR binding affinity because our structural analysis demonstrated that 1E6 made 3 additional bonds with A2-AQWGPDPAAA compared with A2-ALWGPDPAAA, consistent with the >3-fold stronger binding affinity. DISCUSS |
|
139 163 1E6 TCR binding affinity evidence These data also explain our previous findings that alteration of the anchor residue at peptide position 2 (Leu-Gln) has a direct effect on 1E6 TCR binding affinity because our structural analysis demonstrated that 1E6 made 3 additional bonds with A2-AQWGPDPAAA compared with A2-ALWGPDPAAA, consistent with the >3-fold stronger binding affinity. DISCUSS |
|
176 195 structural analysis experimental_method These data also explain our previous findings that alteration of the anchor residue at peptide position 2 (Leu-Gln) has a direct effect on 1E6 TCR binding affinity because our structural analysis demonstrated that 1E6 made 3 additional bonds with A2-AQWGPDPAAA compared with A2-ALWGPDPAAA, consistent with the >3-fold stronger binding affinity. DISCUSS |
|
247 260 A2-AQWGPDPAAA chemical These data also explain our previous findings that alteration of the anchor residue at peptide position 2 (Leu-Gln) has a direct effect on 1E6 TCR binding affinity because our structural analysis demonstrated that 1E6 made 3 additional bonds with A2-AQWGPDPAAA compared with A2-ALWGPDPAAA, consistent with the >3-fold stronger binding affinity. DISCUSS |
|
275 288 A2-ALWGPDPAAA chemical These data also explain our previous findings that alteration of the anchor residue at peptide position 2 (Leu-Gln) has a direct effect on 1E6 TCR binding affinity because our structural analysis demonstrated that 1E6 made 3 additional bonds with A2-AQWGPDPAAA compared with A2-ALWGPDPAAA, consistent with the >3-fold stronger binding affinity. DISCUSS |
|
327 343 binding affinity evidence These data also explain our previous findings that alteration of the anchor residue at peptide position 2 (Leu-Gln) has a direct effect on 1E6 TCR binding affinity because our structural analysis demonstrated that 1E6 made 3 additional bonds with A2-AQWGPDPAAA compared with A2-ALWGPDPAAA, consistent with the >3-fold stronger binding affinity. DISCUSS |
|
56 57 2 residue_number We have recently demonstrated how a suboptimal position 2 anchor in a melanoma-derived antigen can improve TCR binding through a similar mechanism. DISCUSS |
|
58 64 anchor structure_element We have recently demonstrated how a suboptimal position 2 anchor in a melanoma-derived antigen can improve TCR binding through a similar mechanism. DISCUSS |
|
107 110 TCR complex_assembly We have recently demonstrated how a suboptimal position 2 anchor in a melanoma-derived antigen can improve TCR binding through a similar mechanism. DISCUSS |
|
94 98 pMHC complex_assembly These results challenge the notion that the most potent peptide antigens exhibit the greatest pMHC stability and have implications for the design of anchor residue–modified heteroclitic peptides for vaccination. DISCUSS |
|
6 28 thermodynamic analysis experimental_method Early thermodynamic analysis of TCR-pMHC interactions suggested a common energetic signature, driven by favorable enthalpy (generally mediated through an increase in electrostatic interactions) and unfavorable entropy (changes from disorder to order). DISCUSS |
|
32 40 TCR-pMHC complex_assembly Early thermodynamic analysis of TCR-pMHC interactions suggested a common energetic signature, driven by favorable enthalpy (generally mediated through an increase in electrostatic interactions) and unfavorable entropy (changes from disorder to order). DISCUSS |
|
114 122 enthalpy evidence Early thermodynamic analysis of TCR-pMHC interactions suggested a common energetic signature, driven by favorable enthalpy (generally mediated through an increase in electrostatic interactions) and unfavorable entropy (changes from disorder to order). DISCUSS |
|
210 217 entropy evidence Early thermodynamic analysis of TCR-pMHC interactions suggested a common energetic signature, driven by favorable enthalpy (generally mediated through an increase in electrostatic interactions) and unfavorable entropy (changes from disorder to order). DISCUSS |
|
35 50 structural data evidence These parameters aligned well with structural data, demonstrating that TCRs engaged pMHC using an induced fit binding mode. DISCUSS |
|
71 75 TCRs complex_assembly These parameters aligned well with structural data, demonstrating that TCRs engaged pMHC using an induced fit binding mode. DISCUSS |
|
84 88 pMHC complex_assembly These parameters aligned well with structural data, demonstrating that TCRs engaged pMHC using an induced fit binding mode. DISCUSS |
|
42 46 TCRs complex_assembly However, more recent data have shown that TCRs can utilize a range of energetic strategies during pMHC binding, currently with no obvious pattern in terms of TCR affinity, binding mechanism, or specificity (pathogen, cancer, or self-ligands). DISCUSS |
|
98 102 pMHC complex_assembly However, more recent data have shown that TCRs can utilize a range of energetic strategies during pMHC binding, currently with no obvious pattern in terms of TCR affinity, binding mechanism, or specificity (pathogen, cancer, or self-ligands). DISCUSS |
|
158 170 TCR affinity evidence However, more recent data have shown that TCRs can utilize a range of energetic strategies during pMHC binding, currently with no obvious pattern in terms of TCR affinity, binding mechanism, or specificity (pathogen, cancer, or self-ligands). DISCUSS |
|
63 67 TCRs complex_assembly Although no energetic signature appears to exist for different TCRs, we used thermodynamic analysis here to explore whether changes in energetics could help explain ligand discrimination by a single TCR. DISCUSS |
|
77 99 thermodynamic analysis experimental_method Although no energetic signature appears to exist for different TCRs, we used thermodynamic analysis here to explore whether changes in energetics could help explain ligand discrimination by a single TCR. DISCUSS |
|
199 202 TCR complex_assembly Although no energetic signature appears to exist for different TCRs, we used thermodynamic analysis here to explore whether changes in energetics could help explain ligand discrimination by a single TCR. DISCUSS |
|
67 97 Pearson’s correlation analysis experimental_method This analysis demonstrated a strong relationship (according to the Pearson’s correlation analysis) between the energetic signature used by the 1E6 TCR and the sensitivity of the 1E6 T cell clone to different APLs. DISCUSS |
|
143 150 1E6 TCR complex_assembly This analysis demonstrated a strong relationship (according to the Pearson’s correlation analysis) between the energetic signature used by the 1E6 TCR and the sensitivity of the 1E6 T cell clone to different APLs. DISCUSS |
|
208 212 APLs chemical This analysis demonstrated a strong relationship (according to the Pearson’s correlation analysis) between the energetic signature used by the 1E6 TCR and the sensitivity of the 1E6 T cell clone to different APLs. DISCUSS |
|
11 14 APL chemical The weaker APL ligands were characterized by favorable enthalpy and unfavorable entropy, whereas the stronger ligands progressively shifted to favorable entropy. DISCUSS |
|
55 63 enthalpy evidence The weaker APL ligands were characterized by favorable enthalpy and unfavorable entropy, whereas the stronger ligands progressively shifted to favorable entropy. DISCUSS |
|
80 87 entropy evidence The weaker APL ligands were characterized by favorable enthalpy and unfavorable entropy, whereas the stronger ligands progressively shifted to favorable entropy. DISCUSS |
|
153 160 entropy evidence The weaker APL ligands were characterized by favorable enthalpy and unfavorable entropy, whereas the stronger ligands progressively shifted to favorable entropy. DISCUSS |
|
80 89 unligated protein_state These differences were consistent with a greater degree of movement between the unligated and ligated pMHCs for the weaker ligands, suggesting a greater requirement for disorder-to-order changes during TCR binding. DISCUSS |
|
94 101 ligated protein_state These differences were consistent with a greater degree of movement between the unligated and ligated pMHCs for the weaker ligands, suggesting a greater requirement for disorder-to-order changes during TCR binding. DISCUSS |
|
102 107 pMHCs complex_assembly These differences were consistent with a greater degree of movement between the unligated and ligated pMHCs for the weaker ligands, suggesting a greater requirement for disorder-to-order changes during TCR binding. DISCUSS |
|
202 205 TCR complex_assembly These differences were consistent with a greater degree of movement between the unligated and ligated pMHCs for the weaker ligands, suggesting a greater requirement for disorder-to-order changes during TCR binding. DISCUSS |
|
272 280 ΔG value evidence Thus, the enhanced antigen potency was probably mediated through a shift from an induced fit to a lock-and-key interaction between the stronger ligands (less requirement for energetically unfavorable disorder-to-order changes), resulting in a more energetically favorable ΔG value. DISCUSS |
|
17 30 preproinsulin protein Importantly, the preproinsulin-derived epitope was one of the least potent peptides, demonstrating that the 1E6 T cell clone had the ability to respond to different peptide sequences with far greater potency. DISCUSS |
|
4 14 RQFGPDWIVA chemical The RQFGPDWIVA peptide, which was substantially more potent than the preproinsulin peptide, is within the proteome of a common human pathogen (C. asparagiforme), demonstrating the potential for an encounter between a naive 1E6-like T cell and a foreign peptide with a more potent ligand that might then break self-tolerance. DISCUSS |
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69 82 preproinsulin protein The RQFGPDWIVA peptide, which was substantially more potent than the preproinsulin peptide, is within the proteome of a common human pathogen (C. asparagiforme), demonstrating the potential for an encounter between a naive 1E6-like T cell and a foreign peptide with a more potent ligand that might then break self-tolerance. DISCUSS |
|
127 132 human species The RQFGPDWIVA peptide, which was substantially more potent than the preproinsulin peptide, is within the proteome of a common human pathogen (C. asparagiforme), demonstrating the potential for an encounter between a naive 1E6-like T cell and a foreign peptide with a more potent ligand that might then break self-tolerance. DISCUSS |
|
143 159 C. asparagiforme species The RQFGPDWIVA peptide, which was substantially more potent than the preproinsulin peptide, is within the proteome of a common human pathogen (C. asparagiforme), demonstrating the potential for an encounter between a naive 1E6-like T cell and a foreign peptide with a more potent ligand that might then break self-tolerance. DISCUSS |
|
81 86 human species Indeed, we found over 50 decamer peptides from the proteome of likely, or known, human viral pathogens alone that contained both the conserved central GPD motif and anchor residues at positions 2 and 10 that would enable binding to HLA-A*02:01. DISCUSS |
|
87 92 viral taxonomy_domain Indeed, we found over 50 decamer peptides from the proteome of likely, or known, human viral pathogens alone that contained both the conserved central GPD motif and anchor residues at positions 2 and 10 that would enable binding to HLA-A*02:01. DISCUSS |
|
133 142 conserved protein_state Indeed, we found over 50 decamer peptides from the proteome of likely, or known, human viral pathogens alone that contained both the conserved central GPD motif and anchor residues at positions 2 and 10 that would enable binding to HLA-A*02:01. DISCUSS |
|
151 160 GPD motif structure_element Indeed, we found over 50 decamer peptides from the proteome of likely, or known, human viral pathogens alone that contained both the conserved central GPD motif and anchor residues at positions 2 and 10 that would enable binding to HLA-A*02:01. DISCUSS |
|
165 180 anchor residues structure_element Indeed, we found over 50 decamer peptides from the proteome of likely, or known, human viral pathogens alone that contained both the conserved central GPD motif and anchor residues at positions 2 and 10 that would enable binding to HLA-A*02:01. DISCUSS |
|
194 195 2 residue_number Indeed, we found over 50 decamer peptides from the proteome of likely, or known, human viral pathogens alone that contained both the conserved central GPD motif and anchor residues at positions 2 and 10 that would enable binding to HLA-A*02:01. DISCUSS |
|
200 202 10 residue_number Indeed, we found over 50 decamer peptides from the proteome of likely, or known, human viral pathogens alone that contained both the conserved central GPD motif and anchor residues at positions 2 and 10 that would enable binding to HLA-A*02:01. DISCUSS |
|
232 243 HLA-A*02:01 protein Indeed, we found over 50 decamer peptides from the proteome of likely, or known, human viral pathogens alone that contained both the conserved central GPD motif and anchor residues at positions 2 and 10 that would enable binding to HLA-A*02:01. DISCUSS |
|
83 88 human species Further experiments will be required to determine whether any naturally presented, human pathogen–derived peptides act as active ligands for 1E6, but our work presented here demonstrates that it is at least feasible for an autoimmune TCR to bind to a different peptide sequence that could be present in a pathogen proteome with substantially higher affinity and potency than the interaction it might use to attack self-tissue. DISCUSS |
|
234 237 TCR complex_assembly Further experiments will be required to determine whether any naturally presented, human pathogen–derived peptides act as active ligands for 1E6, but our work presented here demonstrates that it is at least feasible for an autoimmune TCR to bind to a different peptide sequence that could be present in a pathogen proteome with substantially higher affinity and potency than the interaction it might use to attack self-tissue. DISCUSS |
|
349 357 affinity evidence Further experiments will be required to determine whether any naturally presented, human pathogen–derived peptides act as active ligands for 1E6, but our work presented here demonstrates that it is at least feasible for an autoimmune TCR to bind to a different peptide sequence that could be present in a pathogen proteome with substantially higher affinity and potency than the interaction it might use to attack self-tissue. DISCUSS |
|
150 155 human species In summary, this investigation into the molecular basis of T cell cross-reactivity using a clinically relevant cytotoxic CD8+ T cell clone that kills human pancreatic β cells provides answers to a number of previously outstanding questions. DISCUSS |
|
36 39 TCR complex_assembly First, our data shows that a single TCR has the potential to functionally (assessed through T cell activation) bind to different ligands with affinities ranging across 3 orders of magnitude. DISCUSS |
|
142 152 affinities evidence First, our data shows that a single TCR has the potential to functionally (assessed through T cell activation) bind to different ligands with affinities ranging across 3 orders of magnitude. DISCUSS |
|
96 101 human species Second, this is the first example in which ligands have been identified and characterized for a human autoreactive TCR that are substantially more potent than the natural self-ligand, demonstrating the potential for a pathogenic ligand to break self-tolerance and prime self-reactive T cells. DISCUSS |
|
115 118 TCR complex_assembly Second, this is the first example in which ligands have been identified and characterized for a human autoreactive TCR that are substantially more potent than the natural self-ligand, demonstrating the potential for a pathogenic ligand to break self-tolerance and prime self-reactive T cells. DISCUSS |
|
18 37 structural analysis experimental_method Third, this first structural analysis of a cross-reactive human MHCI–restricted autoimmune TCR showed that degeneracy was mediated through TCR-pMHC anchoring by a conserved minimal binding peptide motif. DISCUSS |
|
58 63 human species Third, this first structural analysis of a cross-reactive human MHCI–restricted autoimmune TCR showed that degeneracy was mediated through TCR-pMHC anchoring by a conserved minimal binding peptide motif. DISCUSS |
|
64 68 MHCI complex_assembly Third, this first structural analysis of a cross-reactive human MHCI–restricted autoimmune TCR showed that degeneracy was mediated through TCR-pMHC anchoring by a conserved minimal binding peptide motif. DISCUSS |
|
91 94 TCR complex_assembly Third, this first structural analysis of a cross-reactive human MHCI–restricted autoimmune TCR showed that degeneracy was mediated through TCR-pMHC anchoring by a conserved minimal binding peptide motif. DISCUSS |
|
139 147 TCR-pMHC complex_assembly Third, this first structural analysis of a cross-reactive human MHCI–restricted autoimmune TCR showed that degeneracy was mediated through TCR-pMHC anchoring by a conserved minimal binding peptide motif. DISCUSS |
|
163 172 conserved protein_state Third, this first structural analysis of a cross-reactive human MHCI–restricted autoimmune TCR showed that degeneracy was mediated through TCR-pMHC anchoring by a conserved minimal binding peptide motif. DISCUSS |
|
173 202 minimal binding peptide motif structure_element Third, this first structural analysis of a cross-reactive human MHCI–restricted autoimmune TCR showed that degeneracy was mediated through TCR-pMHC anchoring by a conserved minimal binding peptide motif. DISCUSS |
|
9 12 TCR complex_assembly Finally, TCR ligand discrimination was characterized by an energetic shift from an enthalpically to entropically driven interaction. DISCUSS |
|
80 93 preproinsulin protein Our demonstration of the molecular mechanism governing cross-reactivity by this preproinsulin reactive human CD8+ T cell clone supports the notion first put forward by Wucherpfennig and Strominger that molecular mimicry could mediate autoimmunity and has far-reaching implications for the complex nature of T cell antigen discrimination. DISCUSS |
|
103 108 human species Our demonstration of the molecular mechanism governing cross-reactivity by this preproinsulin reactive human CD8+ T cell clone supports the notion first put forward by Wucherpfennig and Strominger that molecular mimicry could mediate autoimmunity and has far-reaching implications for the complex nature of T cell antigen discrimination. DISCUSS |
|
62 66 APLs chemical The 1E6 T cell clone reacts with a broad sensitivity range to APLs. FIG |
|
47 69 peptide dilution assay experimental_method (A and B) The 1E6 T cell clone was tested in a peptide dilution assay, in triplicate, with MVWGPDPLYV (gray), YLGGPDFPTI (red), ALWGPDPAAA (blue), AQWGPDPAAA (green), RQFGPDWIVA (dark blue), RQWGPDPAAV (purple), YQFGPDFPTA (yellow), and RQFGPDFPTI (cyan) peptides presented by HLA-A*0201–expressing C1R cells for release of MIP-1β (A) and killing (B). FIG |
|
91 101 MVWGPDPLYV chemical (A and B) The 1E6 T cell clone was tested in a peptide dilution assay, in triplicate, with MVWGPDPLYV (gray), YLGGPDFPTI (red), ALWGPDPAAA (blue), AQWGPDPAAA (green), RQFGPDWIVA (dark blue), RQWGPDPAAV (purple), YQFGPDFPTA (yellow), and RQFGPDFPTI (cyan) peptides presented by HLA-A*0201–expressing C1R cells for release of MIP-1β (A) and killing (B). FIG |
|
110 120 YLGGPDFPTI chemical (A and B) The 1E6 T cell clone was tested in a peptide dilution assay, in triplicate, with MVWGPDPLYV (gray), YLGGPDFPTI (red), ALWGPDPAAA (blue), AQWGPDPAAA (green), RQFGPDWIVA (dark blue), RQWGPDPAAV (purple), YQFGPDFPTA (yellow), and RQFGPDFPTI (cyan) peptides presented by HLA-A*0201–expressing C1R cells for release of MIP-1β (A) and killing (B). FIG |
|
128 138 ALWGPDPAAA chemical (A and B) The 1E6 T cell clone was tested in a peptide dilution assay, in triplicate, with MVWGPDPLYV (gray), YLGGPDFPTI (red), ALWGPDPAAA (blue), AQWGPDPAAA (green), RQFGPDWIVA (dark blue), RQWGPDPAAV (purple), YQFGPDFPTA (yellow), and RQFGPDFPTI (cyan) peptides presented by HLA-A*0201–expressing C1R cells for release of MIP-1β (A) and killing (B). FIG |
|
147 157 AQWGPDPAAA chemical (A and B) The 1E6 T cell clone was tested in a peptide dilution assay, in triplicate, with MVWGPDPLYV (gray), YLGGPDFPTI (red), ALWGPDPAAA (blue), AQWGPDPAAA (green), RQFGPDWIVA (dark blue), RQWGPDPAAV (purple), YQFGPDFPTA (yellow), and RQFGPDFPTI (cyan) peptides presented by HLA-A*0201–expressing C1R cells for release of MIP-1β (A) and killing (B). FIG |
|
167 177 RQFGPDWIVA chemical (A and B) The 1E6 T cell clone was tested in a peptide dilution assay, in triplicate, with MVWGPDPLYV (gray), YLGGPDFPTI (red), ALWGPDPAAA (blue), AQWGPDPAAA (green), RQFGPDWIVA (dark blue), RQWGPDPAAV (purple), YQFGPDFPTA (yellow), and RQFGPDFPTI (cyan) peptides presented by HLA-A*0201–expressing C1R cells for release of MIP-1β (A) and killing (B). FIG |
|
191 201 RQWGPDPAAV chemical (A and B) The 1E6 T cell clone was tested in a peptide dilution assay, in triplicate, with MVWGPDPLYV (gray), YLGGPDFPTI (red), ALWGPDPAAA (blue), AQWGPDPAAA (green), RQFGPDWIVA (dark blue), RQWGPDPAAV (purple), YQFGPDFPTA (yellow), and RQFGPDFPTI (cyan) peptides presented by HLA-A*0201–expressing C1R cells for release of MIP-1β (A) and killing (B). FIG |
|
212 222 YQFGPDFPTA chemical (A and B) The 1E6 T cell clone was tested in a peptide dilution assay, in triplicate, with MVWGPDPLYV (gray), YLGGPDFPTI (red), ALWGPDPAAA (blue), AQWGPDPAAA (green), RQFGPDWIVA (dark blue), RQWGPDPAAV (purple), YQFGPDFPTA (yellow), and RQFGPDFPTI (cyan) peptides presented by HLA-A*0201–expressing C1R cells for release of MIP-1β (A) and killing (B). FIG |
|
237 247 RQFGPDFPTI chemical (A and B) The 1E6 T cell clone was tested in a peptide dilution assay, in triplicate, with MVWGPDPLYV (gray), YLGGPDFPTI (red), ALWGPDPAAA (blue), AQWGPDPAAA (green), RQFGPDWIVA (dark blue), RQWGPDPAAV (purple), YQFGPDFPTA (yellow), and RQFGPDFPTI (cyan) peptides presented by HLA-A*0201–expressing C1R cells for release of MIP-1β (A) and killing (B). FIG |
|
277 287 HLA-A*0201 protein (A and B) The 1E6 T cell clone was tested in a peptide dilution assay, in triplicate, with MVWGPDPLYV (gray), YLGGPDFPTI (red), ALWGPDPAAA (blue), AQWGPDPAAA (green), RQFGPDWIVA (dark blue), RQWGPDPAAV (purple), YQFGPDFPTA (yellow), and RQFGPDFPTI (cyan) peptides presented by HLA-A*0201–expressing C1R cells for release of MIP-1β (A) and killing (B). FIG |
|
324 330 MIP-1β protein (A and B) The 1E6 T cell clone was tested in a peptide dilution assay, in triplicate, with MVWGPDPLYV (gray), YLGGPDFPTI (red), ALWGPDPAAA (blue), AQWGPDPAAA (green), RQFGPDWIVA (dark blue), RQWGPDPAAV (purple), YQFGPDFPTA (yellow), and RQFGPDFPTI (cyan) peptides presented by HLA-A*0201–expressing C1R cells for release of MIP-1β (A) and killing (B). FIG |
|
57 66 tetramers oligomeric_state (C) The 1E6 T cell clone was stained, in duplicate, with tetramers composed of each APL (colored as above) presented by HLA-A*0201. (D) The stability of each APL (colored as above) was tested, in duplicate, using CD by recording the peak at 218 nm absorbance from 5°C–90°C. FIG |
|
84 87 APL chemical (C) The 1E6 T cell clone was stained, in duplicate, with tetramers composed of each APL (colored as above) presented by HLA-A*0201. (D) The stability of each APL (colored as above) was tested, in duplicate, using CD by recording the peak at 218 nm absorbance from 5°C–90°C. FIG |
|
120 130 HLA-A*0201 protein (C) The 1E6 T cell clone was stained, in duplicate, with tetramers composed of each APL (colored as above) presented by HLA-A*0201. (D) The stability of each APL (colored as above) was tested, in duplicate, using CD by recording the peak at 218 nm absorbance from 5°C–90°C. FIG |
|
158 161 APL chemical (C) The 1E6 T cell clone was stained, in duplicate, with tetramers composed of each APL (colored as above) presented by HLA-A*0201. (D) The stability of each APL (colored as above) was tested, in duplicate, using CD by recording the peak at 218 nm absorbance from 5°C–90°C. FIG |
|
213 215 CD experimental_method (C) The 1E6 T cell clone was stained, in duplicate, with tetramers composed of each APL (colored as above) presented by HLA-A*0201. (D) The stability of each APL (colored as above) was tested, in duplicate, using CD by recording the peak at 218 nm absorbance from 5°C–90°C. FIG |
|
0 2 Tm evidence Tm values were calculated using a Boltzmann fit to each set of data. FIG |
|
34 67 Boltzmann fit to each set of data experimental_method Tm values were calculated using a Boltzmann fit to each set of data. FIG |
|
0 26 3D and 2D binding analysis experimental_method 3D and 2D binding analysis of the 1E6 TCR with A2-ALW and the APLs. FIG |
|
34 41 1E6 TCR complex_assembly 3D and 2D binding analysis of the 1E6 TCR with A2-ALW and the APLs. FIG |
|
47 53 A2-ALW chemical 3D and 2D binding analysis of the 1E6 TCR with A2-ALW and the APLs. FIG |
|
62 66 APLs chemical 3D and 2D binding analysis of the 1E6 TCR with A2-ALW and the APLs. FIG |
|
6 22 Binding affinity evidence (A–H) Binding affinity of the 1E6 TCR interaction at 25°C using SPR. FIG |
|
30 37 1E6 TCR complex_assembly (A–H) Binding affinity of the 1E6 TCR interaction at 25°C using SPR. FIG |
|
64 67 SPR experimental_method (A–H) Binding affinity of the 1E6 TCR interaction at 25°C using SPR. FIG |
|
30 37 1E6 TCR complex_assembly Eight serial dilutions of the 1E6 TCR were measured (shown in the inset); representative data from 3 independent experiments are plotted. FIG |
|
4 32 equilibrium binding constant evidence The equilibrium binding constant (KD) values were calculated using a nonlinear curve fit (y= [P1x]/[P2 + X]). FIG |
|
34 36 KD evidence The equilibrium binding constant (KD) values were calculated using a nonlinear curve fit (y= [P1x]/[P2 + X]). FIG |
|
69 88 nonlinear curve fit experimental_method The equilibrium binding constant (KD) values were calculated using a nonlinear curve fit (y= [P1x]/[P2 + X]). FIG |
|
41 48 1E6 TCR complex_assembly In order to calculate each response, the 1E6 TCR was also injected over a control sample (HLA-A*0201–ILAKFLHWL) that was deducted from the experimental data. FIG |
|
90 110 HLA-A*0201–ILAKFLHWL complex_assembly In order to calculate each response, the 1E6 TCR was also injected over a control sample (HLA-A*0201–ILAKFLHWL) that was deducted from the experimental data. FIG |
|
4 21 1E6-A2-MVWGPDPLYV complex_assembly (A) 1E6-A2-MVWGPDPLYV (approximate value) |
|
47 64 1E6-A2-YLGGPDFPTI complex_assembly (A) 1E6-A2-MVWGPDPLYV (approximate value) |
|
90 107 1E6-A2-ALWGPDPAAA complex_assembly (A) 1E6-A2-MVWGPDPLYV (approximate value) |
|
113 130 1E6-A2-AQWGPDPAAA complex_assembly (A) 1E6-A2-MVWGPDPLYV (approximate value) |
|
136 153 1E6-A2-RQFGPDWIVA complex_assembly (A) 1E6-A2-MVWGPDPLYV (approximate value) |
|
159 176 1E6-A2-RQWGPDPAAV complex_assembly (A) 1E6-A2-MVWGPDPLYV (approximate value) |
|
182 199 1E6-A2-YQFGPDFPTA complex_assembly (A) 1E6-A2-MVWGPDPLYV (approximate value) |
|
209 226 1E6-A2-RQFGPDFPTI complex_assembly (A) 1E6-A2-MVWGPDPLYV (approximate value) |
|
232 241 ΔG values evidence (A) 1E6-A2-MVWGPDPLYV (approximate value) |
|
259 262 SPR experimental_method (A) 1E6-A2-MVWGPDPLYV (approximate value) |
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294 298 EC50 evidence (A) 1E6-A2-MVWGPDPLYV (approximate value) |
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396 426 Pearson’s coefficient analysis experimental_method (A) 1E6-A2-MVWGPDPLYV (approximate value) |
|
428 429 r evidence (A) 1E6-A2-MVWGPDPLYV (approximate value) |
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435 436 P evidence (A) 1E6-A2-MVWGPDPLYV (approximate value) |
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4 25 Effective 2D affinity evidence (J) Effective 2D affinity (AcKa) calculated using adhesion frequency assays, using at least 5 cell pairs, and calculated as an average of 100 cell cell contacts. FIG |
|
27 31 AcKa evidence (J) Effective 2D affinity (AcKa) calculated using adhesion frequency assays, using at least 5 cell pairs, and calculated as an average of 100 cell cell contacts. FIG |
|
50 75 adhesion frequency assays experimental_method (J) Effective 2D affinity (AcKa) calculated using adhesion frequency assays, using at least 5 cell pairs, and calculated as an average of 100 cell cell contacts. FIG |
|
4 25 Effective 2D affinity evidence (K) Effective 2D affinity plotted against 1/EC50 showing Pearson’s coefficient analysis (r) and P value. FIG |
|
44 48 EC50 evidence (K) Effective 2D affinity plotted against 1/EC50 showing Pearson’s coefficient analysis (r) and P value. FIG |
|
57 87 Pearson’s coefficient analysis experimental_method (K) Effective 2D affinity plotted against 1/EC50 showing Pearson’s coefficient analysis (r) and P value. FIG |
|
89 90 r evidence (K) Effective 2D affinity plotted against 1/EC50 showing Pearson’s coefficient analysis (r) and P value. FIG |
|
96 103 P value evidence (K) Effective 2D affinity plotted against 1/EC50 showing Pearson’s coefficient analysis (r) and P value. FIG |
|
4 11 1E6 TCR complex_assembly The 1E6 TCR uses a conserved binding mode to engage A2-ALWGPDPAAA and the APLs. FIG |
|
52 65 A2-ALWGPDPAAA chemical The 1E6 TCR uses a conserved binding mode to engage A2-ALWGPDPAAA and the APLs. FIG |
|
74 78 APLs chemical The 1E6 TCR uses a conserved binding mode to engage A2-ALWGPDPAAA and the APLs. FIG |
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4 17 Superposition experimental_method (A) Superposition of the 1E6 TCR (multicolored illustration) in complex with all 7 APLs (multicolored sticks) and the A2-ALWGPDPAAA ligand using the HLA-A*0201 (gray illustration) molecule to align all of the structures. FIG |
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25 32 1E6 TCR complex_assembly (A) Superposition of the 1E6 TCR (multicolored illustration) in complex with all 7 APLs (multicolored sticks) and the A2-ALWGPDPAAA ligand using the HLA-A*0201 (gray illustration) molecule to align all of the structures. FIG |
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61 76 in complex with protein_state (A) Superposition of the 1E6 TCR (multicolored illustration) in complex with all 7 APLs (multicolored sticks) and the A2-ALWGPDPAAA ligand using the HLA-A*0201 (gray illustration) molecule to align all of the structures. FIG |
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83 87 APLs chemical (A) Superposition of the 1E6 TCR (multicolored illustration) in complex with all 7 APLs (multicolored sticks) and the A2-ALWGPDPAAA ligand using the HLA-A*0201 (gray illustration) molecule to align all of the structures. FIG |
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118 131 A2-ALWGPDPAAA chemical (A) Superposition of the 1E6 TCR (multicolored illustration) in complex with all 7 APLs (multicolored sticks) and the A2-ALWGPDPAAA ligand using the HLA-A*0201 (gray illustration) molecule to align all of the structures. FIG |
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149 159 HLA-A*0201 protein (A) Superposition of the 1E6 TCR (multicolored illustration) in complex with all 7 APLs (multicolored sticks) and the A2-ALWGPDPAAA ligand using the HLA-A*0201 (gray illustration) molecule to align all of the structures. FIG |
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192 197 align experimental_method (A) Superposition of the 1E6 TCR (multicolored illustration) in complex with all 7 APLs (multicolored sticks) and the A2-ALWGPDPAAA ligand using the HLA-A*0201 (gray illustration) molecule to align all of the structures. FIG |
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209 219 structures evidence (A) Superposition of the 1E6 TCR (multicolored illustration) in complex with all 7 APLs (multicolored sticks) and the A2-ALWGPDPAAA ligand using the HLA-A*0201 (gray illustration) molecule to align all of the structures. FIG |
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4 11 1E6 TCR complex_assembly The 1E6 TCR and each peptide are colored according to the APL used in the complex as in Figure 1. (B) Position of the 1E6 TCR CDR loops (multicolored lines) in each complex. FIG |
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58 61 APL chemical The 1E6 TCR and each peptide are colored according to the APL used in the complex as in Figure 1. (B) Position of the 1E6 TCR CDR loops (multicolored lines) in each complex. FIG |
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118 125 1E6 TCR complex_assembly The 1E6 TCR and each peptide are colored according to the APL used in the complex as in Figure 1. (B) Position of the 1E6 TCR CDR loops (multicolored lines) in each complex. FIG |
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126 135 CDR loops structure_element The 1E6 TCR and each peptide are colored according to the APL used in the complex as in Figure 1. (B) Position of the 1E6 TCR CDR loops (multicolored lines) in each complex. FIG |
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4 14 ALWGPDPAAA chemical The ALWGPDPAAA peptide (green sticks) is shown in the HLA-A*0201 binding groove (gray surface). (C) The Cα backbone conformation of each APL (multicolored illustration) in the context of the HLA-A*0201 α1 helices (gray illustration). (D) Crossing angle of the 1E6 TCR (multicolored lines) calculated using previously published parameters in the context of the ALWGPDPAAA peptide (green sticks) bound in the HLA-A*0201 binding groove (gray surface). FIG |
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54 79 HLA-A*0201 binding groove site The ALWGPDPAAA peptide (green sticks) is shown in the HLA-A*0201 binding groove (gray surface). (C) The Cα backbone conformation of each APL (multicolored illustration) in the context of the HLA-A*0201 α1 helices (gray illustration). (D) Crossing angle of the 1E6 TCR (multicolored lines) calculated using previously published parameters in the context of the ALWGPDPAAA peptide (green sticks) bound in the HLA-A*0201 binding groove (gray surface). FIG |
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137 140 APL chemical The ALWGPDPAAA peptide (green sticks) is shown in the HLA-A*0201 binding groove (gray surface). (C) The Cα backbone conformation of each APL (multicolored illustration) in the context of the HLA-A*0201 α1 helices (gray illustration). (D) Crossing angle of the 1E6 TCR (multicolored lines) calculated using previously published parameters in the context of the ALWGPDPAAA peptide (green sticks) bound in the HLA-A*0201 binding groove (gray surface). FIG |
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191 201 HLA-A*0201 protein The ALWGPDPAAA peptide (green sticks) is shown in the HLA-A*0201 binding groove (gray surface). (C) The Cα backbone conformation of each APL (multicolored illustration) in the context of the HLA-A*0201 α1 helices (gray illustration). (D) Crossing angle of the 1E6 TCR (multicolored lines) calculated using previously published parameters in the context of the ALWGPDPAAA peptide (green sticks) bound in the HLA-A*0201 binding groove (gray surface). FIG |
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202 212 α1 helices structure_element The ALWGPDPAAA peptide (green sticks) is shown in the HLA-A*0201 binding groove (gray surface). (C) The Cα backbone conformation of each APL (multicolored illustration) in the context of the HLA-A*0201 α1 helices (gray illustration). (D) Crossing angle of the 1E6 TCR (multicolored lines) calculated using previously published parameters in the context of the ALWGPDPAAA peptide (green sticks) bound in the HLA-A*0201 binding groove (gray surface). FIG |
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238 252 Crossing angle evidence The ALWGPDPAAA peptide (green sticks) is shown in the HLA-A*0201 binding groove (gray surface). (C) The Cα backbone conformation of each APL (multicolored illustration) in the context of the HLA-A*0201 α1 helices (gray illustration). (D) Crossing angle of the 1E6 TCR (multicolored lines) calculated using previously published parameters in the context of the ALWGPDPAAA peptide (green sticks) bound in the HLA-A*0201 binding groove (gray surface). FIG |
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260 267 1E6 TCR complex_assembly The ALWGPDPAAA peptide (green sticks) is shown in the HLA-A*0201 binding groove (gray surface). (C) The Cα backbone conformation of each APL (multicolored illustration) in the context of the HLA-A*0201 α1 helices (gray illustration). (D) Crossing angle of the 1E6 TCR (multicolored lines) calculated using previously published parameters in the context of the ALWGPDPAAA peptide (green sticks) bound in the HLA-A*0201 binding groove (gray surface). FIG |
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360 370 ALWGPDPAAA chemical The ALWGPDPAAA peptide (green sticks) is shown in the HLA-A*0201 binding groove (gray surface). (C) The Cα backbone conformation of each APL (multicolored illustration) in the context of the HLA-A*0201 α1 helices (gray illustration). (D) Crossing angle of the 1E6 TCR (multicolored lines) calculated using previously published parameters in the context of the ALWGPDPAAA peptide (green sticks) bound in the HLA-A*0201 binding groove (gray surface). FIG |
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394 402 bound in protein_state The ALWGPDPAAA peptide (green sticks) is shown in the HLA-A*0201 binding groove (gray surface). (C) The Cα backbone conformation of each APL (multicolored illustration) in the context of the HLA-A*0201 α1 helices (gray illustration). (D) Crossing angle of the 1E6 TCR (multicolored lines) calculated using previously published parameters in the context of the ALWGPDPAAA peptide (green sticks) bound in the HLA-A*0201 binding groove (gray surface). FIG |
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407 432 HLA-A*0201 binding groove site The ALWGPDPAAA peptide (green sticks) is shown in the HLA-A*0201 binding groove (gray surface). (C) The Cα backbone conformation of each APL (multicolored illustration) in the context of the HLA-A*0201 α1 helices (gray illustration). (D) Crossing angle of the 1E6 TCR (multicolored lines) calculated using previously published parameters in the context of the ALWGPDPAAA peptide (green sticks) bound in the HLA-A*0201 binding groove (gray surface). FIG |
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31 40 GPD motif structure_element A conserved interaction with a GPD motif underpins the 1E6 TCR interaction with the APLs. FIG |
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55 62 1E6 TCR complex_assembly A conserved interaction with a GPD motif underpins the 1E6 TCR interaction with the APLs. FIG |
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84 88 APLs chemical A conserved interaction with a GPD motif underpins the 1E6 TCR interaction with the APLs. FIG |
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20 27 1E6 TCR complex_assembly Interaction between 1E6 TCR (gray illustration) residues Tyr97α and Tyr97β (the position of these side chains in the TCR in complex with all 7 APLs, and the previously reported A2-ALWGPDPAAA epitope, is shown in multicolored sticks |
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57 63 Tyr97α residue_name_number Interaction between 1E6 TCR (gray illustration) residues Tyr97α and Tyr97β (the position of these side chains in the TCR in complex with all 7 APLs, and the previously reported A2-ALWGPDPAAA epitope, is shown in multicolored sticks |
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68 74 Tyr97β residue_name_number Interaction between 1E6 TCR (gray illustration) residues Tyr97α and Tyr97β (the position of these side chains in the TCR in complex with all 7 APLs, and the previously reported A2-ALWGPDPAAA epitope, is shown in multicolored sticks |
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117 120 TCR complex_assembly Interaction between 1E6 TCR (gray illustration) residues Tyr97α and Tyr97β (the position of these side chains in the TCR in complex with all 7 APLs, and the previously reported A2-ALWGPDPAAA epitope, is shown in multicolored sticks |
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121 136 in complex with protein_state Interaction between 1E6 TCR (gray illustration) residues Tyr97α and Tyr97β (the position of these side chains in the TCR in complex with all 7 APLs, and the previously reported A2-ALWGPDPAAA epitope, is shown in multicolored sticks |
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143 147 APLs chemical Interaction between 1E6 TCR (gray illustration) residues Tyr97α and Tyr97β (the position of these side chains in the TCR in complex with all 7 APLs, and the previously reported A2-ALWGPDPAAA epitope, is shown in multicolored sticks |
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177 190 A2-ALWGPDPAAA chemical Interaction between 1E6 TCR (gray illustration) residues Tyr97α and Tyr97β (the position of these side chains in the TCR in complex with all 7 APLs, and the previously reported A2-ALWGPDPAAA epitope, is shown in multicolored sticks |
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247 264 GPD peptide motif structure_element Interaction between 1E6 TCR (gray illustration) residues Tyr97α and Tyr97β (the position of these side chains in the TCR in complex with all 7 APLs, and the previously reported A2-ALWGPDPAAA epitope, is shown in multicolored sticks |
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309 313 APLs chemical Interaction between 1E6 TCR (gray illustration) residues Tyr97α and Tyr97β (the position of these side chains in the TCR in complex with all 7 APLs, and the previously reported A2-ALWGPDPAAA epitope, is shown in multicolored sticks |
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318 331 A2-ALWGPDPAAA chemical Interaction between 1E6 TCR (gray illustration) residues Tyr97α and Tyr97β (the position of these side chains in the TCR in complex with all 7 APLs, and the previously reported A2-ALWGPDPAAA epitope, is shown in multicolored sticks |
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332 347 in complex with protein_state Interaction between 1E6 TCR (gray illustration) residues Tyr97α and Tyr97β (the position of these side chains in the TCR in complex with all 7 APLs, and the previously reported A2-ALWGPDPAAA epitope, is shown in multicolored sticks |
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352 359 1E6 TCR complex_assembly Interaction between 1E6 TCR (gray illustration) residues Tyr97α and Tyr97β (the position of these side chains in the TCR in complex with all 7 APLs, and the previously reported A2-ALWGPDPAAA epitope, is shown in multicolored sticks |
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33 36 MHC complex_assembly The rest of the peptide, and the MHCα1 helix, are shown as a gray illustration. FIG |
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36 44 α1 helix structure_element The rest of the peptide, and the MHCα1 helix, are shown as a gray illustration. FIG |
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4 11 1E6 TCR complex_assembly The 1E6 TCR makes distinct peptide contacts with peripheral APL residues. FIG |
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60 63 APL chemical The 1E6 TCR makes distinct peptide contacts with peripheral APL residues. FIG |
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25 32 1E6 TCR complex_assembly Interactions between the 1E6 TCR and peptide residues outside of the conserved GPD motif. FIG |
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69 78 conserved protein_state Interactions between the 1E6 TCR and peptide residues outside of the conserved GPD motif. FIG |
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79 88 GPD motif structure_element Interactions between the 1E6 TCR and peptide residues outside of the conserved GPD motif. FIG |
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4 7 MHC complex_assembly The MHCα1 helix is shown in gray illustrations. FIG |
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7 15 α1 helix structure_element The MHCα1 helix is shown in gray illustrations. FIG |
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0 14 Hydrogen bonds bond_interaction Hydrogen bonds are shown as red dotted lines |
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46 74 van der Waals (vdW) contacts bond_interaction Hydrogen bonds are shown as red dotted lines |
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38 45 1E6 TCR complex_assembly Boxes show total contacts between the 1E6 TCR and each peptide ligand. FIG |
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28 35 1E6 TCR complex_assembly (A) Interaction between the 1E6 TCR (black illustration and sticks) and A2-MVWGPDPLYV (black illustration and sticks). (B) Interaction between the 1E6 TCR (red illustration and sticks) and A2-YLGGPDFPTI (red illustration and sticks). (C) Interaction between the 1E6 TCR (blue illustration and sticks) and A2-ALWGPDPAAA (blue illustration and sticks) reproduced from previous published data. FIG |
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72 85 A2-MVWGPDPLYV chemical (A) Interaction between the 1E6 TCR (black illustration and sticks) and A2-MVWGPDPLYV (black illustration and sticks). (B) Interaction between the 1E6 TCR (red illustration and sticks) and A2-YLGGPDFPTI (red illustration and sticks). (C) Interaction between the 1E6 TCR (blue illustration and sticks) and A2-ALWGPDPAAA (blue illustration and sticks) reproduced from previous published data. FIG |
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147 154 1E6 TCR complex_assembly (A) Interaction between the 1E6 TCR (black illustration and sticks) and A2-MVWGPDPLYV (black illustration and sticks). (B) Interaction between the 1E6 TCR (red illustration and sticks) and A2-YLGGPDFPTI (red illustration and sticks). (C) Interaction between the 1E6 TCR (blue illustration and sticks) and A2-ALWGPDPAAA (blue illustration and sticks) reproduced from previous published data. FIG |
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189 202 A2-YLGGPDFPTI chemical (A) Interaction between the 1E6 TCR (black illustration and sticks) and A2-MVWGPDPLYV (black illustration and sticks). (B) Interaction between the 1E6 TCR (red illustration and sticks) and A2-YLGGPDFPTI (red illustration and sticks). (C) Interaction between the 1E6 TCR (blue illustration and sticks) and A2-ALWGPDPAAA (blue illustration and sticks) reproduced from previous published data. FIG |
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262 269 1E6 TCR complex_assembly (A) Interaction between the 1E6 TCR (black illustration and sticks) and A2-MVWGPDPLYV (black illustration and sticks). (B) Interaction between the 1E6 TCR (red illustration and sticks) and A2-YLGGPDFPTI (red illustration and sticks). (C) Interaction between the 1E6 TCR (blue illustration and sticks) and A2-ALWGPDPAAA (blue illustration and sticks) reproduced from previous published data. FIG |
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305 318 A2-ALWGPDPAAA chemical (A) Interaction between the 1E6 TCR (black illustration and sticks) and A2-MVWGPDPLYV (black illustration and sticks). (B) Interaction between the 1E6 TCR (red illustration and sticks) and A2-YLGGPDFPTI (red illustration and sticks). (C) Interaction between the 1E6 TCR (blue illustration and sticks) and A2-ALWGPDPAAA (blue illustration and sticks) reproduced from previous published data. FIG |
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28 35 1E6 TCR complex_assembly (A) Interaction between the 1E6 TCR (black illustration and sticks) and A2-MVWGPDPLYV (black illustration and sticks). (B) Interaction between the 1E6 TCR (red illustration and sticks) and A2-YLGGPDFPTI (red illustration and sticks). (C) Interaction between the 1E6 TCR (blue illustration and sticks) and A2-ALWGPDPAAA (blue illustration and sticks) reproduced from previous published data. FIG |
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72 85 A2-MVWGPDPLYV chemical (A) Interaction between the 1E6 TCR (black illustration and sticks) and A2-MVWGPDPLYV (black illustration and sticks). (B) Interaction between the 1E6 TCR (red illustration and sticks) and A2-YLGGPDFPTI (red illustration and sticks). (C) Interaction between the 1E6 TCR (blue illustration and sticks) and A2-ALWGPDPAAA (blue illustration and sticks) reproduced from previous published data. FIG |
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147 154 1E6 TCR complex_assembly (A) Interaction between the 1E6 TCR (black illustration and sticks) and A2-MVWGPDPLYV (black illustration and sticks). (B) Interaction between the 1E6 TCR (red illustration and sticks) and A2-YLGGPDFPTI (red illustration and sticks). (C) Interaction between the 1E6 TCR (blue illustration and sticks) and A2-ALWGPDPAAA (blue illustration and sticks) reproduced from previous published data. FIG |
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189 202 A2-YLGGPDFPTI chemical (A) Interaction between the 1E6 TCR (black illustration and sticks) and A2-MVWGPDPLYV (black illustration and sticks). (B) Interaction between the 1E6 TCR (red illustration and sticks) and A2-YLGGPDFPTI (red illustration and sticks). (C) Interaction between the 1E6 TCR (blue illustration and sticks) and A2-ALWGPDPAAA (blue illustration and sticks) reproduced from previous published data. FIG |
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262 269 1E6 TCR complex_assembly (A) Interaction between the 1E6 TCR (black illustration and sticks) and A2-MVWGPDPLYV (black illustration and sticks). (B) Interaction between the 1E6 TCR (red illustration and sticks) and A2-YLGGPDFPTI (red illustration and sticks). (C) Interaction between the 1E6 TCR (blue illustration and sticks) and A2-ALWGPDPAAA (blue illustration and sticks) reproduced from previous published data. FIG |
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305 318 A2-ALWGPDPAAA chemical (A) Interaction between the 1E6 TCR (black illustration and sticks) and A2-MVWGPDPLYV (black illustration and sticks). (B) Interaction between the 1E6 TCR (red illustration and sticks) and A2-YLGGPDFPTI (red illustration and sticks). (C) Interaction between the 1E6 TCR (blue illustration and sticks) and A2-ALWGPDPAAA (blue illustration and sticks) reproduced from previous published data. FIG |
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28 35 1E6 TCR complex_assembly (D) Interaction between the 1E6 TCR (green illustration and sticks) and A2-AQWGPDPAAA (green illustration and sticks). (E) Interaction between the 1E6 TCR (dark blue illustration and sticks) and A2-RQFGPDWIVA (dark blue illustration and sticks). (F) Interaction between the 1E6 TCR (purple illustration and sticks) and A2-RQWGPDPAAV (purple illustration and sticks). (G) Interaction between the 1E6 TCR (yellow illustration and sticks) and A2-YQFGPDFPTA (yellow illustration and sticks). (H) Interaction between the 1E6 TCR (cyan illustration and sticks) and A2-RQFGPDFPTI (cyan illustration and sticks). FIG |
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72 85 A2-AQWGPDPAAA chemical (D) Interaction between the 1E6 TCR (green illustration and sticks) and A2-AQWGPDPAAA (green illustration and sticks). (E) Interaction between the 1E6 TCR (dark blue illustration and sticks) and A2-RQFGPDWIVA (dark blue illustration and sticks). (F) Interaction between the 1E6 TCR (purple illustration and sticks) and A2-RQWGPDPAAV (purple illustration and sticks). (G) Interaction between the 1E6 TCR (yellow illustration and sticks) and A2-YQFGPDFPTA (yellow illustration and sticks). (H) Interaction between the 1E6 TCR (cyan illustration and sticks) and A2-RQFGPDFPTI (cyan illustration and sticks). FIG |
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147 154 1E6 TCR complex_assembly (D) Interaction between the 1E6 TCR (green illustration and sticks) and A2-AQWGPDPAAA (green illustration and sticks). (E) Interaction between the 1E6 TCR (dark blue illustration and sticks) and A2-RQFGPDWIVA (dark blue illustration and sticks). (F) Interaction between the 1E6 TCR (purple illustration and sticks) and A2-RQWGPDPAAV (purple illustration and sticks). (G) Interaction between the 1E6 TCR (yellow illustration and sticks) and A2-YQFGPDFPTA (yellow illustration and sticks). (H) Interaction between the 1E6 TCR (cyan illustration and sticks) and A2-RQFGPDFPTI (cyan illustration and sticks). FIG |
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195 208 A2-RQFGPDWIVA chemical (D) Interaction between the 1E6 TCR (green illustration and sticks) and A2-AQWGPDPAAA (green illustration and sticks). (E) Interaction between the 1E6 TCR (dark blue illustration and sticks) and A2-RQFGPDWIVA (dark blue illustration and sticks). (F) Interaction between the 1E6 TCR (purple illustration and sticks) and A2-RQWGPDPAAV (purple illustration and sticks). (G) Interaction between the 1E6 TCR (yellow illustration and sticks) and A2-YQFGPDFPTA (yellow illustration and sticks). (H) Interaction between the 1E6 TCR (cyan illustration and sticks) and A2-RQFGPDFPTI (cyan illustration and sticks). FIG |
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274 281 1E6 TCR complex_assembly (D) Interaction between the 1E6 TCR (green illustration and sticks) and A2-AQWGPDPAAA (green illustration and sticks). (E) Interaction between the 1E6 TCR (dark blue illustration and sticks) and A2-RQFGPDWIVA (dark blue illustration and sticks). (F) Interaction between the 1E6 TCR (purple illustration and sticks) and A2-RQWGPDPAAV (purple illustration and sticks). (G) Interaction between the 1E6 TCR (yellow illustration and sticks) and A2-YQFGPDFPTA (yellow illustration and sticks). (H) Interaction between the 1E6 TCR (cyan illustration and sticks) and A2-RQFGPDFPTI (cyan illustration and sticks). FIG |
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319 332 A2-RQWGPDPAAV chemical (D) Interaction between the 1E6 TCR (green illustration and sticks) and A2-AQWGPDPAAA (green illustration and sticks). (E) Interaction between the 1E6 TCR (dark blue illustration and sticks) and A2-RQFGPDWIVA (dark blue illustration and sticks). (F) Interaction between the 1E6 TCR (purple illustration and sticks) and A2-RQWGPDPAAV (purple illustration and sticks). (G) Interaction between the 1E6 TCR (yellow illustration and sticks) and A2-YQFGPDFPTA (yellow illustration and sticks). (H) Interaction between the 1E6 TCR (cyan illustration and sticks) and A2-RQFGPDFPTI (cyan illustration and sticks). FIG |
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395 402 1E6 TCR complex_assembly (D) Interaction between the 1E6 TCR (green illustration and sticks) and A2-AQWGPDPAAA (green illustration and sticks). (E) Interaction between the 1E6 TCR (dark blue illustration and sticks) and A2-RQFGPDWIVA (dark blue illustration and sticks). (F) Interaction between the 1E6 TCR (purple illustration and sticks) and A2-RQWGPDPAAV (purple illustration and sticks). (G) Interaction between the 1E6 TCR (yellow illustration and sticks) and A2-YQFGPDFPTA (yellow illustration and sticks). (H) Interaction between the 1E6 TCR (cyan illustration and sticks) and A2-RQFGPDFPTI (cyan illustration and sticks). FIG |
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440 453 A2-YQFGPDFPTA chemical (D) Interaction between the 1E6 TCR (green illustration and sticks) and A2-AQWGPDPAAA (green illustration and sticks). (E) Interaction between the 1E6 TCR (dark blue illustration and sticks) and A2-RQFGPDWIVA (dark blue illustration and sticks). (F) Interaction between the 1E6 TCR (purple illustration and sticks) and A2-RQWGPDPAAV (purple illustration and sticks). (G) Interaction between the 1E6 TCR (yellow illustration and sticks) and A2-YQFGPDFPTA (yellow illustration and sticks). (H) Interaction between the 1E6 TCR (cyan illustration and sticks) and A2-RQFGPDFPTI (cyan illustration and sticks). FIG |
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516 523 1E6 TCR complex_assembly (D) Interaction between the 1E6 TCR (green illustration and sticks) and A2-AQWGPDPAAA (green illustration and sticks). (E) Interaction between the 1E6 TCR (dark blue illustration and sticks) and A2-RQFGPDWIVA (dark blue illustration and sticks). (F) Interaction between the 1E6 TCR (purple illustration and sticks) and A2-RQWGPDPAAV (purple illustration and sticks). (G) Interaction between the 1E6 TCR (yellow illustration and sticks) and A2-YQFGPDFPTA (yellow illustration and sticks). (H) Interaction between the 1E6 TCR (cyan illustration and sticks) and A2-RQFGPDFPTI (cyan illustration and sticks). FIG |
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559 572 A2-RQFGPDFPTI chemical (D) Interaction between the 1E6 TCR (green illustration and sticks) and A2-AQWGPDPAAA (green illustration and sticks). (E) Interaction between the 1E6 TCR (dark blue illustration and sticks) and A2-RQFGPDWIVA (dark blue illustration and sticks). (F) Interaction between the 1E6 TCR (purple illustration and sticks) and A2-RQWGPDPAAV (purple illustration and sticks). (G) Interaction between the 1E6 TCR (yellow illustration and sticks) and A2-YQFGPDFPTA (yellow illustration and sticks). (H) Interaction between the 1E6 TCR (cyan illustration and sticks) and A2-RQFGPDFPTI (cyan illustration and sticks). FIG |
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28 35 1E6 TCR complex_assembly (D) Interaction between the 1E6 TCR (green illustration and sticks) and A2-AQWGPDPAAA (green illustration and sticks). (E) Interaction between the 1E6 TCR (dark blue illustration and sticks) and A2-RQFGPDWIVA (dark blue illustration and sticks). (F) Interaction between the 1E6 TCR (purple illustration and sticks) and A2-RQWGPDPAAV (purple illustration and sticks). (G) Interaction between the 1E6 TCR (yellow illustration and sticks) and A2-YQFGPDFPTA (yellow illustration and sticks). (H) Interaction between the 1E6 TCR (cyan illustration and sticks) and A2-RQFGPDFPTI (cyan illustration and sticks). FIG |
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72 85 A2-AQWGPDPAAA chemical (D) Interaction between the 1E6 TCR (green illustration and sticks) and A2-AQWGPDPAAA (green illustration and sticks). (E) Interaction between the 1E6 TCR (dark blue illustration and sticks) and A2-RQFGPDWIVA (dark blue illustration and sticks). (F) Interaction between the 1E6 TCR (purple illustration and sticks) and A2-RQWGPDPAAV (purple illustration and sticks). (G) Interaction between the 1E6 TCR (yellow illustration and sticks) and A2-YQFGPDFPTA (yellow illustration and sticks). (H) Interaction between the 1E6 TCR (cyan illustration and sticks) and A2-RQFGPDFPTI (cyan illustration and sticks). FIG |
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147 154 1E6 TCR complex_assembly (D) Interaction between the 1E6 TCR (green illustration and sticks) and A2-AQWGPDPAAA (green illustration and sticks). (E) Interaction between the 1E6 TCR (dark blue illustration and sticks) and A2-RQFGPDWIVA (dark blue illustration and sticks). (F) Interaction between the 1E6 TCR (purple illustration and sticks) and A2-RQWGPDPAAV (purple illustration and sticks). (G) Interaction between the 1E6 TCR (yellow illustration and sticks) and A2-YQFGPDFPTA (yellow illustration and sticks). (H) Interaction between the 1E6 TCR (cyan illustration and sticks) and A2-RQFGPDFPTI (cyan illustration and sticks). FIG |
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195 208 A2-RQFGPDWIVA chemical (D) Interaction between the 1E6 TCR (green illustration and sticks) and A2-AQWGPDPAAA (green illustration and sticks). (E) Interaction between the 1E6 TCR (dark blue illustration and sticks) and A2-RQFGPDWIVA (dark blue illustration and sticks). (F) Interaction between the 1E6 TCR (purple illustration and sticks) and A2-RQWGPDPAAV (purple illustration and sticks). (G) Interaction between the 1E6 TCR (yellow illustration and sticks) and A2-YQFGPDFPTA (yellow illustration and sticks). (H) Interaction between the 1E6 TCR (cyan illustration and sticks) and A2-RQFGPDFPTI (cyan illustration and sticks). FIG |
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274 281 1E6 TCR complex_assembly (D) Interaction between the 1E6 TCR (green illustration and sticks) and A2-AQWGPDPAAA (green illustration and sticks). (E) Interaction between the 1E6 TCR (dark blue illustration and sticks) and A2-RQFGPDWIVA (dark blue illustration and sticks). (F) Interaction between the 1E6 TCR (purple illustration and sticks) and A2-RQWGPDPAAV (purple illustration and sticks). (G) Interaction between the 1E6 TCR (yellow illustration and sticks) and A2-YQFGPDFPTA (yellow illustration and sticks). (H) Interaction between the 1E6 TCR (cyan illustration and sticks) and A2-RQFGPDFPTI (cyan illustration and sticks). FIG |
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319 332 A2-RQWGPDPAAV chemical (D) Interaction between the 1E6 TCR (green illustration and sticks) and A2-AQWGPDPAAA (green illustration and sticks). (E) Interaction between the 1E6 TCR (dark blue illustration and sticks) and A2-RQFGPDWIVA (dark blue illustration and sticks). (F) Interaction between the 1E6 TCR (purple illustration and sticks) and A2-RQWGPDPAAV (purple illustration and sticks). (G) Interaction between the 1E6 TCR (yellow illustration and sticks) and A2-YQFGPDFPTA (yellow illustration and sticks). (H) Interaction between the 1E6 TCR (cyan illustration and sticks) and A2-RQFGPDFPTI (cyan illustration and sticks). FIG |
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395 402 1E6 TCR complex_assembly (D) Interaction between the 1E6 TCR (green illustration and sticks) and A2-AQWGPDPAAA (green illustration and sticks). (E) Interaction between the 1E6 TCR (dark blue illustration and sticks) and A2-RQFGPDWIVA (dark blue illustration and sticks). (F) Interaction between the 1E6 TCR (purple illustration and sticks) and A2-RQWGPDPAAV (purple illustration and sticks). (G) Interaction between the 1E6 TCR (yellow illustration and sticks) and A2-YQFGPDFPTA (yellow illustration and sticks). (H) Interaction between the 1E6 TCR (cyan illustration and sticks) and A2-RQFGPDFPTI (cyan illustration and sticks). FIG |
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440 453 A2-YQFGPDFPTA chemical (D) Interaction between the 1E6 TCR (green illustration and sticks) and A2-AQWGPDPAAA (green illustration and sticks). (E) Interaction between the 1E6 TCR (dark blue illustration and sticks) and A2-RQFGPDWIVA (dark blue illustration and sticks). (F) Interaction between the 1E6 TCR (purple illustration and sticks) and A2-RQWGPDPAAV (purple illustration and sticks). (G) Interaction between the 1E6 TCR (yellow illustration and sticks) and A2-YQFGPDFPTA (yellow illustration and sticks). (H) Interaction between the 1E6 TCR (cyan illustration and sticks) and A2-RQFGPDFPTI (cyan illustration and sticks). FIG |
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516 523 1E6 TCR complex_assembly (D) Interaction between the 1E6 TCR (green illustration and sticks) and A2-AQWGPDPAAA (green illustration and sticks). (E) Interaction between the 1E6 TCR (dark blue illustration and sticks) and A2-RQFGPDWIVA (dark blue illustration and sticks). (F) Interaction between the 1E6 TCR (purple illustration and sticks) and A2-RQWGPDPAAV (purple illustration and sticks). (G) Interaction between the 1E6 TCR (yellow illustration and sticks) and A2-YQFGPDFPTA (yellow illustration and sticks). (H) Interaction between the 1E6 TCR (cyan illustration and sticks) and A2-RQFGPDFPTI (cyan illustration and sticks). FIG |
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559 572 A2-RQFGPDFPTI chemical (D) Interaction between the 1E6 TCR (green illustration and sticks) and A2-AQWGPDPAAA (green illustration and sticks). (E) Interaction between the 1E6 TCR (dark blue illustration and sticks) and A2-RQFGPDWIVA (dark blue illustration and sticks). (F) Interaction between the 1E6 TCR (purple illustration and sticks) and A2-RQWGPDPAAV (purple illustration and sticks). (G) Interaction between the 1E6 TCR (yellow illustration and sticks) and A2-YQFGPDFPTA (yellow illustration and sticks). (H) Interaction between the 1E6 TCR (cyan illustration and sticks) and A2-RQFGPDFPTI (cyan illustration and sticks). FIG |
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14 21 ligated protein_state Comparison of ligated and unligated APLs. FIG |
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26 35 unligated protein_state Comparison of ligated and unligated APLs. FIG |
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36 40 APLs chemical Comparison of ligated and unligated APLs. FIG |
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0 13 Superposition experimental_method Superposition of each APL in unligated form and ligated to the 1E6 TCR. FIG |
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22 25 APL chemical Superposition of each APL in unligated form and ligated to the 1E6 TCR. FIG |
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29 38 unligated protein_state Superposition of each APL in unligated form and ligated to the 1E6 TCR. FIG |
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48 55 ligated protein_state Superposition of each APL in unligated form and ligated to the 1E6 TCR. FIG |
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63 70 1E6 TCR complex_assembly Superposition of each APL in unligated form and ligated to the 1E6 TCR. FIG |
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4 13 unligated protein_state All unligated pMHCs are shown as light green illustrations. FIG |
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14 19 pMHCs complex_assembly All unligated pMHCs are shown as light green illustrations. FIG |
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44 53 structure evidence Peptide sequences are shown underneath each structure aligned with the peptide structure. FIG |
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79 88 structure evidence Peptide sequences are shown underneath each structure aligned with the peptide structure. FIG |
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4 17 A2-MVWGPDPLYV chemical (A) A2-MVWGPDPLYV (black sticks). FIG |
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46 50 Tyr8 residue_name_number A large conformational shift was observed for Tyr8 in the ligated versus unligated states (black circle). (B) A2-YLGGPDFPTI (red sticks). (C) A2-ALWGPDPAAA (blue sticks) reproduced from previous published data. (D) A2-AQWGPDPAAA (green sticks). (E) A2-RQFGPDWIVA (dark blue sticks). (F) A2-RQWGPDPAAV (purple sticks). (G) A2-YQFGPDFPTA (yellow sticks). (H) A2-RQFGPDFPTI (cyan sticks). FIG |
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58 65 ligated protein_state A large conformational shift was observed for Tyr8 in the ligated versus unligated states (black circle). (B) A2-YLGGPDFPTI (red sticks). (C) A2-ALWGPDPAAA (blue sticks) reproduced from previous published data. (D) A2-AQWGPDPAAA (green sticks). (E) A2-RQFGPDWIVA (dark blue sticks). (F) A2-RQWGPDPAAV (purple sticks). (G) A2-YQFGPDFPTA (yellow sticks). (H) A2-RQFGPDFPTI (cyan sticks). FIG |
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73 82 unligated protein_state A large conformational shift was observed for Tyr8 in the ligated versus unligated states (black circle). (B) A2-YLGGPDFPTI (red sticks). (C) A2-ALWGPDPAAA (blue sticks) reproduced from previous published data. (D) A2-AQWGPDPAAA (green sticks). (E) A2-RQFGPDWIVA (dark blue sticks). (F) A2-RQWGPDPAAV (purple sticks). (G) A2-YQFGPDFPTA (yellow sticks). (H) A2-RQFGPDFPTI (cyan sticks). FIG |
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110 123 A2-YLGGPDFPTI chemical A large conformational shift was observed for Tyr8 in the ligated versus unligated states (black circle). (B) A2-YLGGPDFPTI (red sticks). (C) A2-ALWGPDPAAA (blue sticks) reproduced from previous published data. (D) A2-AQWGPDPAAA (green sticks). (E) A2-RQFGPDWIVA (dark blue sticks). (F) A2-RQWGPDPAAV (purple sticks). (G) A2-YQFGPDFPTA (yellow sticks). (H) A2-RQFGPDFPTI (cyan sticks). FIG |
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142 155 A2-ALWGPDPAAA chemical A large conformational shift was observed for Tyr8 in the ligated versus unligated states (black circle). (B) A2-YLGGPDFPTI (red sticks). (C) A2-ALWGPDPAAA (blue sticks) reproduced from previous published data. (D) A2-AQWGPDPAAA (green sticks). (E) A2-RQFGPDWIVA (dark blue sticks). (F) A2-RQWGPDPAAV (purple sticks). (G) A2-YQFGPDFPTA (yellow sticks). (H) A2-RQFGPDFPTI (cyan sticks). FIG |
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215 228 A2-AQWGPDPAAA chemical A large conformational shift was observed for Tyr8 in the ligated versus unligated states (black circle). (B) A2-YLGGPDFPTI (red sticks). (C) A2-ALWGPDPAAA (blue sticks) reproduced from previous published data. (D) A2-AQWGPDPAAA (green sticks). (E) A2-RQFGPDWIVA (dark blue sticks). (F) A2-RQWGPDPAAV (purple sticks). (G) A2-YQFGPDFPTA (yellow sticks). (H) A2-RQFGPDFPTI (cyan sticks). FIG |
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249 262 A2-RQFGPDWIVA chemical A large conformational shift was observed for Tyr8 in the ligated versus unligated states (black circle). (B) A2-YLGGPDFPTI (red sticks). (C) A2-ALWGPDPAAA (blue sticks) reproduced from previous published data. (D) A2-AQWGPDPAAA (green sticks). (E) A2-RQFGPDWIVA (dark blue sticks). (F) A2-RQWGPDPAAV (purple sticks). (G) A2-YQFGPDFPTA (yellow sticks). (H) A2-RQFGPDFPTI (cyan sticks). FIG |
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287 300 A2-RQWGPDPAAV chemical A large conformational shift was observed for Tyr8 in the ligated versus unligated states (black circle). (B) A2-YLGGPDFPTI (red sticks). (C) A2-ALWGPDPAAA (blue sticks) reproduced from previous published data. (D) A2-AQWGPDPAAA (green sticks). (E) A2-RQFGPDWIVA (dark blue sticks). (F) A2-RQWGPDPAAV (purple sticks). (G) A2-YQFGPDFPTA (yellow sticks). (H) A2-RQFGPDFPTI (cyan sticks). FIG |
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322 335 A2-YQFGPDFPTA chemical A large conformational shift was observed for Tyr8 in the ligated versus unligated states (black circle). (B) A2-YLGGPDFPTI (red sticks). (C) A2-ALWGPDPAAA (blue sticks) reproduced from previous published data. (D) A2-AQWGPDPAAA (green sticks). (E) A2-RQFGPDWIVA (dark blue sticks). (F) A2-RQWGPDPAAV (purple sticks). (G) A2-YQFGPDFPTA (yellow sticks). (H) A2-RQFGPDFPTI (cyan sticks). FIG |
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357 370 A2-RQFGPDFPTI chemical A large conformational shift was observed for Tyr8 in the ligated versus unligated states (black circle). (B) A2-YLGGPDFPTI (red sticks). (C) A2-ALWGPDPAAA (blue sticks) reproduced from previous published data. (D) A2-AQWGPDPAAA (green sticks). (E) A2-RQFGPDWIVA (dark blue sticks). (F) A2-RQWGPDPAAV (purple sticks). (G) A2-YQFGPDFPTA (yellow sticks). (H) A2-RQFGPDFPTI (cyan sticks). FIG |
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4 11 1E6 TCR complex_assembly The 1E6 TCR makes distinct peptide contacts with the MHC surface depending on the peptide cargo. FIG |
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53 64 MHC surface site The 1E6 TCR makes distinct peptide contacts with the MHC surface depending on the peptide cargo. FIG |
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25 32 1E6 TCR complex_assembly Interactions between the 1E6 TCR and the MHC α1 helix residues Arg65, Lys66, and Gln72. FIG |
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41 44 MHC complex_assembly Interactions between the 1E6 TCR and the MHC α1 helix residues Arg65, Lys66, and Gln72. FIG |
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45 53 α1 helix structure_element Interactions between the 1E6 TCR and the MHC α1 helix residues Arg65, Lys66, and Gln72. FIG |
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63 68 Arg65 residue_name_number Interactions between the 1E6 TCR and the MHC α1 helix residues Arg65, Lys66, and Gln72. FIG |
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70 75 Lys66 residue_name_number Interactions between the 1E6 TCR and the MHC α1 helix residues Arg65, Lys66, and Gln72. FIG |
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81 86 Gln72 residue_name_number Interactions between the 1E6 TCR and the MHC α1 helix residues Arg65, Lys66, and Gln72. FIG |
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0 14 Hydrogen bonds bond_interaction Hydrogen bonds are shown as red dotted lines |
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46 49 vdW bond_interaction Hydrogen bonds are shown as red dotted lines |
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0 3 MHC complex_assembly MHCα1 helix are shown in gray illustrations. FIG |
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3 11 α1 helix structure_element MHCα1 helix are shown in gray illustrations. FIG |
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38 45 1E6 TCR complex_assembly Boxes show total contacts between the 1E6 TCR and these key residues (green boxes are MHC residues |
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86 89 MHC complex_assembly Boxes show total contacts between the 1E6 TCR and these key residues (green boxes are MHC residues |
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116 119 TCR complex_assembly Boxes show total contacts between the 1E6 TCR and these key residues (green boxes are MHC residues |
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0 22 Thermodynamic analysis experimental_method Thermodynamic analysis of the 1E6 TCR with A2-ALWGPDPAAA and the APLs. FIG |
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30 37 1E6 TCR complex_assembly Thermodynamic analysis of the 1E6 TCR with A2-ALWGPDPAAA and the APLs. FIG |
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43 56 A2-ALWGPDPAAA chemical Thermodynamic analysis of the 1E6 TCR with A2-ALWGPDPAAA and the APLs. FIG |
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65 69 APLs chemical Thermodynamic analysis of the 1E6 TCR with A2-ALWGPDPAAA and the APLs. FIG |
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30 37 1E6 TCR complex_assembly Eight serial dilutions of the 1E6 TCR were injected, in duplicate, over each immobilized APL and A2-ALW at 5°C, 13°C, 18°C, 25°C, 30°C, and 37°C. FIG |
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89 92 APL chemical Eight serial dilutions of the 1E6 TCR were injected, in duplicate, over each immobilized APL and A2-ALW at 5°C, 13°C, 18°C, 25°C, 30°C, and 37°C. FIG |
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97 103 A2-ALW chemical Eight serial dilutions of the 1E6 TCR were injected, in duplicate, over each immobilized APL and A2-ALW at 5°C, 13°C, 18°C, 25°C, 30°C, and 37°C. FIG |
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4 32 equilibrium binding constant evidence The equilibrium binding constant (KD) values were calculated using a nonlinear curve fit (y = [P1x]/[P2 + X]), and thermodynamic parameters were calculated according to the Gibbs-Helmholtz equation (ΔG° = ΔH − TΔS°). FIG |
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34 36 KD evidence The equilibrium binding constant (KD) values were calculated using a nonlinear curve fit (y = [P1x]/[P2 + X]), and thermodynamic parameters were calculated according to the Gibbs-Helmholtz equation (ΔG° = ΔH − TΔS°). FIG |
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69 88 nonlinear curve fit experimental_method The equilibrium binding constant (KD) values were calculated using a nonlinear curve fit (y = [P1x]/[P2 + X]), and thermodynamic parameters were calculated according to the Gibbs-Helmholtz equation (ΔG° = ΔH − TΔS°). FIG |
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173 197 Gibbs-Helmholtz equation experimental_method The equilibrium binding constant (KD) values were calculated using a nonlinear curve fit (y = [P1x]/[P2 + X]), and thermodynamic parameters were calculated according to the Gibbs-Helmholtz equation (ΔG° = ΔH − TΔS°). FIG |
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199 202 ΔG° evidence The equilibrium binding constant (KD) values were calculated using a nonlinear curve fit (y = [P1x]/[P2 + X]), and thermodynamic parameters were calculated according to the Gibbs-Helmholtz equation (ΔG° = ΔH − TΔS°). FIG |
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205 207 ΔH evidence The equilibrium binding constant (KD) values were calculated using a nonlinear curve fit (y = [P1x]/[P2 + X]), and thermodynamic parameters were calculated according to the Gibbs-Helmholtz equation (ΔG° = ΔH − TΔS°). FIG |
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210 214 TΔS° evidence The equilibrium binding constant (KD) values were calculated using a nonlinear curve fit (y = [P1x]/[P2 + X]), and thermodynamic parameters were calculated according to the Gibbs-Helmholtz equation (ΔG° = ΔH − TΔS°). FIG |
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4 25 binding free energies evidence The binding free energies, ΔG° (ΔG° = RTlnKD), were plotted against temperature (K) using nonlinear regression to fit the 3-parameters van’t Hoff equation (RT ln KD = ΔH° – TΔS° + ΔCp°[T-T0] – TΔCp° ln [T/T0] with T0 = 298 K). FIG |
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27 30 ΔG° evidence The binding free energies, ΔG° (ΔG° = RTlnKD), were plotted against temperature (K) using nonlinear regression to fit the 3-parameters van’t Hoff equation (RT ln KD = ΔH° – TΔS° + ΔCp°[T-T0] – TΔCp° ln [T/T0] with T0 = 298 K). FIG |
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32 35 ΔG° evidence The binding free energies, ΔG° (ΔG° = RTlnKD), were plotted against temperature (K) using nonlinear regression to fit the 3-parameters van’t Hoff equation (RT ln KD = ΔH° – TΔS° + ΔCp°[T-T0] – TΔCp° ln [T/T0] with T0 = 298 K). FIG |
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90 110 nonlinear regression experimental_method The binding free energies, ΔG° (ΔG° = RTlnKD), were plotted against temperature (K) using nonlinear regression to fit the 3-parameters van’t Hoff equation (RT ln KD = ΔH° – TΔS° + ΔCp°[T-T0] – TΔCp° ln [T/T0] with T0 = 298 K). FIG |
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135 154 van’t Hoff equation experimental_method The binding free energies, ΔG° (ΔG° = RTlnKD), were plotted against temperature (K) using nonlinear regression to fit the 3-parameters van’t Hoff equation (RT ln KD = ΔH° – TΔS° + ΔCp°[T-T0] – TΔCp° ln [T/T0] with T0 = 298 K). FIG |
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156 164 RT ln KD evidence The binding free energies, ΔG° (ΔG° = RTlnKD), were plotted against temperature (K) using nonlinear regression to fit the 3-parameters van’t Hoff equation (RT ln KD = ΔH° – TΔS° + ΔCp°[T-T0] – TΔCp° ln [T/T0] with T0 = 298 K). FIG |
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167 170 ΔH° evidence The binding free energies, ΔG° (ΔG° = RTlnKD), were plotted against temperature (K) using nonlinear regression to fit the 3-parameters van’t Hoff equation (RT ln KD = ΔH° – TΔS° + ΔCp°[T-T0] – TΔCp° ln [T/T0] with T0 = 298 K). FIG |
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173 177 TΔS° evidence The binding free energies, ΔG° (ΔG° = RTlnKD), were plotted against temperature (K) using nonlinear regression to fit the 3-parameters van’t Hoff equation (RT ln KD = ΔH° – TΔS° + ΔCp°[T-T0] – TΔCp° ln [T/T0] with T0 = 298 K). FIG |
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180 184 ΔCp° evidence The binding free energies, ΔG° (ΔG° = RTlnKD), were plotted against temperature (K) using nonlinear regression to fit the 3-parameters van’t Hoff equation (RT ln KD = ΔH° – TΔS° + ΔCp°[T-T0] – TΔCp° ln [T/T0] with T0 = 298 K). FIG |
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193 198 TΔCp° evidence The binding free energies, ΔG° (ΔG° = RTlnKD), were plotted against temperature (K) using nonlinear regression to fit the 3-parameters van’t Hoff equation (RT ln KD = ΔH° – TΔS° + ΔCp°[T-T0] – TΔCp° ln [T/T0] with T0 = 298 K). FIG |
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4 21 1E6-A2-ALWGPDPAAA complex_assembly (A) 1E6-A2-ALWGPDPAAA |
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27 44 1E6-A2-AQWGPDPAAA complex_assembly (A) 1E6-A2-ALWGPDPAAA |
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50 67 1E6-A2-RQFGPDWIVA complex_assembly (A) 1E6-A2-ALWGPDPAAA |
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73 90 1E6-A2-RQWGPDPAAV complex_assembly (A) 1E6-A2-ALWGPDPAAA |
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96 113 1E6-A2-YQFGPDFPTA complex_assembly (A) 1E6-A2-ALWGPDPAAA |
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123 140 1E6-A2-RQFGPDFPTI complex_assembly (A) 1E6-A2-ALWGPDPAAA |
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0 12 1E6 TCR-pMHC complex_assembly 1E6 TCR-pMHC contacts, affinity measurements and thermodynamics TABLE |
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23 44 affinity measurements experimental_method 1E6 TCR-pMHC contacts, affinity measurements and thermodynamics TABLE |
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49 63 thermodynamics experimental_method 1E6 TCR-pMHC contacts, affinity measurements and thermodynamics TABLE |
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