cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7956149.v1
title: Figure 5: Fractal assemblies capture and release greater amounts of cargo compared to globular assemblies

description: <b>Figure 5: Fractal assemblies capture and release greater amounts of cargo compared to globular assemblies. </b>Scheme for the envisioned reversible capture of cargo proteins for the (<b>A</b>) fractal and (<b>B</b>) globular structures. The red stars denote an example cargo protein (antibody). (<b>C</b>) % protein capture was measured for 3:2 fractal (assemblies obtained with 3 AtzA-pY: 2 AtzC-SH2), 3:2 GS linker (globular assemblies obtained at the same stoichiometry with fusion proteins containing long GS-rich linkers), and 3:1 fractal (assemblies obtained with 3 AtzA-pY: 1 AtzC-SH2). The 3:2 fractal captured more IgG antibody (red bars) and GFP-SH2 (green barss), and degraded more substrate TCP (purple bar; reflecting the higher capture efficiency of enzyme DhaA-Sh2) than the 3:2 GS linker assemblies. In addition, 3:2 fractal released more captured antibody compared to the 3:2 GS linker when incubated with YopH phosphatase (blue bars). (<b>D</b>, <b>E</b>) Confocal fluorescence microscopy images of the 3-component assembly with GFP-SH2 showing the topology of incorporation of GFP-SH2 in fractal and (<b>F-G</b>) the incorporation of GFP-SH2 into the globular assemblies. (<b>H-I</b>) the IgG antibody Alexa Fluor 568 incorporation into the fractal assembly and (<b>J-K</b>) the incorporation into the globular assembly.<b></b>
DOI: 10.6084/m9.figshare.7956158.v1
title: Dataset S1

description: Within-patient Non-typeable Haemophilus influenzae differential expression analysis comparing nasopharynx against bronchoalveolar isolates
DOI: 10.6084/m9.figshare.7956194.v2
title: Table S2 - WGS and RNAseq summary information

description: Whole-genome sequencing and RNA sequencing summary information.
DOI: 10.6084/m9.figshare.7956050
title: Supplementary Figure 17 Rate of assembly formation is dependent on ATP concentration

description: Article: Stimulus-responsive Self-Assembly of Protein-Based Fractals by Computational Design Pre-print: bioRxiv 274183; doi: https://doi.org/10.1101/274183 Fig. S17. Rate of assembly formation is dependent on ATP concentration. (A) Volume mean of sample from 0 – 1500 sec. Each point represents average of triplicates. (B) Number mean of sample from 0 – 1500 sec. Each point represents average of triplicates. Curve fitting performed using sloping spline with smoothness parameter (p) and adjusted R2 5 value given in Table S1 (highest concentration of ATP to lowest, starting from top to bottom at time 0 for both graphs). See Table S2 for curve fitting data for figure S17. Note that this figure provides data for Fig 2E. (SI 2.9) Phosphorylation, assembly formation, and disassembly – The phosphorylation protocol was based upon Src kinase activity assay by Sigma (Catalog # S1076). In a final reaction volume of 150μL, 3μM AtzAM1 was mixed into 1X Kinase Activity Buffer (4mM MgCl2, 2.5mM MnCl2, 0.25mM DTT, 5mM MOPS, 2.5mM glycerol-2-phosphate, 1mM EGTA, 400nM EDTA, pH 7.6), 2.5 mM MnCl2,HNG, 2 mM ATP, 800ng Src kinase, and incubated for 7 – 16 hr at 25°C for phosphorylation to occur. After phosphorylating, AtzCM1 was added to a final 2μM concentration. Assembly was allowed to form at 2hr 25°C. Disassembly was performed by adding 4.8μg of YopH phosphatase into the 150μL reaction mixture after assembly formation occurred. Size measurements using DLS were performed to determine assembly formation/disassembly. (SI 2.10) Dynamic light scattering (DLS) – 50 μL of an assembly sample was used for size determination using a Malvern Zetasizer and a quartz cuvette (ZEN2112, Malvern). Ten spectra measures were recorded for eleven replicates at 25 °C. The standard operating procedure accounted for 5% glycerol in solution. % volume was collected and reported. (SI 2.13) DLS Kinetics (varying ATP) Experiment – An assembly mixture of 3 µM non35 pyAtzA and 2 µM AtzCM1 was prepared (as described previously) and syringe-filtered at 0.22 µm. To each 50 µL reaction volume, 1.2 µg of src kinase was added. Size was monitored continuously for 30 min at 25°C in a low-volume quartz sizing cuvette (Malvern; ZEN2112) using a Zetasizer Nano ZS (Malvern) at 50 µL/sample. Measurements were performed in triplicates. Each sample was read and averaged five times over the course of 25 seconds for a single time point. Curve fitting was performed in MATLAB (R2016b; Mathworks) using sloping spline function, with varying smoothing parameters. Adjusted R2 was used to determine model validity.<br>
DOI: 10.6084/m9.figshare.12878636.v8
title: Additional file of Expression of microRNA and their gene targets are dysregulated in preinvasive breast cancer

description: Additional file of Expression of microRNA and their gene targets are dysregulated in preinvasive breast cancer
DOI: 10.6084/m9.figshare.7956104.v1
title: Supplementary Figure 35, 36, and 37 Enzymatic activity of the three-component atrazine-degradation assembly and comparison of fractal vs globular assembly

description: Supp Figure 35: (A) Atrazine degradation pathway, enzymatic conversion of atrazine to cyanuric acid, and further enzymatic conversion to NH3 and CO2. (B) AtzB was added as an SH2-domain fusion to the two-component (AtzA-AtzC) assembly. c and d, Three-component assembly formation was validated using HIM (C), and the incorporation of AtzB was confirmed with fluorescence microscopy (using an Alexa-658-labeled AtzB) (D). (E) and (F), Assemblies were found to be more thermotolerant, as detected by incubation at a given temperature for 30 min followed by activity assays, and more robust to mechanical shearing forces, as detected by ability to withstand shaking. (G), <b>Assemblies and free enzymes were incorporated into a Basotect® polymer foam with different TEOS % layers, to trap proteins, and assayed for cyanuric acid production. </b>Proteins can be lost during the wash step after crosslinking and the % of protein lost under each condition is indicated on top of the bars. Supp Figure 36: <b>Phase contrast micrographs of the Basotect® polymer foam with and without assemblies for the AtzAM1, AtzBSH2, and AtzCM1 components. </b>(A and B) The microporous polymer foam with no assemblies. (C and D) The assemblies have been immobilized into the polymer foam, red arrows depict locations with assemblies. Images were taken with a Leica DM4000 B LED microscope, 10X objective (100X total magnification). Supp Figure 37: <b>The fractal-like assemblies (Reg-Assembly) and the extended linker globular assemblies (ExtLinker-Assembly) enzymatic conversion of atrazine to cyanuric acid demonstrates no enzymatic benefit of a globular assembly. </b>(A) AtzB was incorporated into the two-component assembly as an SH2-domain fusion as previously described to create the three-component assembly for both the fractal and globular assemblies. The activity of the fractal assembly was similar than the extended linker assemblies (GS linker) under different shaking speeds. Note: All enzymatic data from excel is then taken into graph pad for analyses, converted to Relative Yield %, addition of error bars, exported in vector format, and edited in Illustrator for final figure.<br>
DOI: 10.6084/m9.figshare.7956194.v3
title: Table S2 - WGS and RNAseq summary information

description: Whole-genome sequencing and RNA sequencing summary information.
DOI: 10.6084/m9.figshare.7956044
title: Supplementary Figure 14 Inhibition of assembly at 0.66 µM AtzC-SH2, 1 µM pY-AtzA, 0-6 µM SH2-DhaA

description: Article: Stimulus-responsive Self-Assembly of Protein-Based Fractals by Computational Design<br> Pre-print: bioRxiv 274183; doi: https://doi.org/10.1101/274183 Figure: S14. Inhibition of assembly at 0.66 µM AtzC-SH2, 1 µM pY-AtzA, 0-6 µM SH2-DhaA. (A) Inhibition graph of SH2-DhaA on 0.66 µM AtzC-SH2, 1 µM pY-AtzA assembly. Size recorded represents most predominant DLS sizing peak. Data are presented as mean ± 1 standard deviation. IC50 = 3.05 µM. Adjusted R2 5 = 0.98. (B) DLS traces of assembly from 0 - 6 µM SH2-DhaA. DLS traces are of triplicate samples, each read 3 times. (SI 2.9) Phosphorylation, assembly formation, and disassembly – The phosphorylation protocol was based upon Src kinase activity assay by Sigma (Catalog # S1076). In a final reaction volume of 150μL, 3μM AtzAM1 was mixed into 1X Kinase Activity Buffer (4mM MgCl2, 2.5mM MnCl2, 0.25mM DTT, 5mM MOPS, 2.5mM glycerol-2-phosphate, 1mM EGTA, 400nM EDTA, pH 7.6), 2.5 mM MnCl2,HNG, 2 mM ATP, 800ng Src kinase, and incubated for 7 – 16 hr at 25°C for phosphorylation to occur. After phosphorylating, AtzCM1 was added to a final 2μM concentration. Assembly was allowed to form at 2hr 25°C. Disassembly was performed by adding 4.8μg of YopH phosphatase into the 150μL reaction mixture after assembly formation occurred. Size measurements using DLS were performed to determine assembly formation/disassembly. (SI 2.10) Dynamic light scattering (DLS) – 50 μL of an assembly sample was used for size determination using a Malvern Zetasizer and a quartz cuvette (ZEN2112, Malvern). Ten spectra measures were recorded for eleven replicates at 25 °C. The standard operating procedure accounted for 5% glycerol in solution.<br>
DOI: 10.6084/m9.figshare.7956047
title: Supplementary Figure 15 Inhibition of assembly at 2 µM AtzC-SH2, 3 µM pY-AtzA with 0-15 µM inhibitor

description: Article: Stimulus-responsive Self-Assembly of Protein-Based Fractals by Computational Design Pre-print: bioRxiv 274183; doi: https://doi.org/10.1101/274183 Figure: S15. Inhibition of assembly at 2 µM AtzC-SH2, 3 µM pY-AtzA with 0-15 µM inhibitor. All DLS traces were performed in triplicate (A) Inhibition graph of SH2-DhaA of 2 µM AtzC-SH2, 3 µM pY-AtzA assembly. Size recorded represents most predominant DLS sizing peak. Data are presented as mean ± 1 standard deviation. IC50 (SH2) = 6.18 µM, IC50 (SH2-DhaA) = 6.13 µM. Adjusted R2 (SH2) = 0.97. Adjusted R2 8 (SH2-DhaA) = 0.99. (B) DLS traces of assembly from 0-15 µM SH2. (C) DLS traces of assembly from 0-15 µM SH2-DhaA (SI 2.9) Phosphorylation, assembly formation, and disassembly – The phosphorylation protocol was based upon Src kinase activity assay by Sigma (Catalog # S1076). In a final reaction volume of 150μL, 3μM AtzAM1 was mixed into 1X Kinase Activity Buffer (4mM MgCl2, 2.5mM MnCl2, 0.25mM DTT, 5mM MOPS, 2.5mM glycerol-2-phosphate, 1mM EGTA, 400nM EDTA, pH 7.6), 2.5 mM MnCl2,HNG, 2 mM ATP, 800ng Src kinase, and incubated for 7 – 16 hr at 25°C for phosphorylation to occur. After phosphorylating, AtzCM1 was added to a final 2μM concentration. Assembly was allowed to form at 2hr 25°C. Disassembly was performed by adding 4.8μg of YopH phosphatase into the 150μL reaction mixture after assembly formation occurred. Size measurements using DLS were performed to determine assembly formation/disassembly. (SI 2.10) Dynamic light scattering (DLS) – 50 μL of an assembly sample was used for size determination using a Malvern Zetasizer and a quartz cuvette (ZEN2112, Malvern). Ten spectra measures were recorded for eleven replicates at 25 °C. The standard operating procedure accounted for 5% glycerol in solution.<br>
DOI: 10.6084/m9.figshare.7956041
title: Supplementary Figure 20 Average size of particle formed by pY-AtzA and super-binder AtzC-SH2

description: Article: Stimulus-responsive Self-Assembly of Protein-Based Fractals by Computational Design Pre-print: bioRxiv 274183; doi: https://doi.org/10.1101/274183 Figure: Fig. S20. Average size of particle formed by pY-AtzA and super-binder AtzC-SH2. (A) Heat map showing volume-weighted mean size of particles found from 50-3000 nM pY-AtzA and 50-2000 nM AtzC-SH2. Value shown is average of two physical samples. Histogram illustrates distribution of sizes found on heatmap. (B) Volume distributions of heat map. Distributions shown are representative of other traces in the sample. (SI 2.9) Phosphorylation, assembly formation, and disassembly – The phosphorylation protocol was based upon Src kinase activity assay by Sigma (Catalog # S1076). In a final reaction volume of 150μL, 3μM AtzAM1 was mixed into 1X Kinase Activity Buffer (4mM MgCl2, 2.5mM MnCl2, 0.25mM DTT, 5mM MOPS, 2.5mM glycerol-2-phosphate, 1mM EGTA, 400nM EDTA, pH 7.6), 2.5 mM MnCl2,HNG, 2 mM ATP, 800ng Src kinase, and incubated for 7 – 16 hr at 25°C for phosphorylation to occur. After phosphorylating, AtzCM1 was added to a final 2μM concentration. Assembly was allowed to form at 2hr 25°C. Disassembly was performed by adding 4.8μg of YopH phosphatase into the 150μL reaction mixture after assembly formation occurred. Size measurements using DLS were performed to determine assembly formation/disassembly. (SI 2.10) Dynamic light scattering (DLS) – 50 μL of an assembly sample was used for size determination using a Malvern Zetasizer and a quartz cuvette (ZEN2112, Malvern). Ten spectra measures were recorded for eleven replicates at 25 °C. The standard operating procedure accounted for 5% glycerol in solution. % volume was collected and reported. (SI 2.12) DLS Titration Experiment – 6 µM, 3 µM, 1.5 µM, 0.5 µM, 0.1 µM pyAtzA was phosphorylated (as described previously) with an incubation time of overnight at 25°C. Either AtzCM1 wildtype (WT) or AtzCM1 superbinder (SB) was added to each sample at 2 µM, 1 µM, 0.5 µM, 0.25 µM, 0.50 µM final concentration. The sample was allowed to incubate for 2 hr at 25°C. Therefore, the final concentrations of all components was from 3 µM – 0.05 µM pyAtzA, 2 µM – 0.05 µM AtzCM1-WT or AtzCM1-SB. DLS was performed at 25°C, 50 µL/sample volume, in a low-volume quartz sizing cuvette (Malvern; ZEN2112) using a Zetasizer Nano ZS (Malvern). Measurements were performed in duplicate with each sample read and averaged 15 times.<br>
DOI: 10.6084/m9.figshare.7956050.v1
title: Supplementary Figure 17 Rate of assembly formation is dependent on ATP concentration

description: Article: Stimulus-responsive Self-Assembly of Protein-Based Fractals by Computational Design Pre-print: bioRxiv 274183; doi: https://doi.org/10.1101/274183 Fig. S17. Rate of assembly formation is dependent on ATP concentration. (A) Volume mean of sample from 0 – 1500 sec. Each point represents average of triplicates. (B) Number mean of sample from 0 – 1500 sec. Each point represents average of triplicates. Curve fitting performed using sloping spline with smoothness parameter (p) and adjusted R2 5 value given in Table S1 (highest concentration of ATP to lowest, starting from top to bottom at time 0 for both graphs). See Table S2 for curve fitting data for figure S17. Note that this figure provides data for Fig 2E. (SI 2.9) Phosphorylation, assembly formation, and disassembly – The phosphorylation protocol was based upon Src kinase activity assay by Sigma (Catalog # S1076). In a final reaction volume of 150μL, 3μM AtzAM1 was mixed into 1X Kinase Activity Buffer (4mM MgCl2, 2.5mM MnCl2, 0.25mM DTT, 5mM MOPS, 2.5mM glycerol-2-phosphate, 1mM EGTA, 400nM EDTA, pH 7.6), 2.5 mM MnCl2,HNG, 2 mM ATP, 800ng Src kinase, and incubated for 7 – 16 hr at 25°C for phosphorylation to occur. After phosphorylating, AtzCM1 was added to a final 2μM concentration. Assembly was allowed to form at 2hr 25°C. Disassembly was performed by adding 4.8μg of YopH phosphatase into the 150μL reaction mixture after assembly formation occurred. Size measurements using DLS were performed to determine assembly formation/disassembly. (SI 2.10) Dynamic light scattering (DLS) – 50 μL of an assembly sample was used for size determination using a Malvern Zetasizer and a quartz cuvette (ZEN2112, Malvern). Ten spectra measures were recorded for eleven replicates at 25 °C. The standard operating procedure accounted for 5% glycerol in solution. % volume was collected and reported. (SI 2.13) DLS Kinetics (varying ATP) Experiment – An assembly mixture of 3 µM non35 pyAtzA and 2 µM AtzCM1 was prepared (as described previously) and syringe-filtered at 0.22 µm. To each 50 µL reaction volume, 1.2 µg of src kinase was added. Size was monitored continuously for 30 min at 25°C in a low-volume quartz sizing cuvette (Malvern; ZEN2112) using a Zetasizer Nano ZS (Malvern) at 50 µL/sample. Measurements were performed in triplicates. Each sample was read and averaged five times over the course of 25 seconds for a single time point. Curve fitting was performed in MATLAB (R2016b; Mathworks) using sloping spline function, with varying smoothing parameters. Adjusted R2 was used to determine model validity.<br>
DOI: 10.6084/m9.figshare.7956194.v5
title: Table S2 - WGS and RNAseq summary information

description: Whole-genome sequencing and RNA sequencing summary information.
DOI: 10.6084/m9.figshare.7956038
title: Supplementary Figure 10 Biolayer interferometry (BLI) binding profiles of AtzC wildtype SH2 fusion (AtzC9 wtSH2) and AtzC superbinder SH2 fusion (AtzC-SH2) to phosphorylated SH2 binding peptide AtzA fusion (pY-AtzA)

description: Article: Stimulus-responsive Self-Assembly of Protein-Based Fractals by Computational Design Pre-print: bioRxiv 274183; doi: https://doi.org/10.1101/274183 Figure: S10. Biolayer interferometry (BLI) binding profiles of AtzC wildtype SH2 fusion (AtzC9 wtSH2) and AtzC superbinder SH2 fusion (AtzC-SH2) to phosphorylated SH2 binding peptide AtzA fusion (pY-AtzA). (A) Binding profile of AtzC-wtSH2 to pY-AtzA. PY-AtzA was loaded onto the biosensor via a streptavidin-biotin interaction. AtzC-wtSH2 was flowed into the sample. KD = 41.79 ± 0.32 nM. (B) Binding profile of AtzCM1 (superbinder) to pY-AtzA. PY AtzA was loaded onto the biosensor via a streptavidin-biotin interaction. AtzC-SH2 was flowed into the sample. KD = 7.67 ± 0.52 nM. Comment. KD was calculated using ForteBio BLItz software. KD statistical analysis provided in datafile. (SI 2.8) Bio-layer interferometry (BLI) – AtzAM1 was phosphorylated using the conditions described below. pY-AtzAM1 was then biotinylated at 10mM Sulfo-NHS-Biotin (APExBIO) for 30min at 25°C. Excess biotin was buffer exchanged with a PD-10 desalting column (GE Healthcare) equilibrated with HNG. Biotinylated pY-AtzAM1 was loaded onto streptavidin (SA) coated biosensors (ForteBio) and used for BLI. AtzCM1 was flowed in from 4nM to 4μM. BLI experiments were performed using the BLItz System (ForteBio).****Note: This work was part of the Rutgers Biomod 2016 Project (M. Liu, A. Permaul, O. Dineen, M. Khalid, M. Shea, G.L. Bilker). See reference below.
DOI: 10.6084/m9.figshare.7956044.v1
title: Supplementary Figure 14 Inhibition of assembly at 0.66 µM AtzC-SH2, 1 µM pY-AtzA, 0-6 µM SH2-DhaA

description: Article: Stimulus-responsive Self-Assembly of Protein-Based Fractals by Computational Design<br> Pre-print: bioRxiv 274183; doi: https://doi.org/10.1101/274183 Figure: S14. Inhibition of assembly at 0.66 µM AtzC-SH2, 1 µM pY-AtzA, 0-6 µM SH2-DhaA. (A) Inhibition graph of SH2-DhaA on 0.66 µM AtzC-SH2, 1 µM pY-AtzA assembly. Size recorded represents most predominant DLS sizing peak. Data are presented as mean ± 1 standard deviation. IC50 = 3.05 µM. Adjusted R2 5 = 0.98. (B) DLS traces of assembly from 0 - 6 µM SH2-DhaA. DLS traces are of triplicate samples, each read 3 times. (SI 2.9) Phosphorylation, assembly formation, and disassembly – The phosphorylation protocol was based upon Src kinase activity assay by Sigma (Catalog # S1076). In a final reaction volume of 150μL, 3μM AtzAM1 was mixed into 1X Kinase Activity Buffer (4mM MgCl2, 2.5mM MnCl2, 0.25mM DTT, 5mM MOPS, 2.5mM glycerol-2-phosphate, 1mM EGTA, 400nM EDTA, pH 7.6), 2.5 mM MnCl2,HNG, 2 mM ATP, 800ng Src kinase, and incubated for 7 – 16 hr at 25°C for phosphorylation to occur. After phosphorylating, AtzCM1 was added to a final 2μM concentration. Assembly was allowed to form at 2hr 25°C. Disassembly was performed by adding 4.8μg of YopH phosphatase into the 150μL reaction mixture after assembly formation occurred. Size measurements using DLS were performed to determine assembly formation/disassembly. (SI 2.10) Dynamic light scattering (DLS) – 50 μL of an assembly sample was used for size determination using a Malvern Zetasizer and a quartz cuvette (ZEN2112, Malvern). Ten spectra measures were recorded for eleven replicates at 25 °C. The standard operating procedure accounted for 5% glycerol in solution.<br>
DOI: 10.6084/m9.figshare.7956047.v1
title: Supplementary Figure 15 Inhibition of assembly at 2 µM AtzC-SH2, 3 µM pY-AtzA with 0-15 µM inhibitor

description: Article: Stimulus-responsive Self-Assembly of Protein-Based Fractals by Computational Design Pre-print: bioRxiv 274183; doi: https://doi.org/10.1101/274183 Figure: S15. Inhibition of assembly at 2 µM AtzC-SH2, 3 µM pY-AtzA with 0-15 µM inhibitor. All DLS traces were performed in triplicate (A) Inhibition graph of SH2-DhaA of 2 µM AtzC-SH2, 3 µM pY-AtzA assembly. Size recorded represents most predominant DLS sizing peak. Data are presented as mean ± 1 standard deviation. IC50 (SH2) = 6.18 µM, IC50 (SH2-DhaA) = 6.13 µM. Adjusted R2 (SH2) = 0.97. Adjusted R2 8 (SH2-DhaA) = 0.99. (B) DLS traces of assembly from 0-15 µM SH2. (C) DLS traces of assembly from 0-15 µM SH2-DhaA (SI 2.9) Phosphorylation, assembly formation, and disassembly – The phosphorylation protocol was based upon Src kinase activity assay by Sigma (Catalog # S1076). In a final reaction volume of 150μL, 3μM AtzAM1 was mixed into 1X Kinase Activity Buffer (4mM MgCl2, 2.5mM MnCl2, 0.25mM DTT, 5mM MOPS, 2.5mM glycerol-2-phosphate, 1mM EGTA, 400nM EDTA, pH 7.6), 2.5 mM MnCl2,HNG, 2 mM ATP, 800ng Src kinase, and incubated for 7 – 16 hr at 25°C for phosphorylation to occur. After phosphorylating, AtzCM1 was added to a final 2μM concentration. Assembly was allowed to form at 2hr 25°C. Disassembly was performed by adding 4.8μg of YopH phosphatase into the 150μL reaction mixture after assembly formation occurred. Size measurements using DLS were performed to determine assembly formation/disassembly. (SI 2.10) Dynamic light scattering (DLS) – 50 μL of an assembly sample was used for size determination using a Malvern Zetasizer and a quartz cuvette (ZEN2112, Malvern). Ten spectra measures were recorded for eleven replicates at 25 °C. The standard operating procedure accounted for 5% glycerol in solution.<br>