bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polar zippers: Their role in human disease
Authors: Perutz Max 
Published: February 2009

AbstractAscaris hemoglobin consists of 8 subunits, each of which contains a C‐terminal peptide with the sequence Glu‐Glu‐Lys‐His repeated 4 times. When plotted on a β‐strand, this sequence leads to alternate lysines and glutamates on one side of the strand, and alternate glutamates and histidines on the other side, suggestive of a polar zipper that links the subunits together. A computer search of the protein database showed that the same or similar sequences also occur in other proteins. Some contain long repeats of Asp‐Arg or Glu‐Arg, among them the small nuclear ribonucleo‐U1 70K protein, which is an autoantigen in systemic lupus erythematosis. These repeats appear to constitute the dominant epitopes in the autoimmune reaction. Single chains with Asp‐Arg repeats may form α‐helices in which alternate positively charged ridges and negatively charged grooves compensate each other. Several separate chains with Asp‐Arg repeats could compensate each other's charges optimally by zipping together to β‐sheets.Several homeodomains of Drosophila, as well as the human transcription factor SP1, contain repeats of glutamines. Molecular modeling, circular dichroism, and electron and X‐ray diffraction studies of a synthetic poly(L‐glutamine) showed that it forms β‐sheets held together by hydrogen bonds between the main‐chain and side‐chain amides. Published data suggest that the function of these glutamine repeats consists of joining essential transcription factors bound to distant segments of DNA.The study of the structure and function of glutamine repeats has assumed medical importance with the discovery that Huntington's disease and 3 other dominantly inherited diseases are associated with a lengthening of glutamine repeats in the proteins coded for by the affected genes.
Control of nucleation of protein crystals
Authors: Blow D.M. , Chayen N.E. , Lloyd L.F. , Saridakis E. 
Published: February 2009

AbstractControl of nucleation may be needed to obtain a reliable supply of large protein crystals, when standard techniques give many small or twinned crystals. Heterogeneous nucleation may be controlled by the use of fine filters, with the elimination of airborne contaminants by working under paraffin oil. The area of contact with the supporting vessel also has an important effect. A heterogeneous nucleant for lysozyme (identified earlier) has been shown to be effective for carboxypeptidase G2. Control of homogeneous nucleation (previously demonstrated by dilutions of a nucleating sample after various times of incubation) may also be achieved by incubating a sample at 1 temperature, where nucleation can occur, and changing the temperature to conditions where there is growth but no nucleation.
Protein crystallography and infectious diseases
Authors: Verlinde Christophe L.M.J. , Merritt Ethan A. , Van Den Akker Focco , Kim Hidong , Feil Ingeborg , Delboni Luis F. , Mande Shekhar C. , Sarfaty Steve , Petra Philip H. , Hol Wim G.J. 
Published: February 2009

AbstractThe current rapid growth in the number of known 3‐dimensional protein structures is producing a database of structures that is increasingly useful as a starting point for the development of new medically relevant molecules such as drugs, therapeutic proteins, and vaccines. This development is beautifully illustrated in the recent book, Protein structure: New approaches to disease and therapy (Perutz, 1992). There is a great and growing promise for the design of molecules for the treatment or prevention of a wide variety of diseases, an endeavor made possible by the insights derived from the structure and function of crucial proteins from pathogenic organisms and from man.We present here 2 illustrations of structure‐based drug design. The first is the prospect of developing antitrypanosomal drugs based on crystallographic, ligand‐binding, and molecular modeling studies of glycolytic glycosomal enzymes from Trypanosomatidae. These unicellular organisms are responsible for several tropical diseases, including African and American trypanosomiases, as well as various forms of leishmaniasis. Because the target enzymes are also present in the human host, this project is a pioneering study in selective design. The second illustrative case is the prospect of designing anti‐cholera drugs based on detailed analysis of the structure of cholera toxin and the closely related Escherichia coli heat‐labile enterotoxin. Such potential drugs can be targeted either at inhibiting the toxin's receptor binding site or at blocking the toxin's intracellular catalytic activity.Study of the Vibrio cholerae and E. coli toxins serves at the same time as an example of a general approach to structure‐based vaccine design. These toxins exhibit a remarkable ability to stimulate the mucosal immune system, and early results have suggested that this property can be maintained by engineered fusion proteins based on the native toxin structure. The challenge is thus to incorporate selected epitopes from foreign pathogens into the native framework of the toxin such that crucial features of both the epitope and the toxin are maintained. That is, the modified toxin must continue to evoke a strong mucosal immune response, and this response must be directed against an epitope conformation characteristic of the original pathogen.
Influenza virus neuraminidase: Structure, antibodies, and inhibitors
Authors: Colman P.M. 
Published: February 2009

AbstractThe determination of the 3‐dimensional structure of the influenza virus neuraminidase in 1983 has served as a platform for understanding interactions between antibodies and protein antigens, for investigating antigenic variation in influenza viruses, and for devising new inhibitors of the enzyme. That work is reviewed here, together with more recent developments that have resulted in one of the inhibitors entering clinical trials as an anti‐influenza virus drug.
Comparison of the intermediate complexes of human growth hormone bound to the human growth hormone and prolactin receptors
Authors: Kossiakoff Anthony A. , Somers William , Ultsch Mark , Andow Kerrie , Muller Yves A. , De Vos Abraham M. 
Published: February 2009

AbstractThe crystal structures of complexes of human growth hormone (hGH) with the growth hormone and prolactin receptors (hGHR and hPRLR, respectively), together with the mutational data available for these systems, suggest that an extraordinary combination of conformational adaptability, together with finely tuned specificity, governs the molecular recognition processes operative in these systems. On the one hand, in the active 1:2 ligand‐receptor complexes, 2 copies of the same receptor use the identical set of binding determinants to recognize topographically different surfaces on the hormone. On the other hand, comparing the 1:1 hGH‐hGHR and hGH‐hPRLR complexes, 2 distinct receptors use this same set of binding determinants to interact with the identical binding site on the ligand, even though few residues among the binding determinants are conserved. The structural evidence demonstrates that this versatility is accomplished by local conformational flexibility of the binding loops, allowing adaptation to different binding environments, together with rigid‐body movements of the receptor domains, necessary for the creation of specific interactions with the same binding site.
Quantification of tertiary structural conservation despite primary sequence drift in the globin fold
Authors: Aronson Hans‐Erik G. , Hendrickson Wayne A. , Royer William E. 
Published: February 2009

AbstractThe globin family of protein structures was the first for which it was recognized that tertiary structure can be highly conserved even when primary sequences have diverged to a virtually undetectable level of similarity. This principle of structural inertia in molecular evolution is now evident for many other protein families. We have performed a systematic comparison of the sequences and structures of 6 representative hemoglobin subunits as diverse in origin as plants, clams, and humans. Our analysis is based on a 97‐residue helical core in common to all 6 structures. Amino acid sequence identities range from 12.4% to 42.3% in pairwise comparisons, and, despite these variations, the maximal RMS deviation in α‐carbon positions is 3.02 Å. Overall, sequence similarity and structural deviation are significantly anticorrelated, with a correlation coefficient of —0.71, but for a set of structures having under 20% pairwise identity, this anticorrelation falls to —0.38, which emphasizes the weak connection between a specific sequence and the tertiary fold. There is substantial variability in structure outside the helical core, and functional characteristics of these globins also differ appreciably. Nevertheless, despite variations in detail that the sequence dissimilarities and functional differences imply, the core structures of these globins remain remarkably preserved.
Electrostatic effects in the control of glycogen phosphorylase by phosphorylation
Authors: Johnson L.N. , Barford D. 
Published: February 2009

AbstractElectrostatic effects are important in the initial activation mechanism of glycogen phosphorylase by phosphorylation. Analysis of the electrostatic surface potential of glycogen phosphorylase with the program GRASP shows that in the unphosphorylated state, the N‐terminal 20 residues, which include a number of basic amino acids, are located close to a position on the surface of the molecule that is highly acidic. Upon phosphorylation by phosphorylase kinase at Ser 14, the N‐terminal residues change their position and conformation so that the Ser‐P is directed away from the acidic patch and to an intersubunit site where 2 arginines bind the phosphate. This recognition site is created through tertiary and quaternary structural changes that accompany the activation mechanism.
Structure‐function relationship in the globular type III antifreeze protein: Identification of a cluster of surface residues required for binding to ice
Authors: Chao Heman , DeLuca Carl I. , Davies Peter L. , Sykes Brian D. , Sönnichsen Frank D. 
Published: February 2009

AbstractAntifreeze proteins (AFPs) depress the freezing point of aqueous solutions by binding to and inhibiting the growth of ice. Whereas the ice‐binding surface of some fish AFPs is suggested by their linear, repetitive, hydrogen bonding motifs, the 66‐amino‐acid‐long Type III AFP has a compact, globular fold without any obvious periodicity. In the structure, 9 β‐strands are paired to form 2 triple‐stranded antiparallel sheets and 1 double‐stranded anti‐parallel sheet, with the 2 triple sheets arranged as an orthogonal β‐sandwich (Sönnichsen FD, Sykes BD, Chao H, Davies PL, 1993, Science 259:1154–1157). Based on its structure and an alignment of Type III AFP isoform sequences, a cluster of conserved, polar, surface‐accessible amino acids (N14, T18, Q44, and N46) was noted on and around the triple‐stranded sheet near the C‐terminus. At 3 of these sites, mutations that switched amide and hydroxyl groups caused a large decrease in antifreeze activity, but amide to carboxylic acid changes produced AFPs that were fully active at pH 3 and pH 6. This is consistent with the observation that Type III AFP is optimally active from pH 2 to pH 11. At a concentration of 1 mg/mL, Q44T, N14S, and T18N had 50%, 25%, and 10% of the activity of wild‐type antifreeze, respectively. The effects of the mutations were cumulative, such that the double mutant N14S/Q44T had 10% of the wild‐type activity and the triple mutant N14S/T18N/Q44T had no activity. All mutants with reduced activity were shown to be correctly folded by NMR spectroscopy. Moreover, a complete characterization of the triple mutant by 2‐dimensional NMR spectroscopy indicated that the individual and combined mutations did not significantly alter the structure of these proteins. These results suggest that the C‐terminal β‐sheet of Type III AFP is primarily responsible for antifreeze activity, and they identify N14, T18, and Q44 as key residues for the AFP‐ice interaction.
Structural studies of the engrailed homeodomain
Authors: Clarke Neil D. , Kissinger Charles R. , Desjarlais John , Gilliland Gary L. , Pabo Carl O. 
Published: February 2009

AbstractThe structure of the Drosophila engrailed homeodomain has been solved by molecular replacement and refined to an R‐factor of 19.7% at a resolution of 2.1 Å. This structure offers a high‐resolution view of an important family of DNA‐binding proteins and allows comparison to the structure of the same protein bound to DNA. The most significant difference between the current structure and that of the 2.8‐Å engrailed‐DNA complex is the close packing of an extended strand against the rest of the protein in the unbound protein. Structural features of the protein not previously noted include a “herringbone” packing of 4 aromatic residues in the core of the protein and an extensive network of salt bridges that covers much of the helix 1‐helix 2 surface. Other features that may play a role in stabilizing the native state include the interaction of buried carbonyl oxygen atoms with the edge of Phe 49 and a bias toward statistically preferred side‐chain dihedral angles. There is substantial disorder at both ends of the 61 amino acid protein. A 51‐amino acid variant of engrailed (residues 6–56) was synthesized and shown by CD and thermal denaturation studies to be structurally and thermodynamically similar to the full‐length domain.
Formation of a native‐like subdomain in a partially folded intermediate of bovine pancreatic trypsin inhibitor
Authors: Staley Jonathan P. , Kim Peter S. 
Published: February 2009

AbstractIn the folding of bovine pancreatic trypsin inhibitor (BPTI), the single‐disulfide intermediate [30–51] plays a key role. We have investigated a recombinant analog of [30–51] using 2‐dimensional nuclear magnetic resonance (2D‐NMR). This recombinant analog, named [30–51]Ala, contains a disulfide bond between Cys‐30 and Cys‐51, but contains alanine in place of the other cysteines in BPTI to prevent the formation of other intermediates. By 2D‐NMR, [30–51]Ala consists of 2 regions —one folded and one predominantly unfolded. The folded region resembles a previously characterized peptide model of [30–51], named PαPβ, that contains a native‐like subdomain with tertiary packing. The unfolded region includes the first 14 N‐terminal residues of [30–51] and is as unfolded as an isolated peptide containing these residues. Using protein dissection, we demonstrate that the folded and unfolded regions of [30–51]Ala are structurally independent. The partially folded structure of [30–51]Ala explains many of the properties of authentic [30–51] in the folding pathway of BPTI. Moreover, direct structural characterization of [30–51]Ala has revealed that a crucial step in the folding pathway of BPTI coincides with the formation of a native‐like subdomain, supporting models for protein folding that emphasize the formation of cooperatively folded subdomains.
A common structural motif incorporating a cystine knot and a triple‐stranded β‐sheet in toxic and inhibitory polypeptides
Authors: Pallaghy Paul K. , Norton Raymond S. , Nielsen Katherine J. , Craik David J. 
Published: February 2009

AbstractA common structural motif consisting of a cystine knot and a small triple‐stranded β‐sheet has been defined from comparison of the 3‐dimensional structures of the polypeptides ω‐conotoxin GVIA (Conus geographus), kalata BI (Oldenlandia affinis DC), and CMTI‐I (Curcurbita maxima). These 3 polypeptides have diverse biological activities and negligible amino acid sequence identity, but each contains 3 disulfide bonds that give rise to a cystine knot. This knot consists of a ring formed by the first 2 bonds (1–4 and 2–5) and the intervening polypeptide backbone, through which the third disulfide (3–6) passes. The other component of this motif is a triple‐stranded, anti‐parallel β‐sheet containing a minimum of 10 residues, XXC2, XC5X, XXC6X (where the numbers on the half‐cystine residues refer to their positions in the disulfide pattern). The presence in these polypeptides of both the cystine knot and antiparallel β‐sheet suggests that both structural features are required for the stability of the motif. This structural motif is also present in other protease inhibitors and a spider toxin. It appears to be one of the smallest stable globular domains found in proteins and is commonly used in toxins and inhibitors that act by blocking the function of larger protein receptors such as ion channels or proteases.
Three‐dimensional model and quaternary structure of the human eye lens protein γS‐crystallin based on β‐ and γ‐crystallin X‐ray coordinates and ultracentrifugation
Authors: Zarina S. , Zaidi Z.H. , Driessen H. , Srinivasan N. , Slingsby C. , Jaenicke R. 
Published: February 2009

AbstractA 3‐dimensional model of the human eye lens protein γS‐crystallin has been constructed using comparative modeling approaches encoded in the program COMPOSER on the basis of the 3‐dimensional structure of γ‐crystallin and β‐crystallin. The model is biased toward the monomeric γB‐crystallin, which is more similar in sequence. Bovine γS‐crystallin was shown to be monomeric by analytical ultracentrifugation without any tendency to form assemblies up to concentrations in the millimolar range. The connecting peptide between domains was therefore built assuming an intramolecular association as in the monomeric γ‐crystallins. Because the linker has 1 extra residue compared with γB and βB2, the conformation of the connecting peptide was constructed by using a fragment from a protein database. γS‐crystallin differs from γB‐crystallin mainly in the interface region between domains. The charged residues are generally paired, although in a different way from both β‐ and γ‐crystallins, and may contribute to the different roles of these proteins in the lens.
Multiple protein structure alignment
Authors: Taylor William R. , Flores Tomas P. , Orengo Christine A. 
Published: February 2009

AbstractA method was developed to compare protein structures and to combine them into a multiple structure consensus. Previous methods of multiple structure comparison have only concatenated pairwise alignments or produced a consensus structure by averaging coordinate sets. The current method is a fusion of the fast structure comparison program SSAP and the multiple sequence alignment program MULTAL. As in MULTAL, structures are progressively combined, producing intermediate consensus structures that are compared directly to each other and all remaining single structures. This leads to a hierarchic “condensation,” continually evaluated in the light of the emerging conserved core regions.Following the SSAP approach, all interatomic vectors were retained with well‐conserved regions distinguished by coherent vector bundles (the structural equivalent of a conserved sequence position). Each bundle of vectors is summarized by a resultant, whereas vector coherence is captured in an error term, which is the only distinction between conserved and variable positions. Resultant vectors are used directly in the comparison, which is weighted by their error values, giving greater importance to the matching of conserved positions. The resultant vectors and their errors can also be used directly in molecular modeling.Applications of the method were assessed by the quality of the resulting sequence alignments, phylogenetic tree construction, and databank scanning with the consensus. Visual assessment of the structural superpositions and consensus structure for various well‐characterized families confirmed that the consensus had identified a reasonable core.
A quantitative methodology for the de novo design of proteins
Authors: Brenner Steven E. , Berry Alan 
Published: February 2009

AbstractWe have developed a general quantitative methodology for designing proteins de novo, which automatically produces sequences for any given plausible protein structure. The method incorporates statistical information, a theoretical description of protein structure, and motifs described in the literature. A model system embodying a portion of the quantitative methodology has been used to design many protein sequences for the phage 434 Cro and fibronectin type III domain folds, as well as several other structures. Residue sequences selected by this prototype share no significant identity with any natural protein. Nonetheless, 3‐dimensional models of the designed sequences appear generally plausible. When examined using secondary structure prediction methods and profile analysis, the designed sequences generally score considerably better than the natural ones. The designed sequences are also in reasonable agreement with a sequence template. This quantitative methodology is likely to be capable of successfully designing new proteins and yielding fundamental insights about the determinants of protein structure.
Malate dehydrogenase: A model for structure, evolution, and catalysis
Authors: Goward Christopher R. , Nicholls David J. 
Published: February 2009

AbstractMalate dehydrogenases are widely distributed and alignment of the amino acid sequences show that the enzyme has diverged into 2 main phylogenetic groups. Multiple amino acid sequence alignments of malate dehydrogenases also show that there is a low degree of primary structural similarity, apart from in several positions crucial for nucleotide binding, catalysis, and the subunit interface. The 3‐dimensional structures of several malate dehydrogenases are similar, despite their low amino acid sequence identity. The coenzyme specificity of malate dehydrogenase may be modulated by substitution of a single residue, as can the substrate specificity. The mechanism of catalysis of malate dehydrogenase is similar to that of lactate dehydrogenase, an enzyme with which it shares a similar 3‐dimensional structure. Substitution of a single amino acid residue of a lactate dehydrogenase changes the enzyme specificity to that of a malate dehydrogenase, but a similar substitution in a malate dehydrogenase resulted in relaxation of the high degree of specificity for oxaloacetate. Knowledge of the 3‐dimensional structures of malate and lactate dehydrogenases allows the redesign of enzymes by rational rather than random mutation and may have important commercial implications.
Different protein sequences can give rise to highly similar folds through different stabilizing interactions
Authors: Laurents D. V. , Subbiah S. , Levitt M. 
Published: February 2009

AbstractWe report an interesting case of structural similarity between 2 small, nonhomologous proteins, the third domain of ovomucoid (ovomucoid) and the C‐terminal fragment of ribosomal L7/L12 protein (CTF). The region of similarity consists of a 3‐stranded β‐sheet and an α‐helix. This region is highly similar; the corresponding elements of secondary structure share a common topology, and the RMS difference for “equivalent” Cα atoms is 1.6 Å. Surprisingly, this common structure arises from completely different sequences. For the common core, the sequence identity is less than 3%, and there is neither significant sequence similarity nor similarity in the position or orientation of conserved hydrophobic residues. This superposition raises the question of how 2 entirely different sequences can produce an identical structure. Analyzing this common region in ovomucoid revealed that it is stabilized by disulfide bonds. In contrast, the corresponding structure in CTF is stabilized in the α‐helix by a composition of residues with high helix‐forming propensities. This result suggests that different sequences and different stabilizing interactions can produce an identical structure.