bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preliminary crystallographic analysis of class 3 rat liver aldehyde dehydrogenase
Authors: Rose John P. , Hempel John , Kuo Ingrid , Lindahl Ronald , Wang Bi‐Cheng 
Published: May 2005

AbstractNAD‐linked aldehyde dehydrogenases (A1DH) (EC 1.2.1.3) catalyze the irreversible oxidation of a wide variety of aldehydes to their respective carboxylic acids. Crystals of a class 3 A1DH (from an Escherichia coli expression system) suitable for X‐ray analysis have been obtained. These crystals, which can be grown to a size of 0.8 × 0.3 × 0.2 mm, diffract to 2.5 Å resolution. Analysis of the diffraction pattern indicates that the crystals belong to the monoclinic space group P21, with cell parameters a = 65.11 Å, b = 170.67 Å, c = 47.15 Å, and β = 110.5°. Assuming one dimer per asymmetric unit, the value Vm is calculated to be 2.45 and the solvent content of the crystal is estimated to be 50%. A self‐rotation function study produced significant rotation peaks (58% of the origin) on the K = 180 section at ψ = 90° and ϕ = 71° and 341°, indicating that the pseudo‐dimer axis is (or is very nearly) perpendicular to the b‐axis.
A helix–turn–strand structural motif common in α–β proteins
Authors: Rice Phoebe A. , Goldman Adrian , Steitz Thomas A. 
Published: May 2005

AbstractBy exhaustive structural comparisons, we have found that about one‐third of the α‐helix–turn–β–strand polypeptides in α–β barrel domains share a common structural motif. The chief characteristics of this motif are that first, the geometry of the turn between the α‐helix and the β‐strand is somewhat constrained, and second, the β‐strand contains a hydrophobic patch that fits into a hydrophobic pocket on the α‐helix. The geometry of the turn does not seem to be a major determinant of the α–β unit, because the turns vary in length from four to six residues. However, the motif does not occur when there are few constraints on the geometry of the turn–for instance, when the turns between the α‐helix and the β‐strands are very long. It also occurs much less frequently in flat‐sheet α–β proteins, where the topology is much less regular and the amount of twist on the sheet varies considerably more than in the barrel proteins. The motif may be one of the basic building blocks from which α–β barrels are constructed.
Database of homology‐derived protein structures and the structural meaning of sequence alignment
Authors: Sander Chris , Schneider Reinhard 
Published: May 2005

AbstractThe database of known protein three‐dimensional structures can be significantly increased by the use of sequence homology, based on the following observations. (1) The database of known sequences, currently at more than 12,000 proteins, is two orders of magnitude larger than the database of known structures. (2) The currently most powerful method of predicting protein structures is model building by homology. (3) Structural homology can be inferred from the level of sequence similarity. (4) The threshold of sequence similarity sufficient for structural homology depends strongly on the length of the alignment. Here, we first quantify the relation between sequence similarity, structure similarity, and alignment length by an exhaustive survey of alignments between proteins of known structure and report a homology threshold curve as a function of alignment length. We then produce a database of homology‐derived secondary structure of proteins (HSSP) by aligning to each protein of known structure all sequences deemed homologous on the basis of the threshold curve. For each known protein structure, the derived database contains the aligned sequences, secondary structure, sequence variability, and sequence profile. Tertiary structures of the aligned sequences are implied, but not modeled explicity. The database effectively increases the number of known protein structures by a factor of five to more than 1800. The results may be useful in assessing the structural significance of matches in sequence database searches, in deriving preferences and patterns for structure prediction, in elucidating the structural role of conserved residues, and in modeling three‐dimensional detail by homology.
Role of conserved proline residues in stabilizing tryptophan synthase α subunit: Analysis by mutants with alanine or glycine
Authors: Yutani Katsuhide , Hayashi Seiko , Sugisaki Yoshiko , Ogasahara Kyoko 
Published: May 2005

AbstractTo study the role of Pro residues in the conformation and conformational stability of a protein, nine mutant α subunits of tryptophan synthase from Escherichia coli, in which Ala or Gly was substituted for each of six Pro residues (positions 28, 57, 62, 96, 132, and 207) that are conserved in 10 microoganisms, were constructed by means of site‐directed mutagenesis. The far‐ultraviolet (UV) CD spectra of five mutant α subunits with Ala in place of Pro were identical to the spectrum of the wild‐type protein, the exception being the mutant at position 207 (P207A). CD values in the far‐UV region were less negative for P207A, indicating that the Pro residue at position 207 plays a role in maintaining the intact structure of the α subunit. The negative CD values of the Gly mutants examined (P28G, P96G, and P132G) were also decreased. Calorimetric measurements showed that the two mutants at position 28 (P28G and P28A) gave two peaks in the excess heat capacity curve, whereas the wild type and other Pro mutants had only a single peak. The stability of each mutant protein relative to that of the wild type was about the same for P57A, less for P62A and P132A, and markedly decreased for P96A and P207A, which are substituted at less mobile positions. The changes of denaturation entropy (ΔΔdS) at the denaturation temperature of the wild‐type protein (54.1 °C at pH 9.0) were positive for P57A, P62A, and P132A, but negative for P96A, P207A, and P132G. The present results do not indicate that the differences in stability (ΔdG) among Pro substitutions are caused only by an entropic factor, as might be theoretically expected. The decreases in stability for P96A and P207 were due to the considerable decrease in denaturation enthalpy, although they were partly compensated for by the decrease in entropy. Our results also suggest that Pro‐28 stabilizes the interaction between two domains of the α subunit.
The isolation, purification, and preliminary crystallographic characterization of udp‐galactose‐4‐epimerase from Escherichia coli
Authors: Bauer Alan J. , Rayment Ivan , Frey Perry A. , Holden Hazel M. 
Published: May 2005

AbstractUridine diphosphogalactose‐4‐epimerase from E. coli has been crystallized in a form suitable for a high‐resolution X‐ray crystallographic structural analysis. The enzyme complexed with a substrate analogue, uridine diphosphobenzene (UDP‐benzene), crystallizes readily using polyethylene glycol 8000 as the precipitant. The crystals belong to the orthorhombic space group P212121 with unit cell dimensions, a = 76.3 Å, b = 83.1 Å, and c = 132.1 Å. Based on still setting photographs, the crystals diffract to a nominal resolution of 2.3 Å and are stable in the X‐ray beam. The enzyme used in these experiments was produced by a new expression system and a modified purification scheme.
Preliminary x‐ray analysis of crystals of plasminogen activator inhibitor‐1
Authors: Goldsmith Elizabeth J. , Sheng‐Cheng Chen , Danley Dennis E. , Gerard Robert D. , Geoghegan Kieran F. , Mottonen James , Strand Arne 
Published: May 2005

AbstractCrystals of bacterially expressed plasminogen activator inhibitor (PAI‐1) suitable for X‐ray diffraction analysis have been obtained from 8% (w/v) PEG 1500, pH 8.25. The space group is P1, and the lattice constants are a = 82.17 Å, b = 47.82 Å, c = 62.89 Å, α = 90.00°, β = 106.90°, γ = 106.84°. The diffraction limit is 2.3 Å, and the unit cell contains two molecules of PAI‐1. The crystals contain latent PAI‐1 which can be partly reactivated by exposure to denaturants.
Hydrophobic clustering in nonnative states of a protein: Interpretation of chemical shifts in NMR spectra of denatured states of lysozyme
Authors: Evans Philip A. , Topping Karen D. , Woolfson Derek N. , Dobson Christopher M. 
Published: May 2005

AbstractChemical shifts of resonances of specific protons in the 1H NMR spectrum of thermally denatured hen lysozyme have been determined by exchange correlation with assigned native state resonances in 2D NOESY spectra obtained under conditions where the two states are interconverting. There are subtle but widespread deviations of the measured shifts from the values which would be anticipated for a random coil; in the case of side chain protons these are virtually all net upfield shifts and it is shown that this may be the averaged effect of interactions with aromatic rings in a partially collapsed denatured state. In a very few cases, notably that of two sequential tryptophan residues, it is possible to interpret these effects in terms of specific, local interresidue interactions. Generally, however, there is no correlation with either native state shift perturbations or with sequence proximity to aromatic groups. Diminution of most of the residual shift perturbations on reduction of the disulfide cross‐links confirms that they are not simply effects of residues adjacent in the sequence. Similar effects of chemical denaturants, with the disulfides intact, demonstrate that the shift perturbations reflect an enhanced tendency to side chain clustering in the thermally denatured state. The temperature dependences of the shift perturbations suggest that this clustering is noncooperative and is driven by small, favorable enthalpy changes. While the extent of conformational averaging is clearly much greater than that observed for a homologous protein, α‐lactalbumin, in its partially folded “molten globule” state, the results clearly show that thermally denatured lysozyme differs substantially from a random coil, principally in that it is partially hydrophobically collapsed.
The crystal structure of staphylococcal nuclease refined at 1.7 Å resolution
Authors: Hynes Thomas R. , Fox Robert O. 
Published: May 2005

AbstractThe crystal structure of staphylococcal nuclease has been determined to 1.7 Å resolution with a final R‐factor of 16.2% using stereochemically restrained Hendrickson–Konnert least‐squares refinement. The structure reveals a number of conformational changes relative to the structure of the ternary complex of staphylococcal nuclease1,2 bound with deoxythymidine‐3′,5′‐diphosphate and Ca2+. Tyr‐113 and Tyr‐115, which pack against the nucleotide base in the nuclease complex, are rotated outward creating a more open binding pocket in the absence of nucleotide. The side chains of Ca2+ ligands Asp‐21 and Asp‐40 shift as does Glu‐43, the proposed general base in the hydrolysis of the 5′‐phosphodiester bond. The significance of some changes in the catalytic site is uncertain due to the intrusion of a symmetry related Lys‐70 side chain which hydrogen bonds to both Asp‐21 and Glu‐43. The position of a flexible loop centered around residue 50 is altered, most likely due to conformational changes propagated from the Ca2+ site. The side chains of Arg‐35, Lys‐84, Tyr‐85, and Arg‐87, which hydrogen bond to the 3′‐ and 5′‐phosphates of the nucleotide in the nuclease complex, are unchanged in conformation, with packing interactions with adjacent protein side chains sufficient to fix the geometry in the absence of ligand. The nuclease structure presented here, in combination with the stereochemically restrained refinement of the nuclease complex structure2 at 1.65 Å, provides a wealth of structural information for the increasing number of studies using staphylococal nuclease as a model system of protein structure and function.
1.59 Å structure of trypsin at 120 K: Comparison of low temperature and room temperature structures
Authors: Earnest Thomas , Fauman Eric , Craik Charles S. , Stroud Robert 
Published: May 2005

AbstractThe structure of a rat trypsin mutant [S195C] at a temperature of 120 K has been refined to a crystallographic R factor of 17.4% between 12.0 and 1.59 Å and is compared with the structure of the D102N mutant at 295 K. A reduction in the unit cell dimensions in going from room temperature to low temperature is accompanied by a decrease in molecular surface area and radius of gyration. The overall structure remains similar to that at room temperature. The attainable resolution appears to be improved due to the decrease in the fall off of intensities with resolution [reduction of the temperature factor]. This decreases the uncertainty in the atomic positions and allows the localization of more protein atoms and solvent molecules in the low temperature map. The largest differences between the two models occur at residues with higher than average temperature factors. Several features can be localized in the solvent region of the 120 K map that are not seen in the 295 K map. These include several more water molecules as well as an interstitial sulfate ion and two interstitial benzamidine molecules.
On the multiple‐minima problem in the conformational analysis of polypeptides. V. Application of the self‐consistent electrostatic field and the electrostatically driven monte carlo methods to bovine pancreatic trypsin inhibitor
Authors: Ripoll Daniel R. , Piela Lucjan , Váasquez Max , Scheraga Harold A. 
Published: May 2005

AbstractIn connection with the accompanying paper to test various models for the hydration of polypeptides, we have explored a limited portion of the conformational energy hyperspace of the small protein bovine pancreatic trypsin inhibitor (BPTI) with the aid of two search methods developed in this laboratory. A series of low‐energy conformations was obtained as a result of this study. These conformations constitute a set of local minima in the conformational energy space of the molecule as described by the ECEPP/2 (Empirical Conformational Energy Program for Peptides) potential energy function, without the inclusion of hydration. Five different initial conformations were used in this exploration: the first corresponds to an energy‐refined structure based on the crystallographic coordinates (4PTI) provided by Deisenhofer and Steigemann25 and reported previously by Meirovitch and Scheraga.3 The remaining four initial conformations were obtained by using a Variable‐Target‐Function procedure, applied to the experimental Cartesian coordinates (5PTI) reported by Wlodawer et al.26The self‐consistent electrostatic field (SCEF) and the electrostatically driven Monte Carlo (EDMC) methods were used to search the conformational space. The SCEF and EDMC methodologies assume that a polypeptide or protein molecule is driven toward the native structure mainly by the action of the electrostatic interactions. Application of these methodologies led to a set of conformations (up to 50 kcal/mol lower than the starting ones) with ECEPP/2 energies lower than any of those that we had previously found. Application of both methods to the initial conformation generated from 4PTI led to a series of low‐energy conformations exhibiting similar rms deviations with respect to the experimental data (4PTI) as did the starting conformation. However, statistical analysis of the runs that had started from the conformations generated by using the variable‐target‐function procedure (and applying the EDMC method) indicated that the rms deviations of the atomic positions of the new low‐energy conformations tended to increase as the energy improved, when compared with the X‐ray data from which the starting conformations had been generated. The structures with the lowest energies also had radii of gyration smaller than the experimentally observed one. These results indicated a need to include hydration in the potential function, and provided the conformations used in the accompanying paper to test various hydration models.
Empirical solvation models can be used to differentiate native from near‐native conformations of bovine pancreatic trypsin inhibitor
Authors: Vila J. , Williams R. L. , Vásquez M. , Scheraga H. A. 
Published: May 2005

AbstractSeveral hydration models for peptides and proteins based on solvent accessible surface area have been proposed previously. We have evaluated some of these models as well as four new ones in the context of near‐native conformations of a protein. In addition, we propose an empirical site–site distance‐dependent correction that can be used in conjuction with any of these models.The set of near‐native structures consisted of 39 conformations of bovine pancreatic trypsin inhibitor (BPTI) each of which was a local minimum of an empirical energy function (ECEPP) in the absence of solvent. Root‐mean‐square (rms) deviations from the crystallographically determined structure were in the following ranges: 1.06–1.94 Å for all heavy atoms, 0.77–1.36 Å for all backbone heavy atoms, 0.68–1.33 Å for all α‐carbon atoms, and 1.41–2.72 Å for all side‐chain heavy atoms.We have found that there is considerable variation among the solvent models when evaluated in terms of concordance between the solvation free energy and the rms deviations from the crystallographically determined conformation. The solvation model for which the best concordance (0.939) with the rms deviations of the Cα atoms was found was derived from NMR coupling constants of peptides in water combined with an exponential site–site distance dependence of the potential of mean force.Our results indicate that solvation free energy parameters derived from nonpeptide free energies of hydration may not be transferrable to peptides. Parameters derived from peptide and protein data may be more applicable to conformational analysis of proteins. A general approach to derive parameters for free energy of hydration from ensemble‐averaged properties of peptides in solution is described.
Proline in α‐helix: Stability and conformation studied by dynamics simulation
Authors: Yun R. H. , Anderson Amil , Hermans Jan 
Published: May 2005

AbstractFree‐energy simulations have been used to estimate the change in the conformational stability of short polyalanine α‐helices when one of the alanines is replaced by a proline residue. For substituting proline in the middle of the helix the change in free energy of folding (ΔΔG°) was calculated as 14 kJ/mol (3.4 kcal/mol), in excellent agreement with the one available experimental value. The helix containing proline was found to be strongly kinked; the free energy for reducing the angle of the kink from 40° to 15° was calculated, and found to be small. A tendency to alternate hydrogen bonding schemes was observed in the proline‐containing helix. These observations for the oligopeptide agree well with the observation of a range of kink angles (18–35°) and variety of hydrogen bonding schemes, in the rare instances where proline occurs in helices in globular proteins. For substituting proline at the N‐terminus of the helix the change in free energy of folding (ΔΔG°) was calculated as −4 kJ/mol in the first helical position (N1) and +6 kJ/mol in the second helical position (N2). The observed frequent occurrence of proline in position N1 in α‐helices in proteins therefore has its origin in stability differences of secondary structure. The conclusion reached here that proline may be a better helix former in position N1 than (even) alanine, and thus be a helix initiator may be testable experimentally by measurements of fraction helical conformation of individual residues in oligopeptides of appropriate sequence. The relevance of these results in regards to the frequent occurrence of proline‐containing helices in certain membrane proteins is discussed.
Structure of ricin A‐chain at 2.5 Å
Authors: Katzin Betsy J. , Collins Edward J. , Robertus Jon D. 
Published: May 2005

AbstractRicin has been refined in a crystallographic sense to 2.5 Å resolution and the model for the A‐chain (RTA) is described in detail. Because RTA is the first member of the class of plant toxins to be analyzed, this model probably defines the major structural characteristics of the entire family of these medically important proteins. Explanations are provided to rationalize amino acids that are conserved between RTA and a number of homologous plant and bacterial toxins. Eight invariant residues appear to be involved in creating or stabilizing the active site. In the active site Arg180 and Glu177 are hydrogen bonded to each other and also coordinate a water molecule; each of these groups may be important in the N‐glycosidation reaction. Several other polar residues may play lesser roles in the mechanism, including tyrosines 80 and 123 and asparagines 78 and 209. A number of conserved hydrophobic residues are seen to cluster within several patches and probably drive the overall folding of the toxin molecule.
Site‐directed mutagenesis of ricin A‐chain and implications for the mechanism of action
Authors: Ready Michael P. , Kim Youngsoo , Robertus Jon D. 
Published: May 2005

AbstractRicin A‐chain is an N‐glycosidase that attacks ribosomal RNA at a highly conserved adenine residue. The enzyme is representative of a large family of medically significant proteins used in the design of anticancer agents and in the treatment of HIV infection. The x‐ray structure has been used as a guide to create several active site mutations by directed mutagenesis of the cloned gene. Glu177 is a key catalytic residue, and conversion to Gln reduces activity 180‐fold. Asn209 is shown to participate in substrate binding by kinetic analysis. Conversion to Ser increases Km sixfold but has no effect on kcat. Conversion of Tyr80 and Tyr123 to Phe decreases activity by 15‐ and 7‐fold respectively. A mechanism of action is proposed that involves binding of the substrate adenine in a syn configuration that resembles the transition state; the putative oxycarbonium ion is probably stabilized by interaction with Glu177.
Physical reasons for secondary structure stability: α‐Helices in short peptides
Authors: Finkelstein A. V. , Badretdinov A. Y. , Ptitsyn O. B. 
Published: May 2005

AbstractIt was recently found that some short peptides (including C‐ and S‐peptide fragments of RNase A) can have considerable helicity in solution, 1–12 which was considered to be surprising. Does the observed helicity require a new explanation, or is it consistent with previous understanding? In this work we show that this helicity is consistent with the physical theory of secondary structure12–19 based on an extension of the conventional Zimm‐Bragg model.20 Without any special modifications, this theory explains reasonably well almost all the experimentally observed dependencies of helicity on pH, temperature, and amino acid replacements. We conclude that the observed “general level” of helicity of C‐ and S‐peptides (5–30% at room temperature and 10–50% near 0°C) is “normal” for short peptides consisting mainly of helix‐forming and helix‐indifferent residues. The helicity is modified by a multitude of weak specific side chain interactions, many of which are taken into account by the present theory;13–19 some discrepancies between the theory and experiment can be explained by weak side‐chain‐side chain interactions that were neglected. A reasonable coincidence of the theory with experiment suggests that it had been used to investigate the role of local interactions in the formation of α‐helical “embryos” in unfolded protein chains.