bluuebunny/crossref_metadata_2025_split huggingface dataset:
An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
Authors: Lawrence Charles E. , Reilly Andrew A. 
Published: May 2005

AbstractStatistical methodology for the identification and characterization of protein binding sites in a set of unaligned DNA fragments is presented. Each sequence must contain at least one common site. No alignment of the sites is required. Instead, the uncertainty in the location of the sites is handled by employing the missing information principle to develop an “expectation maximization” (EM) algorithm. This approach allows for the simultaneous identification of the sites and characterization of the binding motifs. The reliability of the algorithm increases with the number of fragments, but the computations increase only linearly. The method is illustrated with an example, using known cyclic adenosine monophophate receptor protein (CRP) binding sites. The final motif is utilized in a search for undiscovered CRP binding sites.
Polyproline, β‐turn helices. Novel secondary structures proposed for the tandem repeats within rhodopsin, synaptophysin, synexin, gliadin, RNA polymerase II, hordein, and gluten
Authors: Matsushima Norio , Creutz Carl. E. , Kretsinger Robert H. 
Published: May 2005

AbstractSeven proteins each contain 8 to 52 tandem repeats of a unique class of oligopeptide. The consensus peptide for each is

rhodopsin Tyr Pro Pro Gln Gly
synapto‐physin Tyr Gly Pro Gln Gly
synexin Tyr Pro Pro Pro Pro Gly
gliadin Tyr Pro Pro Pro Gln Pro
RNA polymerase II Tyr Ser Pro Thr Ser Pro Ser
hordein Phe Pro Gln Gln Pro Gln Gln Pro
gluten Tyr Pro Thr Ser Pro Gln Gn Gly Tyr
Although there is obvious variations of sequence and of length, the penta‐to nonapeptides share an initial Tyr(or Phe) and have high Pro contents and abundant Gly, Gln, and Ser. We have evaluated helical models that both recognize the uniqueness of these sequence repeats and accommodate variations on the basic theme.We have developed a group of related heical model for these proteins with about three oligopeptide repeats per turn of 10–20 Å. These models share several common features: Most of the ϕ dihedral angels are −54°, to accommodate Pro at all positions expect the first (Tyr). Except for the β‐turns, most ψ dihedral angles are near +140° as found in polyproline. Each oligopeptide has at least one β‐turn; several have two. Some contains a cis‐Tyr, Pro peptide bond; a few have a cis‐bond plus one β‐turn. Tyr side chains vary from totally exposed to buried within the helices and could mode to accommodate either external hydrophobic interactions or phosphorylation. The several related structures seem to be readily interconverted without major change in the overall helical parameters, and therein may lie the key to their functions.
Substrate recognition by the EcoRI endonuclease
Authors: Heitman Joseph , Model Peter 
Published: May 2005

AbstractThe EcoRI restriction endonuclease is one of the most widely used tools for recombinant DNA manipulations. Because the EcoRI enzyme has been extremely well characterized biochemically and its structure is known at 3 Å resolution as an enzyme–DNA complex, EcoRI also serves as an important model of DNA–protein interactions. To facilitate a genetic analysis of the EcoRI enzyme, we devised an in vivo DNA scission assay based on our finding that DNA double‐strand breaks induce the Escherichia coli SOS response and thereby increase β‐galactosidase expression from SOS::lacZ gene fusions. By site‐directed mutagenesis, 50 of 60 possible point mutations were generated at three amino acids (E144, R145, and R200) implicated in substrate recognition by the crystal structure. Although several of these mutant enzymes retain partial endonuclease activity, none are altered in substrate specificity in vivo or in vitro. These findings argue that, in addition to the hydrogen bond interactions revealed by the crystal structure, the EcoRI enzyme must make additional contacts to recognize its substrate.
Modelling of the human intercellular adhesion molecule‐1, the human rhinovirus major group receptor
Authors: Giranda Vincent L. , Chapman Michael S. , Rossmann Michael G. 
Published: May 2005

AbstractA model has been built of the amino‐terminal domain of the intercellular adhesion molecule‐1 (ICAM‐1), the receptor for most human rhinovirus serotypes. The model was based on sequence and presumed structural homology to immunoglobulin constant domains. It fits well into the putative receptors attachment site, the canyon, on the human rhinovirus‐14 (HRV14) surface in a manner consistent with most of the mutational data for ICMA‐1 (Staunton, D. E., Dustin, M. L., Erickson, H. P., Springer, T. A. Cell, in press, 1989) and HRV14 (Colonno, R. J., Condra, J. H., Mizutani, S., Callahan, P. L., Davies, M. E., Murcko, M. A. Proc. Natl. Acad. Sci. U.S.A. 85: 5449‐5453, 1988).
Automated docking of substrates to proteins by simulated annealing
Authors: Goodsell David S. , Olson Arthur J. 
Published: May 2005

AbstractThe Metropolis technique of conformation searching is combined with rapid energy evaluation using molecular affinity potentials to give an efficient procedure for docking substrates to macromolecules of known structure. The procedure works well on a number of crystallographic test systems, functionally reproducing the observed binding modes of several substrates.
Models of δ‐hemolysin membrane channels and crystal structures
Authors: Raghunathan G. , Seetharamulu P. , Brooks B. R. , Guy H. R. 
Published: May 2005

AbstractMolecular modeling and energy calculations have been used to study how δ‐hemolysin and melittin helices may aggregate on membrane surfaces and insert through membranes to form channels. In these models adjacent antiparallel amphipathic helices form planar “raft” structures, in which one surface is hydrophobic and the other hydrophilic. Models of δ‐hemolysin crystal structure were developed using these “rafts.” These models are based on the unit cell constants and the crystal symmetry obtained from the preliminary crystal data. Energy calculations favor channel models of δ‐hemolysin with six or eight monomers per channel.
Changes in secondary structure follow the dissociation of human insulin hexamers: A circular dichroism study
Authors: Melberg Steen G. , Johnson W. Curtis 
Published: May 2005

AbstractVacuum UV circular dichroism spectra measured down to 178 nm for hexameric 2‐zinc human insulin, zinc‐free human insulin, and the two engineered and biologically active monomeric mutants, [B/S9D] and [BS9D, T27E] human insulin, show significant differences. The secondary structure analysis of the 2‐zinc human insulin (T6) in neutral solution was determined: 57% helix, 1% β‐strand, 18% turn, and 24% random coil. This is very close to the corresponding crystal structure showing that the solution and solid structures are similar. The secondary structure of the monomer shows a 10–15% increase in antiparallel β‐structure and a corresponding reduction in random coil structure. These structural changes are consistent with an independent analysis of the corresponding difference spectra. The advantage of secondary structure analyses of difference spectra is that the contribution of odd spectral features stemming mainly from side chain chromophores is minimized and the sensitivity of the analyses improved. Analysis of the CD spectra of T6 2‐zinc, zinc‐free human insulin and monomeric mutant insulin by singular value decomposition indicates that the secondary structure changes following the dissociation of hexamers into dimers and monomers are two‐state processes.
The effect of solvent viscosity on the rate‐determining step of fatty acid synthetase
Authors: Kyushiki Hiroyuki , Ikai Atsushi 
Published: May 2005

AbstractThe overall activity of animal fatty acid synthetase at the saturation level of substrate concentration decreased when the solvent viscosity, η, of the reaction mixture was increased with viscogens such as glycerol, sucrose, and polyethylene glycol. The activity of the enzyme changed roughly proportional to η−p, where p = 1.0 for glycerol, p = 0.66 for sucrose, and p < 0.6 for polyethylene glycol with different molecular sizes. The thioesterase activity, which catalyzes the final partial reaction in the multifunctional enzyme, was not affected by 5‐fold increase of solvent viscosity with sucrose. These results suggested that the rate‐determining step of the enzyme other than the thioesterase reaction involves a microscopic transport step, the rate of which is influenced by the solvent viscosity. The microscopic transport step may be related to the transfer of the reaction intermediate from one active site to another or to the motion of a larger part of the enzyme requisite for the catalytic reaction. In the solution containing glycerol, the rate‐determining motion was primarily diffusion limited since the inverse of the initial rate was proportional to η, i.e., p = 1. Since the substrate concentration was at a saturation level in this experiment, the viscosity‐dependent step cannot be the encounter between the enzyme and substrates, but must be intramolecular in origin, most probably the reaction catalyzed by β‐ketoacyl synthetase. In solutions containing other viscogens, however, p was less than 1.0, indicating a significant involvement of chemical steps in the rate‐determining step as well. Bovine serum albumin, when used as a proteinic viscogen, also decreased the initial rate. In the living cells therefore, the rate‐determining intramolecular motion of fatty acid synthetase could be affected by the presence of high concentrations of cytoplasmic proteins.
Hormone phage: An enrichment method for variant proteins with altered binding properties
Authors: Bass Steven , Greene Ronald , Wells James A. 
Published: May 2005

AbstractHuman growth hormone (hGH), a 191 residue protein containing two disulfide bonds, was fused to the carboxyl‐terminal domain of the gene III protein, a minor coat protein exposed at one end of the filamentous phage M13. The gene fusion was cloned into a plasmid containing origins of replication for Escherichia coli and filamentous phage and was packaged into phagemid particles upon infection by an M13KO7 helper phage. Transcription of the hGH‐gene III fusion was controlled so that usually no more than one copy of the fusion protein was displayed along with the four copies of the wild‐type gene III protein. The hGH‐gene III fusion protein was properly folded, as judged by reactivity with six hGH monoclonal antibodies whose epitopes are sensitive to the folded conformation of hGH. Moreover, the hGH–gene III phagemid particles were enriched over 5000‐fold from non‐hGH phage, and 8‐fold from a mutant hGH phagemid following a single hGH‐specific elution step from hGH receptor‐coated beads. The hGH phagemid should be useful for isolating new receptor binding mutants of hGH. More generally, this expression system may allow other large proteins with discontinuous binding epitopes to be displayed, and binding selections applied to their mutated gene III fusions on filamentous phage.
Fragment peptide library for classification and functional prediction of proteins
Authors: Seto Yasuhiko , Ikeuchi Yoshinori , Kanehisa Minoru 
Published: May 2005

AbstractFrom protein sequence comparison data found in the literature, a library was organized using peptide fragment sequences which are common to related proteins. Each of the fragments was then examined for its occurrence in all the protein superfamilies defined by the NBRF‐PIR data base. We have selected those fragment peptides that appear exclusively in one or a few superfamilies, and thus made a library of fragment peptides that characterize specific superfamilies. Such characteristic peptides are, in general, five to seven residues long and contain unusually high proportions of glycine and cysteine. This collection is a useful resource for the classification and functional prediction of protein molecules.
Refinement of the NMR structures for acyl carrier protein with scalar coupling data
Authors: Kim Yangmee , Prestegard James H. 
Published: May 2005

AbstractStructure determination of small proteins using NMR data is most commonly pursued by combining NOE derived distance constraints with inherent constraints based on chemical bonding. Ideally, one would make use of a variety of experimental observation, not just distance constraints. Here, coupling constant constraints have been added to molecular mechanics and molecular dynamics protocols for structure determination in the form of a psuedoenergy function that is minimized in a search for an optimum molecular conformation. Application is made to refinement of a structure for a 77 amino acid protein involved in fatty acid synthesis, Escherichia coli acyl carrier protein (ACP). 54 3JHNα coupling constants, 12 coupling constants for stereospecifically assigned side chain protons, and 450 NOE distance contraints were used to calculate the 3‐D structure of ACP. A three‐step protocol for a molecular dynamics calculation is described, in analogy to the protocol previously used in molecular mechanics calculations. The structures calculated with the molecular mechanics approach and the molecular dynamics apporach using a rigid model for the protein show similar molecular energies and similar agreement with experimental distance and coupling constant constraints. The molecular dynamics approach shows some advantage in overcoming local minimum problems, but only when a two‐state averaging model for the protein was used, did molecular energies drop significantly.
Modeling of agonist binding to the ligand‐gated ion channel superfamily of receptors
Authors: Cockcroft Victor B. , Osguthorpe David J. , Barnard Eric A. , Lunt George G. 
Published: May 2005

AbstractA generalized model is presented of agonist binding to ligand‐gated ion channels (LGICs). Broad similarity in the structure of agonists suggests that the binding sites of LGICs may have evolved from a protobinding site. Aligned sequence data identified as a candidate for such a site a highly conserved 15 residue stretch of primary structure in the N‐terminal extracellular region of all known LGIC subunits. We modeled this subregion, termed the cys‐loop, as a rigid, amphiphilic β‐hairpin and propose that it may form a major determinant of a conserved structural binding cleft.In the model of the binding complex (1) an invariant aspartate residue at position 11 of the cys‐loop is the anionic site interacting with the positively charged amine group of agonists, (2) a local dipole within the π‐electron system of agonists is favorably oriented in the electrostatic field of the invariant aspartate, (3) the ε ring‐proton of a conserved aromatic residue at the turn of the cys‐loop interacts orthogonally with the agonist α‐electron density at its electronegative center, and (4) selective recognition is partly a result of the type of amino acid residue at position 6 of the cys‐loop. Additionally, the formation of a hydrogen bond between the electronegative atom of the π‐electron system of agonist and a complementary group in the receptor may be important in the high‐affinity binding of agonists.
Predicted three‐dimensional structure of the protease inhibitor domain of the Alzheimer's disease β‐amyloid precursor
Authors: Struthers R. Scott , Kitson David H. , Hagler Arnold T. 
Published: May 2005

AbstractAlzheimer's disease is characterized by the deposition of amyloid β‐protein as plaques and tangles in the brains of its victims. The amyloid precursor can be expressed with or without the inclusion of a protease inhibitor domain, the potential role of which in amyloidogenesis has prompted the generation of a model of its three‐dimensional structure based on the known structure of a related inhibitor. The model structure predicts that the mutated residues are almost entirely on the surface of the inhibitor domain, while conserved residues constitute the hydrophobic core. In addition, several pairs of structurally complementary, or concerted, mutations are seen. These structural features provide strong evidence for the validity of the modeled structure, and it is suggested that the presence of complementary mutations may be used as a criterion for evaluating protein structures built by homology, in addition to the (spatial) location of the mutations. The terminal residues delimiting the domain are among those furthest from the protease binding site and are in close proximity to one another, thus suggesting the ability of the domain to function as a structural cassette within the context of a larger protein. The electrostatic potentials of the inhibitor and of the related bovine pancreatic trypsin inhibitor reveal how two inhibitors with very different net charges can bind with approximately the same binding constant to trypsin and suggest a mutation of trypsin that might selectively enhance the binding of the amyloid inhibitor domain. The model provides a structural basis for understanding the functional roles of residues in the domain and for designing simpler molecules to test as pharmacologic agents for intervention in Alzheimer's disease.
Assignment of the nucleotide binding sites and the mechanism of substrate inhibition of Escherichia coli adenylate kinase
Authors: Liang Peng , Phillips George N. , Glaser Michael 
Published: May 2005

AbstractSite‐directed mutagenesis of key amino acids of adenylate kinase has been used to suggest a new model for the location of the AMP and ATP binding sites. Phe‐86 and Tyr‐133, which are in close contact with the inhibitor Ap5A according to previous crystallographic results, have been independently changed to tryptophan and other amino acids. The Phe‐86→Trp mutant had a 3‐ to 6‐fold change in the Km for ATP and a 44‐fold increase in the Km for AMP with a simultaneous loss of AMP substrate inhibition. Thus Phe‐86 is probably in close contact with bound AMP. The Tyr‐133→Trp mutant showed no large effects on enzyme kinetics and suggests that the previous assignment of Ap5A occupying natural adenosine binding sites is probably incorrect. A temperature‐sensitive Leu‐107→Gln mutant showed a 6‐fold decrease in the Km for ATP and no effect on AMP binding, suggesting that this amino acid is near the ATP binding site.Changes in the fluorescence of single tryptophan‐containing mutant enzymes provided specific information about AMP and ATP binding. The fluorescence results are consistent with the kinetic studies, and also suggest that AMP substrate inhibition is caused by the formation of an abortive complex that prevents the release of product.
Distribution and complementarity of hydropathy in mutisunit proteins
Authors: Korn Alex P. , Burnett Roger M. 
Published: May 2005

AbstractA survey of 40 multisubunit proteins and 2 protein–protein complexes was performed to assay quantitatively the distribution of hydropathy among the exterior surface, interior, contact surface, and noncontact exterior surface of the isolated subunits. We suggest a useful way to present this distribution by using a “hydropathy level diagram.” Additionally, we have devised a function called “hydropathy complementarity” to quantitate the degree to which interacting surfaces have matching hydropathy distributions. Our survey revealed the following patters: (1) The difference in hydropathy between the interior and exterior of subunits is a fairly invariant quantity. (2) On average, the hydropathy of the contact surface is higher than that of the exterior surface, but is not greater than that of the protein as a whole. There was variation, however, among the proteins. In some instances, the contact surface was more hydrophilic than the noncontact exterior, and in a few cases the contact surface was as hydrophobic as the protein interior. (3) The average interface manifests significant hydropathy complementarity, signifying that proteins interact by placing hydrophobic centers of one surface against hydrophobic centers of the other surface, and by similarly matching hydrophilic centers. As a measure of recognition and specificity, hydropathy complementarity could be a useful tool for predicting correct docking of interacting proteins. We suggest that high hydropathy complementarity is associated with static inflexible interactions. (4) We have found that some subunits that bind predominantly through hydrophilic forces, such as hydrogen bonds, ionic pairs, and water and metal bridges, are involved in dynamic quaternary organization and allostery.
Refined structure of melittin bound to perdeuterated dodeclylphoscholine micelles as studied by 2D‐NMR and distance geometry calculation
Authors: Ikura Teikichi , Gō Nobuhiro , Inagaki Fuyuhiko 
Published: May 2005

AbstractIn our previous paper we reported the conformation of melittin bound to perdeuterated dodecylphosphocholine micelles as studied by 1H NMR experiment and distance geometry calculation. No hydrogen bonds were taken into consideration explicitly in the calculation. However, mostly α‐helical conformations were obtained as results of the calculation even with no explicitly assumed hydrogen bonds. In the present paper we refined the distance geometry calculation by incorporating hydrogen bonds suggested by the previous calculation. As a result, we obtained the conformation of melittin, which was consistent with both NMR data and the additional hydrogen bonding data. The α‐helical rod in the refined conformation also has a kink at Thr‐11 and Gly‐12, but its bent angle is now a bit narrowly distributed in 135° × 15°. In the present study another distortion at Trp‐19 and IIe‐20 becomes conspicuous. The average root‐mean‐square displacement of atoms is now much smaller and is 1.5 Å for all backbone atoms. In the present paper side chain conformations are also analyzed.
The three‐dimensional structure of glutathione reductase from Escherichia coli at 3.0 Å resolution
Authors: Ermler Ulrich , Schulz Georg E. 
Published: May 2005

AbstractThe structure of glutathione reductase from Escherichia coli has been solved at 3 Å resolution using multiple isomorphous replacement, solvent flattening, and molecular replacement on the basis of the homologous (53% identical residues) and structurally well‐established human enzyme. The structures of both enzyme species agree with each other in a global way; there is no domain rearrangement. In detail, clear structural differences can be observed. The structure analysis of the E. coli enzyme was tackled in order to understand sitedirected mutants, the most spectacular of which changed the cofactor specificity of this enzyme from NADP to NAD (Scrutton et al., 1990, Nature 343:38–43).