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PubMed1990

Hydrogen bond stereochemistry in protein structure and function.

Fifty high resolution protein structures from the Brookhaven Protein Data Bank have been analyzed for recurring motifs in hydrogen bond stereochemistry. Although an exhaustive analysis of hydrogen bond statistics has been presented by Baker & Hubbard, a detailed stereochemical analysis of classical donor (N-H, O-H, or S-H) and acceptor (N:, O:, or S:) structure within proteins is lacking. Here, we describe the preferential hydrogen bond stereochemistry for the side-chains of glutamate and aspartate (carboxylate), glutamine and asparagine (carboxamide), arginine (guanidinium), histidine (imidazole/imidazolium), tryptophan (indole), tyrosine (phenolic hydroxyl), lysine (ammonium), serine and threonine (alkyl hydroxyl), cysteine (thiol), methionine (thioether) and cystine (disulfide). Preferential hydrogen bond stereochemistry is governed by (1) the electronic configuration of acceptor atoms, (2) the steric accessibility of donor atoms and (3) the conformation of amino acid side-chains. Applications of hydrogen bond stereochemistry are useful in the interpretation of protein structure, function and stability. Additionally, this stereochemistry is a prerequisite to the interpretation of protein-other molecule recognition and biological catalysis.

Amino Acids↗

PubMed1995

Mapping and sequence of the gene encoding protein p17, a major African swine fever virus structural protein.

The gene encoding protein p17, a major structural protein of African swine fever virus, has been mapped and sequenced. Protein p17 was purified from dissociated virus by reverse-phase HPLC and the amino acid sequence of a peptide obtained after digestion of protein p17 with cyanogen bromide was determined by automated Edman degradation. To map the gene encoding protein p17, a mixture of 17-mer oligonucleotides based upon a part of the amino acid sequence was hybridized to cloned African swine fever virus DNA restriction fragments. This allowed the location of the gene in the fragment EcoRI D of the viral genome. The nucleotide sequence of a Sa/l/KpnI fragment revealed an open reading frame designated D117R encoding a protein of 117 amino acids with a deduced molecular mass of about 13,000 Da. A transcriptional analysis revealed that the p17 gene is expressed late in the viral infection cycle.

Africa↗

PubMed2003

Development of an ab initio protein structure prediction system ABLE.

An ab initio protein structure prediction system called ABLE is described. It is based on the fragment assembly method, which consists of two steps: dividing a target sequence into overlapping subsequences (fragments) of short length and assigning a local structure to each fragment; and generating models by assembling the local structures and selecting the models with low potential energy. One of the most important problems in conventional fragment assembly methods is the difficulty of selecting native-like structures by energy minimization only. ABLE thus employs a structural clustering method to select the native-like models from among the generated models. By applying the unit-vector root mean square distance (URMS) as a measure of structure similarity, we achieve more robust, effective structural clustering. When no enough clusters of good quality are obtained, ABLE runs the energy minimization procedure again by incorporating structural restraint conditions obtained from the consensus substructures in the previously generated models. This approach is based on our observation that there is a high probability that the consensus substructures of the generated models have native-like structures. Another feature of ABLE is that in assigning local structures to fragments, it assigns mainchain dihedral angles (phi, psi) to the central residue of each fragment according to a probability distribution map built from candidate sequences similar to each fragment. This enables the system to generate appropriate local structures that may not already exist in a protein structure database. We applied our system to 25 small proteins and obtain near-native folds for more than half of them. We also demonstrate the performance of our structural clustering method, which can be applied to other protein structure prediction systems.

Cluster Analysis↗

PubMed2001

EVA: continuous automatic evaluation of protein structure prediction servers.

UNLABELLED: Evaluation of protein structure prediction methods is difficult and time-consuming. Here, we describe EVA, a web server for assessing protein structure prediction methods, in an automated, continuous and large-scale fashion. Currently, EVA evaluates the performance of a variety of prediction methods available through the internet. Every week, the sequences of the latest experimentally determined protein structures are sent to prediction servers, results are collected, performance is evaluated, and a summary is published on the web. EVA has so far collected data for more than 3000 protein chains. These results may provide valuable insight to both developers and users of prediction methods. AVAILABILITY: http://cubic.bioc.columbia.edu/eva. CONTACT: eva@cubic.bioc.columbia.edu

Automation↗

PubMed1989

Improved strategies for the determination of protein structures from NMR data: the solution structure of acyl carrier protein.

The hybrid method that combines the early stages of a distance geometry program with simulated annealing in the presence of NMR constraints was optimized to obtain structures fully consistent with the observed NMR data. This was achieved by using more restrictive bounds of the NOE constraints than those usually used in the literature and by grouping the NOEs into classes dependent on the quality of the experimental NOE data. The 'floating' stereospecific assignment introduced at the simulated annealing stage of the calculations further improved the definition of the local conformation. An improved sampling and convergence property of the hybrid method was obtained by means of fitting the substructure obtained from the distance geometry program to different conformations. Compared to the standard hybrid methods, this procedure gave superior structures for a 77 amino acid protein, acyl carrier protein from Escherichia coli.

Acyl Carrier Protein↗

PubMedDate not supplied

StructSorter: a method for continuously updating a comprehensive protein structure alignment database.

Advances in protein crystallography and homology modeling techniques are producing vast amounts of high resolution protein structure data at ever increasing rates. As such, the ability to quickly and easily extract structural similarities is a key tool in discovering important functional relationships. We report on an approach for creating and maintaining a database of pairwise structure alignments for a comprehensive database comprising the PDB and homology models for the human and select pathogen genomes. Our approach consists of a novel, multistage method for determining pairwise structural similarity coupled with an efficient clustering protocol that approximates a full NxN assessment in a fraction of the time. Since biologists are commonly interested in recently released structures, and the homology models built from them, an automatically updating database of structural alignments has great value. Our approach yields a querying system that allows scientists to retrieve databank-wide protein structure similarities as easily as retrieving protein sequence similarities via BLAST or PSI-BLAST. Basic, noncommercial access to the database can be requested at https://tip.eidogen-sertanty.com/.

Databases, Protein↗

PubMed2002

Tripeptide analysis of protein structures.

BACKGROUND: An efficient building block for protein structure prediction can be tripeptides. 8000 different tripeptides from a dataset of 1220 high resolution (<or= 2.0 degrees A) structures from the Protein Data Bank (PDB) have been looked at, to determine which are structurally rigid and non-rigid. This data has been statistically analyzed, discussed and summarized. The entire data can be utilized for the building of protein structures. RESULTS: Tripeptides have been classified into three categories: rigid, non-rigid and intermediate, based on the relative structural rigidity between Calpha and Cbeta atoms in a tripeptide. We found that 18% of the tripeptides in the dataset can be classified as rigid, 4% as non-rigid and 78% as intermediate. Many rigid tripeptides are made of hydrophobic residues, however, there are tripeptides with polar side chains forming rigid structures. The bulk of the tripeptides fall in the intermediate class while very small numbers actually fall in the non-rigid class. Structurally all rigid tripeptides essentially form two structural classes while the intermediate and non-rigid tripeptides fall into one structural class. This notion of rigidity and non-rigidity is designed to capture side chain interactions but not secondary structures. CONCLUSIONS: Rigid tripeptides have no correlation with the secondary structures in proteins and hence this work is complementary to such studies. Tripeptide data may be used to predict plausible structures for oligopeptides and for denovo protein design.

Molecular Structure↗

PubMed1993

Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures.

The data base of known protein structures contains a tremendous amount of information on protein-solvent systems. Boltzmann's principle enables the extraction of this information in the form of potentials of mean force. The resulting force field constitutes an energetic model for protein-solvent systems. We outline the basic physical principles of this approach to protein folding and summarize several techniques which are useful in the development of knowledge-based force fields. Among the applications presented are the validation of experimentally determined protein structures, data base searches which aim at the identification of native-like sequence structure pairs, sequence structure alignments and the calculation of protein conformations from amino acid sequences.

Amino Acid Sequence↗

PubMed1993

Effect of growth promoters on pig muscle structural protein and proteolytic enzyme levels in vivo and in vitro.

To elucidate the biochemical mechanism by which the growth hormone porcine somatotrophin (PST) promotes skeletal muscle growth, we have determined the activity of a comprehensive range of protein catabolizing proteolytic enzymes and structural proteins (determined by analytical electrophoresis, SDS-PAGE) in longissimus dorsi muscle from control and PST treated pigs. There was no significant difference in the levels of muscle structural proteins, or in the activity of muscle proteolytic enzymes at point of slaughter in control or PST treated animals. Similarly, in post-mortem muscle proteolysis time course experiments at pH 5.5 or pH 7.5, there was no significant difference in the rate of structural protein degradation by endogenous muscle proteases (determined via SDS-PAGE) using muscle from control or PST treated animals. In addition, investigation of a range of beta-agonist related drugs (clenbuterol, salbutamol, pirbuterol, fenoterol) showed no effect (10(-4)-10(-8) M) in vitro on the activity of individual protease types in control muscle, or on the degradation rate of muscle structural proteins by endogenous proteases in time course experiments at pH 5.5 or pH 7.5.(ABSTRACT TRUNCATED AT 250 WORDS)

Adrenergic beta-Agonists↗

PubMed2002

Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction.

Residual dipolar couplings provide significant structural information for proteins in the solution state, which makes them attractive for the rapid determination of protein structures. While dipolar couplings contain inherent structural ambiguities, these can be reduced via an overlap similarity measure that insists that protein fragments assigned to overlapping regions of the sequence must have self-consistent structures. This allows us to determine a backbone fold (including the correct Calpha-Cbeta bond orientations) using only residual dipolar coupling data from one ordering medium. The resulting backbone structures are of sufficient quality to allow for modeling of sidechain rotamer states using a rotamer prediction algorithm and a force field employing the Surface Generalized Born continuum solvation model. We demonstrate the applicability of the method using experimental data for ubiquitin. These results illustrate the synergies that are possible between protein structural database and molecular modeling methods and NMR spectroscopy, and we expect that the further development of these methods will lead to the extraction of high resolution structural information from minimal NMR data.

Computer Simulation↗

PubMed2004

Automated clustering of ensembles of alternative models in protein structure databases.

Experimentally determined protein structures have been classified in different public databases according to their structural and evolutionary relationships. Frequently, alternative structural models, determined using X-ray crystallography or NMR spectroscopy, are available for a protein. These models can present significant structural dissimilarity. Currently there is no classification available for these alternative structures. In order to classify them, we developed STRuster, an automated method for clustering ensembles of structural models according to their backbone structure. The method is based on the calculation of carbon alpha (Calpha) distance matrices. Two filters are applied in the calculation of the dissimilarity measure in order to identify both large and small (but significant) backbone conformational changes. The resulting dissimilarity value is used for hierarchical clustering and partitioning around medoids (PAM). Hierarchical clustering reflects the hierarchy of similarities between all pairs of models, while PAM groups the models into the 'optimal' number of clusters. The method has been applied to cluster the structures in each SCOP species level and can be easily applied to any other sets of conformers. The results are available at: http://bioinf.mpi-sb.mpg.de/projects/struster/.

Aldehyde-Lyases↗

PubMed1991

Simulated annealing approach to the study of protein structures.

One of the most difficult problems in predicting the three dimensional structure of proteins is how to deal with the local minimum problem. In many cases of practical interest this problem has been reduced to how to select an appropriate set of starting conformations for carrying out energy minimizations. How these starting conformations are selected, however, is often based on the physical intuition of the person doing the calculations, and hence it is hard to avoid bearing some sort of arbitrariness. To improve such a situation, we introduced the simulated annealing Monte Carlo algorithm to locate the optimal starting conformations for energy minimizations. The method developed here is valid for both single and multiple polypeptide chain systems. The annealing process can be conducted with respect to either the internal dihedral angles of a polypeptide chain or the external rotations and translations of various constituent polypeptide chains, and hence is particularly useful for studying the packing arrangements of secondary structures in proteins, such as helix/helix packing, helix/sheet packing and sheet/sheet packing. It was shown via a number of comparative calculations that the final structures obtained through the annealing process not only had lower energies than the corresponding energy-minimized structures reported previously, but also assumed the forms closer to the observations in proteins. All these results indicate that a better result can be obtained in search of low-energy structures of proteins by incorporating the simulated annealing approach.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗

PubMed1975

Translation of the genes for the structural proteins of alphaviruses.

Synthesis of the structural proteins of Semliki Forest virus by a cell-free system derived from mouse L-cells and programmed by intracellular 26S RNA is described. This polycistronic RNA is translated in vitro into several discrete polypeptides. The identity of these polypeptides as the structural proteins of the virus was established by polyacrylamide gel electrophoresis, immunoprecipitation and tryptic peptide mapping. Studies using formyl--e135S]methionyl-tRNAf as precursor, and using diphtheria toxin and NAD to inhibit elongation, showed that 26S RNA contains only a single initiation site at, or near, the 5' end of the core protein cistron. Experiments in infected cells under conditions of synchronous initiation revealed that the order of the structural protein genes in 26S RNA is core-E3-E2-E1 in the 5' leads to 3' direction.

Arboviruses↗

PubMed2001

Free-energy calculations highlight differences in accuracy between X-ray and NMR structures and add value to protein structure prediction.

BACKGROUND: While X-ray crystallography structures of proteins are considerably more reliable than those from NMR spectroscopy, it has been difficult to assess the inherent accuracy of NMR structures, particularly the side chains. RESULTS: For 15 small single-domain proteins, we used a molecular mechanics-/dynamics-based free-energy approach to investigate native, decoy, and fully extended alpha conformations. Decoys were all less energetically favorable than native conformations in nine of the ten X-ray structures and in none of the five NMR structures, but short 150 ps molecular dynamics simulations on the experimental structures caused them to have the lowest predicted free energy in all 15 proteins. In addition, a strong correlation exists (r(2) = 0.86) between the predicted free energy of unfolding, from native to fully extended conformations, and the number of residues. CONCLUSIONS: This work suggests that the approximate treatment of solvent used in solving NMR structures can lead NMR model conformations to be less reliable than crystal structures. This conclusion was reached because of the considerably higher calculated free energies and the extent of structural deviation during aqueous dynamics simulations of NMR models compared to those determined by X-ray crystallography. Also, the strong correlation found between protein length and predicted free energy of unfolding in this work suggests, for the first time, that a free-energy function can allow for identification of the native state based on calculations on an extended state and in the absence of an experimental structure.

Crystallography, X-Ray↗

PubMed2003

Calculation of helix packing angles in protein structures.

UNLABELLED: Software is presented for the calculation of packing angles and geometry of helical secondary structure elements in protein structures. AVAILABILITY: C language source code and documentation is available from http://www.bioinformatics.leeds.ac.uk.

Algorithms↗

PubMed1997

A novel RNA-binding motif in influenza A virus non-structural protein 1.

The solution NMR structure of the RNA-binding domain from influenza virus non-structural protein 1 exhibits a novel dimeric six-helical protein fold. Distributions of basic residues and conserved salt bridges of dimeric NS1(1-73) suggest that the face containing antiparallel helices 2 and 2' forms a novel arginine-rich nucleic acid binding motif.

Binding Sites↗

PubMed1991

Asymmetry in protein structures.

The asymmetry of L-amino acids determines the asymmetrical features of alpha-helices and beta-sheets. These in turn determine two principal aspects of the three-dimensional structure of proteins: the preferred ways in which alpha-helices and beta-sheets pack together, and certain topological features of the paths followed by polypeptide chains through structures. Though the asymmetrical nature of amino acids plays the central role in determining the asymmetrical aspects of protein structures, it has little or no influence on the next level of biological structures--assemblies of protein molecules.

Amino Acids↗

PubMed1989

A holistic approach to protein structure alignment.

A method of protein structure comparison developed previously is extended to incorporate other aspects of protein structure in addition to the inter-atomic vectors on which it was originally based. Each additional aspect, which induced hydrogen bonding, solvent exposure, torsional angles and sequence, was introduced separately and evaluated for its ability to improve alignment quality. The components were then combined, suitably weighted, to produce a more holistic comparison method. The method was tested on a group of remotely related beta/alpha type proteins that share a common feature in their overall chain fold. The results indicated that while the original inter-atomic vector component was sufficient to give the correct alignment of most pairs of topologically equivalent proteins, the inclusion of hydrogen bonds, torsion angles and a measure of solvent exposure led to improvements in the more difficult comparisons. Consideration of amino acid properties, including hydrophobicity, had no beneficial effect. The failure of the latter component was not unexpected considering the almost total lack of sequence similarity among the proteins considered.

Chemistry, Physical↗