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PubMed2004

Hierarchical analysis of promolecular full electron-density distributions: description of protein structure fragments.

A theoretical method is applied to describe protein structures in terms of hierarchically related substructures. The approach is based on the location of local maxima (peaks) in promolecular electron-density (ED) distributions established at various smoothing levels. Promolecular ED distributions are generated using either the Promolecular Atom Shell Approximation (PASA) representation or the ED are calculated using the Cromer-Mann coefficients. The analysis of the decomposition patterns of a protein structure in its native and hypothetical extended conformations showed that the amino-acid residues have a similar decomposition pattern regardless of their position in the protein sequence, the protein conformation and the influence of the crystal packing. A link is proposed with model-building tools in protein structure determination from diffraction data.

Algorithms↗

PubMed1985

Studies on human parainfluenza virus 3: characterization of the structural proteins and in vitro synthesized proteins coded by mRNAs isolated from infected cells.

The structural proteins of human parainfluenza virus 3, a member of the paramyxovirus family, were characterized by SDS-polyacrylamide gel electrophoresis of radiolabeled virus. The purified virion contains at least eight structural proteins, with estimated molecular weights of 251K, 90K, 71K, 68K, 65K, 51K, 35K, and 21K, respectively. Three of the polypeptides (71K, 65K, and 51K) were identified as glycoproteins based on their incorporation of [3H]glucosamine. Disruption of the virus by Triton X-100 in the presence of increasing salt concentrations indicated that the polypeptides of molecular weights 251K, 90K, 68K, and 21K were components of the nucleocapsid. In parainfluenza virus 3 infected BS-C-1 cells, seven virus structural polypeptides were identified. Six structural proteins (90K, 71K, 68K, 51K, 35K, and 21K) were detected in the cell lysate at 7 hr after infection, while at 10 hr an additional polypeptide (251K) was also observed. At least two nonstructural polypeptides of molecular weights 30K and 25K were also detected in infected cells. mRNAs isolated from virus-infected cells were translated in a cell-free protein-synthesizing system. The in vitro translation products were identical to the authentic virion polypeptides as determined by partial digestion with staphylococcal V8 protease.

Animals↗

PubMed1997

An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures.

A single NMR-derived protein structure is usually deposited as an ensemble containing many structures, each consistent with the restraint set used. The number of NMR-derived structures deposited in the Protein Data Bank (PDB) is increasing rapidly. In addition, many of the structures deposited in an ensemble exhibit variation in only some regions of the structure, often with the majority of the structure remaining largely invariant across the family of structures. Therefore it is useful to determine the set of atoms whose positions are 'well defined' across an ensemble (also known as the 'core' atoms). We have developed a computer program, NMRCORE, which automatically defines (i) the core atoms, and (ii) the rigid body(ies), or domain(s), in which they occur. The program uses a sorted list of the variances in individual dihedral angles across the ensemble to define the core, followed by the automatic clustering of the variances in pairwise inter-atom distances across the ensemble to define the rigid body(ies) which comprise the core. The program is freely available via the World Wide Web (http://neon.chem.le.ac.uk/nmrcore/).

Algorithms↗

PubMed2005

Validating the use of database potentials in protein structure determination by NMR.

The refinement of protein structures determined by nuclear magnetic resonance spectroscopy against database potentials of mean force allows for the exclusion of unfavourable conformations of the protein backbone during a structure calculation, resulting in protein structures with a marked improvement in Ramachandran statistics. In this communication, we use multiple sets of residual dipolar couplings as quality assessment criteria for several proteins and show that not only do the Ramachandran and structural quality statistics improve, but a significant improvement in the accuracy of structures is achieved upon refinement.

Data Interpretation, Statistical↗

PubMed1996

Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures.

A method is presented that positions polar hydrogen atoms in protein structures by optimizing the total hydrogen bond energy. For this goal, an empirical hydrogen bond force field was derived from small molecule crystal structures. Bifurcated hydrogen bonds are taken into account. The procedure also predicts ionization states of His, Asp, and Glu residues. During optimization, side-chain conformations of His, Gln, and Asn residues are allowed to change their last chi angle by 180 degrees to compensate for crystallographic misassignments. Crystal structure symmetry is taken into account where appropriate. The results can have significant implications for molecular dynamics simulations, protein engineering, and docking studies. The largest impact, however, is in protein structure verification: over 85% of protein structures tested can be improved by using our procedure.

Amino Acids↗

PubMed1984

Papillomavirus infection of the cervix. III: Relationship of the presence of viral structural proteins to the expression of involucrin.

Forty-two cervical biopsies with cervical intraepithelial neoplasia were compared with respect to the expression of human papillomavirus (HPV) structural proteins and the expression of the cellular structural protein involucrin, a marker of suprabasal squamous differentiation. HPV structural protein and involucrin expression displayed an inverse correlation with the severity of dysplasia. Both of these proteins were detected in 11 of 28 cases (39%) of mild and moderate dysplasia, but in only two of 14 (14%) cases of severe dysplasia. This difference was statistically significant (p less than 0.001). The presence of HPV was also associated with expression of involucrin in the full thickness of the epithelium, including the basal layer, and an altered staining pattern in the more superficial cells, particularly the koilocytotic cells. These findings support the hypothesis that squamous differentiation is required for the expression of viral structural proteins and that HPV infection begins in the basal epithelium. The study also demonstrates the utility of involucrin staining in differentiating virus-induced cytologic atypia from true neoplasia.

Adult↗

PubMed1996

A knowledge-based method for protein structure refinement and prediction.

The native conformation of a protein, in a given environment, is determined entirely by the various interatomic interactions dictated by the amino acid sequence (1-3). We describe here a knowledge-based approach for protein structure assessment and prediction. Using a well-defined set of high-resolution protein structures, we have derived statistical potentials, in the form of atom-pairwise distance probability density functions. These provide a description of pairwise interatomic interactions of native proteins. When applied to highly randomized and noisy structures of proteins distinct from the basis set, native-like structures were obtained to very high precision (< or = 2A). The examples tested include proteins of all sizes (from 38 up to 461 amino acids long) and diverse topological structures (alpha, beta and alpha-beta classes). The potentials appear to be sensitive enough to recognize subtle distortions from a native packing structure and in optimization of structures drive them consistently to a higher probability. Therefore they provide a powerful tool for refinement of X-ray and NMR derived structures at arbitrary degrees of initial precision.

Crystallography, X-Ray↗

PubMed1999

A comparison of sequence and structure protein domain families as a basis for structural genomics.

MOTIVATION: Protein families can be defined based on structure or sequence similarity. We wanted to compare two protein family databases, one based on structural and one on sequence similarity, to investigate to what extent they overlap, the similarity in definition of corresponding families, and to create a list of large protein families with unknown structure as a resource for structural genomics. We also wanted to increase the sensitivity of fold assignment by exploiting protein family HMMs. RESULTS: We compared Pfam, a protein family database based on sequence similarity, to Scop, which is based on structural similarity. We found that 70% of the Scop families exist in Pfam while 57% of the Pfam families exist in Scop. Most families that occur in both databases correspond well to each other, but in some cases they are different. Such cases highlight situations in which structure and sequence approaches differ significantly. The comparison enabled us to compile a list of the largest families that do not occur in Scop; these are suitable targets for structure prediction and determination, and may be useful to guide projects in structural genomics. It can be noted that 13 out of the 20 largest protein families without a known structure are likely transmembrane proteins. We also exploited Pfam to increase the sensitivity of detecting homologs of proteins with known structure, by comparing query sequences to Pfam HMMs that correspond to Scop families. For SWISSPROT+TREMBL, this yielded an increase in fold assignment from 31% to 42% compared to using FASTA only. This method assigned a structure to 22% of the proteins in Saccharomyces cerevisiae, 24% in Escherichia coli, and 16% in Methanococcus jannaschii.

Computational Biology↗

PubMed1994

Enlarged representative set of protein structures.

To reduce redundancy in the Protein Data Bank of 3D protein structures, which is caused by many homologous proteins in the data bank, we have selected a representative set of structures. The selection algorithm was designed to (1) select as many nonhomologous structures as possible, and (2) to select structures of good quality. The representative set may reduce time and effort in statistical analyses.

Amino Acid Sequence↗

PubMed1999

A key driving force in determination of protein structural classes.

The three-dimensional structure of a protein is uniquely dictated by its primary sequence. However, owing to the very high degenerative nature of the sequence-structure relationship, proteins are generally folded into one of only a few structural classes that are closely correlated with the amino-acid composition. This suggests that the interaction among the components of amino acid composition may play a considerable role in determining the structural class of a protein. To quantitatively test such a hypothesis at a deeper level, three potential functions, U((0)), U((1)), and U((2)), were formulated that respectively represent the 0th-order, 1st-order, and 2nd-order approximations for the interaction among the components of the amino acid composition in a protein. It was observed that the correct rates in recognizing protein structural classes by U((2)) are significantly higher than those by U((0)) and U((1)), indicating that an algorithm that can more completely incorporate the interaction contributions will yield better recognition quality, and hence further demonstrate that the interaction among the components of amino acid composition is an important driving force in determining the structural class of a protein during the sequence folding process.

Algorithms↗

PubMed1998

Serological and cellular immune responses to non-structural proteins in animals infected with FMDV.

In order to provide a rational base for the evaluation of FMDV non structural proteins as diagnostic probes, we have performed systematic longitudinal studies of the humoral and cellular immune responses to these proteins in animals infected with different FMDV serotypes. Although primary antibody responses to all the non structural proteins were observed, antibody titres were highly variable, ranging from insignificant in some cases, to clearly positive in others. In general, even the obvious positive responses were of short duration. For this reasons, discrimination between infected and vaccinated cattle is only possible at a herd level, and in our experiments the most useful target was the non structural protein 3A, although addition of 2C and 3C would provide a more sensitive test. As an alternative, with the major advantage of use directly on living cattle in the field, recombinant non structural proteins were evaluated in Delayed Type Hypersensitivity (DTH) skin tests. With this test, which measures Th1 type cellular immune responses, the most T cell immunogenic non structural proteins were 2B, 2C and 3D. Thus, DTH skin test could be a very useful tool to differentiate infected from vaccinated cattle.

Animals↗

PubMed2004

Protein structure prediction using sparse dipolar coupling data.

Residual dipolar coupling (RDC) represents one of the most exciting emerging NMR techniques for protein structure studies. However, solving a protein structure using RDC data alone is still a highly challenging problem. We report here a computer program, RDC-PROSPECT, for protein structure prediction based on a structural homolog or analog of the target protein in the Protein Data Bank (PDB), which best aligns with the (15)N-(1)H RDC data of the protein recorded in a single ordering medium. Since RDC-PROSPECT uses only RDC data and predicted secondary structure information, its performance is virtually independent of sequence similarity between a target protein and its structural homolog/analog, making it applicable to protein targets beyond the scope of current protein threading techniques. We have tested RDC-PROSPECT on all (15)N-(1)H RDC data (representing 43 proteins) deposited in the BioMagResBank (BMRB) database. The program correctly identified structural folds for 83.7% of the target proteins, and achieved an average alignment accuracy of 98.1% residues within a four-residue shift.

Computational Biology↗

PubMed2005

PROTINFO: new algorithms for enhanced protein structure predictions.

We describe new algorithms and modules for protein structure prediction available as part of the PROTINFO web server. The modules, comparative and de novo modelling, have significantly improved back-end algorithms that were rigorously evaluated at the sixth meeting on the Critical Assessment of Protein Structure Prediction methods. We were one of four server groups invited to make an oral presentation (only the best performing groups are asked to do so). These two modules allow a user to submit a protein sequence and return atomic coordinates representing the tertiary structure of that protein. The PROTINFO server is available at http://protinfo.compbio.washington.edu.

Algorithms↗

PubMed2003

3D-Jury: a simple approach to improve protein structure predictions.

MOTIVATION: Consensus structure prediction methods (meta-predictors) have higher accuracy than individual structure prediction algorithms (their components). The goal for the development of the 3D-Jury system is to create a simple but powerful procedure for generating meta-predictions using variable sets of models obtained from diverse sources. The resulting protocol should help to improve the quality of structural annotations of novel proteins. RESULTS: The 3D-Jury system generates meta-predictions from sets of models created using variable methods. It is not necessary to know prior characteristics of the methods. The system is able to utilize immediately new components (additional prediction providers). The accuracy of the system is comparable with other well-tuned prediction servers. The algorithm resembles methods of selecting models generated using ab initio folding simulations. It is simple and offers a portable solution to improve the accuracy of other protein structure prediction protocols. AVAILABILITY: The 3D-Jury system is available via the Structure Prediction Meta Server (http://BioInfo.PL/Meta/) to the academic community. SUPPLEMENTARY INFORMATION: 3D-Jury is coupled to the continuous online server evaluation program, LiveBench (http://BioInfo.PL/LiveBench/)

Algorithms↗

PubMed1986

Cloning full-length dengue type 4 viral DNA sequences: analysis of genes coding for structural proteins.

DNA sequences (approximately 11,000 nucleotides) representing the full-length genome of the dengue virus type 4 were cloned. The sequence of the first 2,429 nucleotides at the 5' terminus which includes the coding region for the structural proteins is presented. The virion structural proteins are encoded in one long open reading frame specifying a polyprotein precursor which is apparently proteolytically cleaved by a mechanism resembling that proposed for expression of structural proteins of other flaviviruses such as yellow fever (YF) and West Nile (WN) viruses. The N terminus for each of the dengue virus structural proteins was tentatively assigned by homology alignment to the corresponding sequence of YF or WN virus. Comparison of sequence homology of structural proteins suggests that dengue virus is more closely related to WN virus than to YF virus or Murray Valley encephalitis virus. Finally, analysis of the extreme 5'- and 3'-terminal nucleotides of the dengue virus genome revealed sequences that may be involved in transcription, replication, and packaging of viral RNA.

Amino Acid Sequence↗

PubMed1986

Calculating three-dimensional changes in protein structure due to amino-acid substitutions: the variable region of immunoglobulins.

A procedure (coupled perturbation procedure, CPP) is introduced as a specific method for calculating the detailed three-dimensional structure of a protein molecule which has a number of amino-acid substitutions relative to some previously determined "parent" protein structure. The accuracy of the procedure is tested by calculating the conformation of a region of the human immunoglobulin fragment Fab Kol based on the analogous region of the human immunoglobulin fragment Fab New. Both structures have previously been determined crystallographically. The calculated model is accurate to the extent that both of the sequence differences in the region are modeled correctly and that conformational changes in a number of nearby residues are correctly identified. CPP is shown to give better results than other commonly used modeling procedures when applied to the same problem.

Amino Acid Sequence↗

PubMed1996

Detection of non-topological motifs in protein structures.

We present an efficient technique for the comparison of protein structures. The algorithm uses a vector representation of the secondary structure elements and searches for spatial configurations of secondary structure elements in proteins. In such recurring protein folds, the order of the secondary structure elements in the protein chains is disregarded. The method is based on the geometric hashing paradigm and implements approaches originating in computer vision. It represents and matches the secondary structure element vectors in a 3-D translation and rotation invariant manner. The matching of a pair of proteins takes on average under 3 s on a Silicon Graphics Indigo2 workstation, allowing extensive all-against-all comparisons of the data set of non-redundant protein structures. Here we have carried out such a comparison for a data set of over 500 protein molecules. The detection of recurring topological and non-topological, secondary structure element order-independent protein folds may provide further insight into evolution. Moreover, as these recurring folding units are likely to be conformationally favourable, the availability of a data set of such topological motifs can serve as a rich input for threading routines. Below, we describe this rapid technique and the results it has obtained. While some of the obtained matches conserve the order of the secondary structure elements, others are entirely order independent. As an example, we focus on the results obtained for Che Y, a signal transduction protein, and on the profilin-beta-actin complex. The Che Y molecule is composed of a five-stranded, parallel beta-sheet flanked by five helices. Here we show its similarity with the Escherichia coli elongation factor, with L-arabinose binding protein, with haloalkane dehalogenase and with adenylate kinase. The profilin-beta-actin contains an antiparallel beta-pleated sheet with alpha-helical termini. Its similarities to lipase, fructose disphosphatase and beta-lactamase are displayed.

Algorithms↗

PubMed2006

OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures.

The large number of experimentally determined protein 3D structures is a rich resource for studying protein function and evolution, and protein structure comparison (PSC) is a key method for such studies. When comparing two protein structures, almost all currently available PSC servers report a single and sequential (i.e. topological) alignment, whereas the existence of good alternative alignments, including those involving permutations (i.e. non-sequential or non-topological alignments), is well known. We have recently developed a novel PSC method that can detect alternative alignments of statistical significance (alignment similarity P-value <10(-5)), including structural permutations at all levels of complexity. OPAAS, the server of this PSC method freely accessible at our website (http://opaas.ibms.sinica.edu.tw), provides an easy-to-read hierarchical layout of output to display detailed information on all of the significant alternative alignments detected. Because these alternative alignments can offer a more complete picture on the structural, evolutionary and functional relationship between two proteins, OPAAS can be used in structural bioinformatics research to gain additional insight that is not readily provided by existing PSC servers.

Internet↗