proteinstructure comparison is a important anddeveloping area in Bioinformatics. Understanding the proteinstructure is very useful, since proteinstructure suffers less evolutionary changes compared to the amino ac...
详细信息
ISBN:
(纸本)9781424441334
proteinstructure comparison is a important anddeveloping area in Bioinformatics. Understanding the proteinstructure is very useful, since proteinstructure suffers less evolutionary changes compared to the amino acid sequences. Thus, comparing proteinstructures provides additional evolution information. However, structure comparison is not straightforward and multiple algorithms for comparison have emerged recently. In this paper we evaluate the performance of algorithms based on contact maps and C alpha, and their respective objective function, which is a measure of biological and evolutionary importance. The contributions are a state-of-the-art review of proteinstructure comparison algorithms that have not been compared with other servers. Further, we compare findings and evaluate them across others methods already proven effective.
The increase in the number of Web-based resources on post-translational modification sites (PTMSs) in proteins is accelerating. The paper presents a set of computational protocols describing how to work with the Inter...
详细信息
The increase in the number of Web-based resources on post-translational modification sites (PTMSs) in proteins is accelerating. The paper presents a set of computational protocols describing how to work with the Internet resources when dealing with PTMSs. The protocols are intended for querying in PTMSs relateddata bases, search of the PTMSs in the protein sequences andstructures, calculating the pI and molecular mass of the PTM isoforms. Thus, the modern bioinformatics prediction tools make feasible to express protein modification in broader quantitative terms. less
Closely related to studying the function of a protein is the analysis of its three-dimensional structure and the identification of interaction sites with its binding partners. An alternative approach to the high-resol...
详细信息
Closely related to studying the function of a protein is the analysis of its three-dimensional structure and the identification of interaction sites with its binding partners. An alternative approach to the high-resolution methods for three-dimensional proteinstructure analysis, such as X-ray crystallography and NMR spectroscopy, consists of covalently connecting two functional groups of the protein(s) under investigation. The location of the created cross-links imposes a distance constraint on the location of the respective side chains and allows one to draw conclusions on the three-dimensional structure of the protein or a protein complex. Recently, chemical cross-linking of proteins has been combined with a mass spectrometric analysis of the created cross-linked products. This review article describes the most popular cross-linking reagents for proteinstructure analysis and gives an overview of the different available strategies that employ chemical cross-linking anddifferent mass spectrometric techniques. The challenges for mass spectrometry caused by the enormous complexity of the cross-linking reaction mixtures are emphasized. The various approaches described in the literature to facilitate the mass spectrometric detection of cross-linked products as well as computer software for data analyses are reviewed. (c) 2006 Wiley Periodicals, Inc.,
In this article we characterize, from a structural point of view, all 16 members of the tubulin gene family of Caeno-rhabditis elegans (9 alpha-tubulins, 6 beta-tubulins, and 1 gamma- tubulin). We obtained their terti...
详细信息
In this article we characterize, from a structural point of view, all 16 members of the tubulin gene family of Caeno-rhabditis elegans (9 alpha-tubulins, 6 beta-tubulins, and 1 gamma- tubulin). We obtained their tertiary structures by computationally modifying the X-ray crystal structure of the pig brain alpha/beta-tubulin dimer published by Nogales et al. [Nature (London) 1998;391:199-203]. Our computational protocol involves changing the amino acids (with MIdAS;Jarvis et al., UCSF MIdAS. University of California, San Francisco, 1986) in the 3dstructure of pig brain alpha/beta-tubulin dimer followed by geometry optimization with the AMBER force field (Perlman et al., AMBER 4. University of California, San Francisco, 1990). We subsequently analyze and compare the resulting structures in terms of the differences in their secondary and tertiary structures. In addition, we compare the pattern of hydrogen bonds and hydrophobic contacts in the guanosine triphosphate (GTP)-binding site for all members of the tubulin family. Our computational results show that, except that the change in the pattern of hydrogen bonds in the GTP-binding site may be used to assess the relative stability of different alpha/beta-tubulin dimers formed by monomers of the tubulin family. (C) 2000 by Elsevier Science Inc.
The experimental and computational techniques for capturing information about proteinstructures and genetic variation within the human genome have advanceddramatically in the past 20 years, generating extensive new ...
详细信息
The experimental and computational techniques for capturing information about proteinstructures and genetic variation within the human genome have advanceddramatically in the past 20 years, generating extensive new data resources. In this review, we discuss these advances, along with new approaches for determining the impact a genetic variant has on protein function. We focus on the potential of new methods that integrate human genetic variation into proteinstructures to discover relationships to disease, including the discovery of mutational hotspots in cancer-relatedproteins, the localization of protein-altering variants within protein regions for common complex diseases, and the assessment of variants of unknown significance for Mendelian traits. We expect that approaches that integratethese data sources will play increasingly important roles in disease gene discovery and variant interpretation.
暂无评论