Identification of a Novel Cysteine-stack Arrangement in Parallel β-helix Proteins using Computational and Knowledge-based Approach
Zeti A.M.H., and Mohd Shahir S., and Gerloff, D.L., (2007) Identification of a Novel Cysteine-stack Arrangement in Parallel β-helix Proteins using Computational and Knowledge-based Approach. Malaysian Journal of Biochemistry and Molecular Biology, 15 (1). pp. 24-29. ISSN ISSN 1511-2616 Full text not available from this repository. Official URL: http://ejum.fsktm.um.edu.my/ArticleInformation.aspx?ArticleID=578 AffiliationsUniversiti Kebangsaan Malaysia. Faculty of Science and Technology. School of Biosciences and Biotechnology
Universiti Teknologi Malaysia. Faculty of Science. Dept. of Biology
University of Edinburgh. Institute of Structural & Molecular Biology AbstractParallel β-helices, a subclass of β-sheet proteins, represent the folding of a polypeptide chain into an elongated topologically simpler fold than globular β-sheets. However, the amino acid sequence rules that specify β-sheet structure in protein remain unelucidated. In this study, a combination of knowledge-based and computational analysis using the novel cysteine staple pattern found in pectin methylesterase A to predict the right-handed parallel β-helix structural motif in primary amino acid sequences is presented. The novel staple pattern was used to find further pectin lyase-like protein families displaying this pattern, and to produce high confidence 3D models for all detectable members of this superfamily. To achieve these goals, candidate sequences were retrieved from GenPept and SUPERFAMILY databases. Possible pectin lyase-like proteins were detected with two different fold recognition algorithms, and stringent criteria were designed to minimise false positive predictions. The filtered datasets were clustered, resulting into two main categories; Category A included all sequences with homologues in the PDB and Category B comprised all sequences with unknown homologues. Four families have been identified as new family, where prior to this study, the proteins in this new family had not been identified nor classified as pectin lyase-like proteins. Multiple sequence alignments were generated from each family in both categories, and were carefully inspected to finally produce highly accurate alignments to be used as input for large-scale automatic modeling. There were 298 high quality 3D models of pectin lyase-like proteins produced, which may be used to provide a valuable resource for biological research in this area. Models inspection has revealed numerous instances of possible cysteine stacks in the β-helix cores, where asparagine ladders are common as well as the existence of disulphide bridges. Repository Staff Only: item control page
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