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题名: Detection and Alignment of 3D Domain Swapping Proteins Using Angle-distance Image-based Secondary Structural Matching Techniques
作者: Chia-Han Chu;Wei-Cheng Lo;Hsin-Wei Wang;Yen-Chu Hsu;Jenn-Kang Hwang;Ping-Chiang Lyu;Tun-Wen Pai;Chuan Yi Tang
贡献者: NTOU:Department of Computer Science and Engineering
國立臺灣海洋大學:資訊工程學系
日期: 2010
上传时间: 2011-10-21T02:35:10Z
出版者: PLoS ONE
摘要: Abstract:This work presents a novel detection method for three-dimensional domain swapping (DS), a mechanism for forming protein quaternary structures that can be visualized as if monomers had ‘‘opened’’ their ‘‘closed’’ structures and exchanged the opened portion to form intertwined oligomers. Since the first report of DS in the mid 1990s, an increasing number of identified cases has led to the postulation that DS might occur in a protein with an unconstrained terminus under appropriate conditions. DS may play important roles in the molecular evolution and functional regulation of proteins and the formation of depositions in Alzheimer’s and prion diseases. Moreover, it is promising for designing auto-assembling biomaterials. Despite the increasing interest in DS, related bioinformatics methods are arely available. Owing to a dramatic conformational difference between the monomeric/closed and oligomeric/open forms, conventional structural comparison methods are inadequate for detecting DS. Hence, there is also a lack of comprehensive datasets for studying DS. Based on angle-distance (A-D) image transformations of secondary structural elements (SSEs), specific patterns within A-D images can be recognized and classified for structural similarities. In this work, a matching algorithm to extract corresponding SSE pairs from A-D images and a novel DS score have been designed and demonstrated to be applicable to the etection of DS relationships. The Matthews correlation coefficient (MCC) and sensitivity of the proposed DS-detecting method were higher than 0.81 even when the sequence identities of the proteins examined were lower than 10%. On average, the alignment percentage and root-mean-square distance (RMSD) computed by the proposed method were 90% and 1.8A° for a set of 1,211 DS-related pairs of proteins. The performances of structural alignments remain high nd stable for DS-related homologs with less than 10% sequence identities.
關聯: 5(10), pp.1-22
URI: http://ntour.ntou.edu.tw/handle/987654321/28017
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