%0 Journal Article
%T Statistical Analysis of Terminal Extensions of Protein ¦Â-Strand Pairs
%A Ning Zhang
%A Shan Gao
%A Lei Zhang
%A Jishou Ruan
%A Tao Zhang
%J Advances in Bioinformatics
%D 2013
%I Hindawi Publishing Corporation
%R 10.1155/2013/909436
%X The long-range interactions, required to the accurate predictions of tertiary structures of ¦Â-sheet-containing proteins, are still difficult to simulate. To remedy this problem and to facilitate ¦Â-sheet structure predictions, many efforts have been made by computational methods. However, known efforts on ¦Â-sheets mainly focus on interresidue contacts or amino acid partners. In this study, to go one step further, we studied ¦Â-sheets on the strand level, in which a statistical analysis was made on the terminal extensions of paired ¦Â-strands. In most cases, the two paired ¦Â-strands have different lengths, and terminal extensions exist. The terminal extensions are the extended part of the paired strands besides the common paired part. However, we found that the best pairing required a terminal alignment, and ¦Â-strands tend to pair to make bigger common parts. As a result, 96.97%£¿ of ¦Â-strand pairs have a ratio of 25% of the paired common part to the whole length. Also 94.26% and 95.98%£¿ of ¦Â-strand pairs have a ratio of 40% of the paired common part to the length of the two ¦Â-strands, respectively. Interstrand register predictions by searching interacting ¦Â-strands from several alternative offsets should comply with this rule to reduce the computational searching space to improve the performances of algorithms. 1. Introduction The issue of protein structure prediction is still extremely challenging in bioinformatics [1, 2]. Usually, structural information for protein sequences with no detectable homology to a protein of known structure could be obtained by predicting the arrangement of their secondary structural elements [3]. As we know, the two predominant protein secondary structures are ¦Á-helices and ¦Â-sheets. However, a combination of the early suitable ¦Á-helical model systems and sustained researches have resulted in a detailed understanding of ¦Á-helix, while comparatively little is known about ¦Â-sheet [4]. Tertiary structures of ¦Â-sheet-containing proteins are especially difficult to simulate [3, 5]. Unlike ¦Á-helices, ¦Â-sheets are more complex resulting from a combination of two or more disjoint peptide segments, called ¦Â-strands. Therefore, the ¦Â-sheet topology is very useful for elucidating protein folding pathways [6, 7] for predicting tertiary structures [3, 8¨C11], and even for designing new proteins [12¨C14]. As fundamental components, ¦Â-sheets are plentifully contained in protein domains. In a ¦Â-sheet, multiple ¦Â-strands held together linked by hydrogen bonds and can be classified into parallel and antiparallel direction styles. Adjacent
%U http://www.hindawi.com/journals/abi/2013/909436/