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https://hdl.handle.net/10216/96316
Author(s): | Miguel M. de Sousa Cristian R. Munteanu Alejandro Pazos Nuno A. Fonseca Rui Camacho A. L. Magalhães |
Title: | Amino acid pair- and triplet-wise groupings in the interior of alpha-helical segments in proteins |
Issue Date: | 2011 |
Abstract: | A statistical approach has been applied to analyse primary structure patterns at inner positions of alpha-helices in proteins. A systematic survey was carried out in a recent sample of non-redundant proteins selected from the Protein Data Bank, which were used to analyse alpha-helix structures for amino acid pairing patterns. Only residues more than three positions apart from both termini of the alpha-helix were considered as inner. Amino acid pairings i, i+k(k = 1, 2, 3,4, 5), were analysed and the corresponding 20 x 20 matrices of relative global propensities were constructed. An analysis of (i, i+4, i+8) and (i, i+3, i+4) triplet patterns was also performed. These analysis yielded information on a series of amino acid patterns (pairings and triplets) showing either high or low preference for alpha-helical motifs and suggested a novel approach to protein alphabet reduction. In addition, it has been shown that the individual amino acid propensities are not enough to define the statistical distribution of these patterns. Global pair propensities also depend on the type of pattern, its composition and orientation in the protein sequence. The data presented should prove useful to obtain and refine useful predictive rules which can further the development and fine-tuning of protein structure prediction algorithms and tools. (C) 2010 Elsevier Ltd. All rights reserved. |
Subject: | Matemática Mathematics |
Scientific areas: | Ciências exactas e naturais::Matemática Natural sciences::Mathematics |
URI: | https://repositorio-aberto.up.pt/handle/10216/96316 |
Document Type: | Artigo em Revista Científica Internacional |
Rights: | restrictedAccess |
Appears in Collections: | FCUP - Artigo em Revista Científica Internacional FEUP - Artigo em Revista Científica Internacional |
Files in This Item:
File | Description | Size | Format | |
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64331.pdf Restricted Access | Amino Acid Pair- and Triplet-wise Groupings in the Interior of Alpha-Helical Segments in Proteins | 594.45 kB | Adobe PDF | Request a copy from the Author(s) |
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