Neighboring-Site Effects of Amino Acid Substitutions in the Mouse Genome

Title:Neighboring-Site Effects of Amino Acid Substitutions in the Mouse Genome

Volume: 10 Issue: 3

Author(s): Mingchuan Fu, Hongxia Pang, Jian Cheng and Shiheng Tao

Affiliation:

Keywords: Amino acid substitution, C- and N-terminal, mice genome, neighboring-site, preference, second protein structure.

Abstract: Nucleotide evolution models benefit a lot from the reported neighbor-dependent nucleotide mutations. Investigations of neighboring-site effects of amino acid substitutions may also promote the development of protein evolution models. Here, the neighboring-site effects of amino acid substitutions in the mouse genome are evaluated by grouping the 20 amino acids into four categories: nonpolar neutral (NON), polar neutral (NEU), positive (POS) and negative (NEG) amino acids. Our data indicate that amino acid substitutions are evidently neighboring-site dependent, and the most prominent bias is the NEG→NEG substitution occurring in NEG_NEG context, the frequency of which is 2-fold higher than that of expectation. The neighboring-site effects are also correlated with some types of protein secondary structures. Through this study, we conclude that like neighbor-dependent nucleotide mutations, amino acid substitutions are also neighboring-site dependent. The mutation bias of nucleotide sequence and natural or functional selection on protein structure might be two underlying reasons for the neighboring-site effects of amino acid substitutions in the mouse genome.

Cite this article as:

Fu Mingchuan, Pang Hongxia, Cheng Jian and Tao Shiheng, Neighboring-Site Effects of Amino Acid Substitutions in the Mouse Genome, Current Bioinformatics 2015; 10 (3) . https://dx.doi.org/10.2174/1574893609666140716171245