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