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Bioinformatics Advance Access published online on May 6, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth297
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received February 26, 2004
Revised April 15, 2004
Accepted April 22, 2004

Discovery note

Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins

Akira R. Kinjo 1 Ken Nishikawa 2*

1 Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, 411-8540, Japan
2 Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, 411-8540, Japan; Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, 411-8540, Japan

* To whom correspondence should be addressed. E-mail: knishika{at}genes.nig.ac.jp.


  Abstract

The pattern of amino acid substitutions and sequence conservation over many structure-based alignments of protein sequences was analyzed as a function of percent sequence identity. The statistics of the amino acid substitutions were converted into the form of log-odds amino acid substitution matrices to which eigenvalue decomposition was applied. It was found that the most important component of the substitution matrices exhibited a sharp transition at the sequence identity of 30-35% which coincides with the twilight zone. Above the transition point, the most dominant component is related to the mutability of amino acids and it acts to disfavor any substitutions, whereas below the transition point, the most dominant component is related to the hydrophobicity of amino acids and substitutions between residues of similar hydrophobic character are positively favored. Implications for protein evolution and sequence analysis are discussed.

Supplementary Information:

http://maccl01.genes.nig.ac.jp/~akinjo/aasm/


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