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Journal of Biochemistry Advance Access originally published online on February 14, 2008
Journal of Biochemistry 2008 143(5):661-665; doi:10.1093/jb/mvn017
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© 2008 The Japanese Biochemical Society.

Vertebrate Genomes Code Excess Proteins with Charge Periodicity of 28 Residues

Runcong Ke*, Noriyuki Sakiyama, Ryusuke Sawada, Masashi Sonoyama and Shigeki Mitaku

Department of Applied Physics, Graduate School of Engineering, Nagoya University, Nagoya, Japan

*To whom correspondence should be addressed. Tel: +81 52 788 6218, Fax: +81 52 788 6215, E-mail: ke{at}bp.nuap.nagoya-u.ac.jp

Received December 9, 2007; Accepted February 1, 2008


  Abstract

All amino acid sequences derived from 248 prokaryotic genomes, 10 invertebrate genomes (plants and fungi) and 10 vertebrate genomes were analysed by the autocorrelation function of charge sequences. The analysis of the total amino acid sequences derived from the 268 biological genomes showed that a significant periodicity of 28 residues is observable for the vertebrate genomes, but not for the other genomes. When proteins with a charge periodicity of 28 residues (PCP28) were selected from the total proteomes, we found that PCP28 in fact exists in all proteomes, but the number of PCP28 is much larger for the vertebrate proteomes than for the other proteomes. Although excess PCP28 in the vertebrate proteomes are only poorly characterized, a detailed inspection of the databases suggests that most excess PCP28 are nuclear proteins.

Key Words: amino acid sequence, autocorrelation function, charge periodicity, nuclear protein, vertebrate

Abbreviations: COG, clusters of orthologous groups; PCP28, proteins with a charge periodicity of 28 residues


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