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Published online before print December 2, 2004
Protein Science, DOI: 10.1110/ps.04984505
 Copyright © 2004 The Protein Society
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Electric charge balance mechanism of extended soluble proteins

Nobuyuki Uchikoga1, Shun-Ya Takahashi2, Runcong Ke1, Masashi Sonoyama1 and Shigeki Mitaku1

1 Nagoya University, Department of Applied Physics, Graduate School of Engineering, Nagoya, Aichi 464-8603, Japan
2 Tokyo University of Agriculture and Technology, Department of Biotechnology, Tokyo 184-8588, Japan

(RECEIVED July 19, 2004; FINAL REVISION August 27, 2004; ACCEPTED August 27, 2004)

Extended proteins such as calmodulin and troponin C have two globular terminal domains linked by a central region that is exposed to water and often acts as a function-regulating element. The mechanisms that stabilize the tertiary structure of extended proteins appear to differ greatly from those of globular proteins. Identifying such differences in physical properties of amino acid sequences between extended proteins and globular proteins can provide clues useful for identification of extended proteins from complete genomes including orphan sequences. In the present study, we examined the structure and amino acid sequence of extended proteins. We found that extended proteins have a large net electric charge, high charge density, and an even balance of charge between the terminal domains, indicating that electrostatic interaction is a dominant factor in stabilization of extended proteins. Additionally, the central domain exposed to water contained many amphiphilic residues. Extended proteins can be identified from these physical properties of the tertiary structure, which can be deduced from the amino acid sequence. Analysis of physical properties of amino acid sequences can provide clues to the mechanism of protein folding. Also, structural changes in extended proteins may be caused by formation of molecular complexes. Long-range effects of electrostatic interactions also appear to play important roles in structural changes of extended proteins.

Keywords: structural classification; extended protein; bioinformatics; structural genomics; mechanism of structural stabilization; physical properties of amino acid residues

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.04984505.

Reprint requests to: Nobuyuki Uchikoga, Department of Applied Physics, Graduate School of Engineering, Nagoya University, Furocho, Chikusaku, Nagoya, Aichi 464-8603, Japan; e-mail: uchikoga{at}bp.nuap.nagoya-u.ac.jp; fax: +81-52-789-3708.


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