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PEDS Advance Access published online on April 8, 2005
Protein Engineering Design and Selection, doi:10.1093/protein/gzi016
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oupjournals.org
Received November 29, 2004
Revised March 5, 2005
Accepted March 5, 2005

Article

Detection of subunit interfacial modifications by tracing the evolution of clamp-loader complex

Mihoko Saito 1, Takuji Oyama 2, and Tsuyoshi Shirai 3*

1 Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
2 Department of Structural Biology, Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
3 Department of Computational Biology, Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan

* To whom correspondence should be addressed.
Tsuyoshi Shirai, E-mail: shirai{at}beri.or.jp


  Abstract

The archaeal and eukaryal clamp-loader and clamp proteins were investigated with the evolutionary trace method. The molecular phylogeny of the proteins suggested that the hetero-pentameric complex of the archaeal clamp-loader with two subunits (RFCL and RFCS) was not a preserved ancestral type, but a degenerated version of the eukaryal complex of five subunits (RFC1-5). The evolutionary trace of amino acid replacements during the course of subunit differentiation revealed that the replacements had accumulated preferentially at the subunit interface regions. Some of the interfacial modifications that might be responsible for the specific interaction between the subunits were conserved in the current complex.

Keywords: evolutionary trace; PCNA; protein complex; protein interface; RFC.
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