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PEDS Advance Access originally published online on April 8, 2005
Protein Engineering Design and Selection 2005 18(3):139-145; 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

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

Mihoko Saito1, Takuji Oyama2 and Tsuyoshi Shirai3,4

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

4 To whom correspondence should be addressed. E-mail: shirai{at}beri.or.jp

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

Received November 29, 2004; revised March 5, 2005; accepted March 5, 2005.

Edited by Haruki Nakamura


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