Mechanism of Selection of Side-Chain Rotamers in alpha-Helices

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A. V. Efimov

Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; fax: (495) 632-7871; E-mail: efimov@protres.ru

Received October 11, 2006

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In this study, a possible mechanism of selection of side-chain rotamers based on the rotamer distributions in known coiled-coil proteins is suggested. According to this mechanism, interhelical hydrophobic, polar, and packing interactions bring alpha-helices closer to each other and this effect squeezes side chains out of the helix-helix interface. As a result, in dimeric coiled coils and long alpha-alpha-hairpins where alpha-helices are packed in a face-to-face manner, most side chains occupying the a-positions have t-rotamers and those in the d-positions g^--rotamers. In tetramers, where alpha-helices are packed side-by-side, most side chains in the a-positions adopt g^--rotamers and those in the d-positions t-rotamers.

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KEY WORDS: alpha-proteins, rotamer preference, stereochemical analysis, alpha-helix packing

DOI: 10.1134/S0006297907020083

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