A Novel Method for Packing Quality Assessment of Transmembrane alpha-Helical Domains in Proteins

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A. O. Chugunov^1,2, V. N. Novoseletsky^1,3, A. S. Arseniev¹, and R. G. Efremov¹

¹Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia; fax: (495) 336-2000; E-mail: batch2k@yandex.ru

²Department of Bioengineering, Biological Faculty, Lomonosov Moscow State University, 119899 Moscow, Russia

³Moscow Institute of Physics and Technology (State University), Institutskii Pereulok 9, 141700 Dolgoprudnyi, Moscow Region, Russia

^* To whom correspondence should be addressed.

Received November 2, 2006; Revision received November 10, 2006

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Here we present a novel method for assessment of packing quality for transmembrane (TM) domains of alpha-helical membrane proteins (MPs), based on analysis of available high-resolution experimental structures of MPs. The presented concept of protein-membrane environment classes permits quantitative description of packing characteristics in terms of membrane accessibility and polarity of the nearest protein groups. We demonstrate that the method allows identification of native-like conformations among the large set of theoretical MP models. The developed “membrane scoring function” will be of use for optimization of TM domain packing in theoretical models of MPs, first of all G-protein coupled receptors.

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KEY WORDS: integral membrane proteins, spatial structure prediction, protein environment, GPCR, visual rhodopsin

DOI: 10.1134/S0006297907030066

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