Biochemistry (Moscow)

, Volume 72, Issue 3, pp 293–300 | Cite as

A novel method for packing quality assessment of transmembrane α-helical domains in proteins

  • A. O. Chugunov
  • V. N. Novoseletsky
  • A. S. Arseniev
  • R. G. Efremov
Article

Abstract

Here we present a novel method for assessment of packing quality for transmembrane (TM) domains of α-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.

Key words

integral membrane proteins spatial structure prediction protein environment GPCR visual rhodopsin 

Abbreviations

GPCR

G-protein coupled receptors

MP

membrane protein

PhP

photosynthetic protein

RMSD

root-mean square deviation

Smem

“membrane score”

TM

transmembrane

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Copyright information

© Pleiades Publishing, Ltd. 2007

Authors and Affiliations

  • A. O. Chugunov
    • 1
    • 2
  • V. N. Novoseletsky
    • 1
    • 3
  • A. S. Arseniev
    • 1
  • R. G. Efremov
    • 1
  1. 1.Shemyakin—Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussia
  2. 2.Department of Bioengineering, Biological FacultyLomonosov Moscow State UniversityMoscowRussia
  3. 3.Moscow Institute of Physics and TechnologyState UniversityDolgoprudnyi, Moscow RegionRussia

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