A novel method for packing quality assessment of transmembrane alpha-helical domains in proteins.
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.
Chugunov
A O
AO
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia. batch2k@yandex.ru
Novoseletsky
V N
VN
Arseniev
A S
AS
Efremov
R G
RG
D000465:Algorithms; D008962:Models, Theoretical; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D012243:Rhodopsin / Q000737:chemistry; D020539:Sequence Analysis, Protein / Q000379:methods*
D011506:Proteins; D012243:Rhodopsin