Application of three-dimensional molecular hydrophobicity potential to the analysis of spatial organization of membrane protein domains. II. Optimization of hydrophobic contacts in transmembrane hairpin structures of Na+, K(+)-ATPase.
A method of packing of transmembrane hairpin helices in proteins is described. The procedure is based on the optimization of hydrophobic contacts calculated using the three-dimensional (3D) molecular hydrophobicity potential technique. To verify the validity of the computational scheme, we calculated relative orientations of membrane-spanning peptides in pairs L2-L3, M2-M3, and M4-M5 from L- and M-subunits of the photoreaction center of Rhodopseudomonas viridis and compared the predicted structures with those derived from atomic coordinates. The results of computer modeling agree with the X-ray data. We applied the approach proposed to study possible interhelical interactions in transmembrane hairpin structures of Na+, K(+)-ATPase.
Efremov
R G
RG
Shemyakin Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow.
Gulyaev
D I
DI
Modyanov
N N
NN
D002462:Cell Membrane / Q000201:enzymology; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003198:Computer Simulation; D004563:Electrochemistry; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D015394:Molecular Structure; D045322:Photosynthetic Reaction Center Complex Proteins / Q000737:chemistry; D017433:Protein Structure, Secondary; D016992:Rhodobacter / Q000737:chemistry; D000254:Sodium-Potassium-Exchanging ATPase / Q000737:chemistry*
D008565:Membrane Proteins; D045322:Photosynthetic Reaction Center Complex Proteins; D000254:Sodium-Potassium-Exchanging ATPase