Prediction of the positioning of the seven transmembrane α-helices of bacteriorhodopsin: A molecular simulation study

• Published in: Journal of molecular biology Vol. 236; no. 4; pp. 1105 - 1122
• Main Authors: Tuffery, P., Etchebest, C., Popot, J.-L., Lavery, R.
• Format: Journal Article
• Language: English
• Published: Oxford Elsevier Ltd 04.03.1994; Elsevier
• Subjects: Analytical, structural and metabolic biochemistry; Bacteriorhodopsins - chemistry; Bacteriorhodopsins - ultrastructure; Biochemistry, Molecular Biology; Biological and medical sciences; Computer Simulation; Fundamental and applied biological sciences. Psychology; Halobacterium salinarum - chemistry; Life Sciences; membrane proteins; Microscopy, Electron; Models, Molecular; Molecular Structure; Non metallic chromoproteins, photoproteins; optimization; Protein Conformation; Protein Structure, Secondary; Proteins; side-chain conformations; Thermodynamics; α-helices; computer simulation; membrane proteins; α-helices; side-chain conformations; optimization; Transmembrane protein; Computer simulation; Archaeobacteria; Halobacterium salinarium; Photoprotein; Optimal estimation; Bacteriorhodopsin; Molecular orientation; Halobacteriales; Bacteria; Helical structure; Halobacteriaceae; Structural analysis; Conformation
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/0022-2836(94)90015-9

We have applied a search strategy for determining the optimal packing of protein secondary structure elements to the rotational positioning of the seven transmembrane helices of bacteriorhodopsin. The search is based on the assumption that the relative orientations of the helices within the bundle are conditioned principally by inter-helix side-chain interactions and that the extra-helical parts of the protein have only a minor influence on the bundle conformation. Our approach performs conformational energy optimization using a predetermined set of side-chain rotamers and appropriate methods for sampling the conformational space of peptide fragments with fixed backbone geometries. The final solution obtained for bacteriorhodopsin places each of the seven helices to a precision of a few degrees in rotation around the helical axis and to a few tenths of an ångström in translation along the helical axis with respect to the best experimental structure obtained by electron diffraction except for helix D, where our results support the suggestion that this helix should be displaced along its axis toward its N terminus. The perspectives of such an approach for the determination of the structures of other transmembrane helical bundles are discussed.