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Prediction of the positioning of the seven transmembrane alpha-helices of bacteriorhodopsin. A molecular simulation study.

Abstract：

: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.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Tuffery P,Etchebest C,Popot JL,Lavery R

doi

10.1016/0022-2836(94)90015-9

subject

Has Abstract

pub_date

1994-03-04 00:00:00

pages

1105-22

issue

4

eissn

0022-2836

issn

1089-8638

pii

0022-2836(94)90015-9

journal_volume

236

pub_type

杂志文章

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