The stability of transmembrane helices: A molecular dynamics study on the isolated helices of bacteriorhodopsin

Iyer, Lakshmanan K and Vishveshwara, Saraswathi (1996) The stability of transmembrane helices: A molecular dynamics study on the isolated helices of bacteriorhodopsin. In: Biopolymers, 38 (3). pp. 401-422.

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Abstract

Bacteriorhodopsin (bR) continues to be a proven testing ground for the study of integral membrane proteins (IMPs). It is important to study the stability of the individual helices of bR, as they are postulated to exist as independently stable transmembmne helices (TMHs) and also for their utility as templates for modeling other IMPs with the postulated seven-helix bundle topology. Toward this purpose, the seven helices of bR have been studied by molecular dynamics simulation in this study. The suitability of using the backbone-dependent rotamer library of side-chain conformations arrived at from the data base of globular protein structures in the case TMHs has been tested by another set of ? helix simulations with the side-chain orientations taken from this library. The influence of the residue's net charge oil the helix stability was examined by simulating the helices III, IV, and VI (from both of the above sets of helices) with zero net charge on the side chains. The results of these 20 simulations demonstrate in general the stability of the isolated helices of bR in conformity with the two-stage hypothesis of IMP folding. However, the helices I, II, V, and VII are more stable than the other three helices. The helical nature of certain regions of III, IV, and VI are influenced by factors such as the net charge and orientation of several residues. It is seen that the residues Arg, Lys, Asp, and Glu (charged residues), and Ser, Thr, Gly, and Pro, play a crucial role in the stability of the helices of bR. The backbone-dependent rotamer library for the side chains is found to be suitable for the study of TMHs in IMP. (C) 1996 John Wiley & Sons, Inc.

Item Type:	Journal Article
Publication:	Biopolymers
Publisher:	John Wiley and Sons
Additional Information:	Copyright of this article belongs to John Wiley and Sons.
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	13 May 2011 06:36
Last Modified:	13 May 2011 06:36
URI:	http://eprints.iisc.ac.in/id/eprint/37637

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