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A hydrogen bonded chain in bactereorhodopsin by computer modeling approach

Sankara-Ramakrishnan, R and Vishveshwara, Saraswathi (1989) A hydrogen bonded chain in bactereorhodopsin by computer modeling approach. In: Journal of Biomolecular Structure & Dynamics, 7 (1). pp. 187-205.

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Abstract

The 7 $\alpha$-helical segments of bacteriorhodopsin (BR) passing through the membrane are investigated for a continuous H bonded chain (HBC)9. The study is carried out by computer modeling approach. It is assumed that the 7 helixes are placed as (AGFEDCB), which has been accepted as the best model by several groups. Helixes A, D, E and G are considered to be present in right handed $\alpha$-helical conformation. The inter-orientation of these helixes are represented by Eulerian angles $\alpha$, $\beta$, and $\gamma$. For the helixes B, C and F which contain proline in the middle, several conformational possibilities were considered. In these cases apart from the Eulerian angles $\alpha$, $\beta$ and $\gamma$, the dihedral angles $\Phi$p-1 and $\Psi$p-1 of the residues that are succeeded by proline residue in the helical regions were also used in fixing the position of the helixes with respect to each other. All these parameters were varied to fit with the top, middle, and bottom distances reported by electron diffraction studies. Good fit was obtained for all right handed $\alpha$-helical conformations and also for helixes B, C and F with a left handed turn at the residue preceding proline. Hence 2 structures were analyzed for continuous HBC, structure I which contained all the 7 helixes in right handed $\alpha$-helical conformation and structure II, which had the helixes A, D, E and G in right handed conformation and the helixes B, C and F in right handed $\alpha$-helical conformation with a left handed turn at the residue preceding proline. All possible staggered conformations were considered for the side chains and the inter at. distances were analyzed for H bonds. It was possible to obtain a continuous chain in both the structures which includes most of the residues found to be important by the expts. However lysine-216 has to be considered in 2 different conformations to connect the cytoplasmic side with the extra cellular side. The overall height spanned by HBC is about 25 .ANG. The chains obtained by both the structures I and II are analyzed in terms of the conformational parameters. It has also been possible to place the retinal in the region as predicted by the expts. The tryptophan residues which affect the spectral characteristics can be aligned on either side of the retinal.

Item Type: Journal Article
Additional Information: Copyright of this article belongs to Adenine Press
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 26 Feb 2008
Last Modified: 27 Aug 2008 13:09
URI: http://eprints.iisc.ernet.in/id/eprint/12876

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