Amino acid interaction preferences in helical membrane proteins

Jha, Anupam Nath and Vishveshwara, Saraswathi and Banavar, Jayanth R (2011) Amino acid interaction preferences in helical membrane proteins. In: Protein Engineering Design and Selection, 24 (8). pp. 579-588.

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Abstract

Membrane proteins are involved in a number of important biological functions. Yet, they are poorly understood from the structure and folding point of view. The external environment being drastically different from that of globular proteins, the intra-protein interactions in membrane proteins are also expected to be different. Hence, statistical potentials representing the features of inter-residue interactions based exclusively on the structures of membrane proteins are much needed. Currently, a reasonable number of structures are available, making it possible to undertake such an analysis on membrane proteins. In this study we have examined the inter-residue interaction propensities of amino acids in the membrane spanning regions of the alpha-helical membrane (HM) proteins. Recently we have shown that valuable information can be obtained on globular proteins by the evaluation of the pair-wise interactions of amino acids by classifying them into different structural environments, based on factors such as the secondary structure or the number of contacts that a residue can make. Here we have explored the possible ways of classifying the intra-protein environment of HM proteins and have developed scoring functions based on different classification schemes. On evaluation of different schemes, we find that the scheme which classifies amino acids to different intra-contact environment is the most promising one. Based on this classification scheme, we also redefine the hydrophobicity scale of amino acids in HM proteins.

Item Type:	Journal Article
Publication:	Protein Engineering Design and Selection
Publisher:	Oxford University Press
Additional Information:	Copyright of this article belongs to Oxford University Press.
Keywords:	contact-based environment;helix environment;hydrophobicity; scoring functions for helical membrane (HM) proteins
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	01 Aug 2011 07:18
Last Modified:	01 Aug 2011 07:18
URI:	http://eprints.iisc.ac.in/id/eprint/39597

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