Orientation-dependent potential of mean force for protein folding

Mukherjee, Arnab and Bhimalapuram, Prabhakar and Bagchi, Biman (2005) Orientation-dependent potential of mean force for protein folding. In: Journal of Chemical Physics, 123 (1).

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Abstract

We present a solvent-implicit minimalistic model potential among the amino acid residues of proteins, obtained by using the known native structures [deposited in the Protein Data Bank (PDB)]. In this model,the amino acid side chains are represented by a single ellipsoidal site, defined by the group of atoms about the center of mass of the side chain. These ellipsoidal sites interact with other sites through an orientation-dependent interaction potential which we construct in the following fashion. First, the site-site potential of mean force(PMF) between heavy atoms is calculated [following F. Melo and E.Feytsman, J. Mol. Biol. 267, 207 (1997)] from statistics of their distance separation obtained from crystal structures. These site-site potentials are then used to calculate the distance and the orientation-dependent potential between side chains of all the amino acid residues (AAR). The distance and orientation dependencies show several interesting results. For example, we find that the PMF betweentwo hydrophobic AARs, such as phenylalanine, is strongly attractive at short distances (after the obvious repulsive region at very shortseparation) and is characterized by a deep minimum, for specific orientations. For the interaction between two hydrophilic AARs, such a deep minimum is absent and in addition, the potential interestingly reveals the combined effect of polar (charge) and hydrophobic interactions among some of these AARs. The effectiveness of our potential has been tested by calculating the Z-scores for a large set of proteins. The calculated Z-scores show high negative values for most of them, signifying the success of the potential to identify the native structure from among a large number of its decoy states.

Item Type:	Journal Article
Publication:	Journal of Chemical Physics
Publisher:	American Institute of Physics
Additional Information:	Copyright for this article belongs to American Institute of Physics.
Department/Centre:	Division of Chemical Sciences > Solid State & Structural Chemistry Unit
Date Deposited:	18 Aug 2005
Last Modified:	19 Sep 2010 04:19
URI:	http://eprints.iisc.ac.in/id/eprint/3525

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