Determination of protein coarse-grain charges from smoothed molecular electrostatic potentials

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Abstract

The design of protein coarse-grain (CG) models and their corresponding interaction potentials is currently an active field of research, especially for solving protein folding or docking problems, … Among the essential parameters involved by CG potentials, electrostatics interactions are of crucial importance since they govern local and global properties such as their stability, their flexibility, …

Following our development of an original approach to decompose hierarchically a protein structure into fragments from its electron density (ED) distribution [1,2], we propose to apply our method to molecular electrostatic potential functions (MEP), calculated from point charges as implemented in well-known force fields. To follow the pattern of local maxima (and minima) in an ED or a MEP distribution, as a function of the degree of smoothing, we adopted the following strategy. First, each atom of a molecule is considered as a starting point (a peak, or a pit for negative charges in a MEP analysis). As the smoothing degree increases, each point moves along a path to reach a location where the ED or MEP gradient value vanishes. Convergences of trajectories lead to a reduction of the number of points.

Practically, to determine the protein backbone representations, we analyze CG models obtained for a strand of polyglycine. The influence of the different amino acid side chains is then studied for different rotamers by substituting the central glycine residue. A fitting algorithm is used to assign charges to the obtained local maxima/minima.

[1] L. Leherte, Acta Crystallogr. D 60 (2004) 1254
[2] L. Leherte, B. Guillot, D. Vercauteren, V. Pichon-Pesme, Ch. Jelsch, A. Lagoutte, Cl. Lecomte, in “Quantum Theory of Atoms in Molecules - From Solid State to DNA and Drug Design”, Eds C. F. Matta, R. J. Boyd, Wiley-VCH (Weinheim), (2006)
Original languageEnglish
Publication statusPublished - 2008
EventAssemblée générale de la SRC - Chimie des matériaux et du vivant : une cohabitation harmonieuse - Namur, FUNDP, Belgium
Duration: 9 Oct 2008 → …

Meeting

MeetingAssemblée générale de la SRC - Chimie des matériaux et du vivant : une cohabitation harmonieuse
CountryBelgium
CityNamur, FUNDP
Period9/10/08 → …

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    Leherte, L., & Vercauteren, D. (2008). Determination of protein coarse-grain charges from smoothed molecular electrostatic potentials. Poster session presented at Assemblée générale de la SRC - Chimie des matériaux et du vivant : une cohabitation harmonieuse, Namur, FUNDP, Belgium.