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Issue 29, 2010
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Simulating ligand-induced conformational changes in proteins using a mechanical disassembly method

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Abstract

Simulating protein conformational changes induced or required by the internal diffusion of a ligand is important for the understanding of their interaction mechanisms. Such simulations are challenging for currently available computational methods. In this paper, the problem is formulated as a mechanical disassembly problem where the protein and the ligand are modeled like articulated mechanisms, and an efficient method for computing molecular disassembly paths is described. The method extends recent techniques developed in the framework of robot motion planning. Results illustrating the capacities of the approach are presented on two biologically interesting systems involving ligand-induced conformational changes: lactose permease (LacY), and the β2-adrenergic receptor.

Graphical abstract: Simulating ligand-induced conformational changes in proteins using a mechanical disassembly method

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Supplementary files

Article information


Submitted
09 Feb 2010
Accepted
25 May 2010
First published
04 Jun 2010

Phys. Chem. Chem. Phys., 2010,12, 8268-8276
Article type
Paper

Simulating ligand-induced conformational changes in proteins using a mechanical disassembly method

J. Cortés, D. Thanh Le, R. Iehl and T. Siméon, Phys. Chem. Chem. Phys., 2010, 12, 8268
DOI: 10.1039/C002811H

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