Journal
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
Volume 12, Issue 29, Pages 8268-8276Publisher
ROYAL SOC CHEMISTRY
DOI: 10.1039/c002811h
Keywords
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Funding
- French National Agency for Research (ANR)
- Region Midi-Pyrenees
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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 beta(2)-adrenergic receptor.
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