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

Juan Cortés 1 Duc Thanh Le 1 Romain Iehl 1 Thierry Simeon 1
1 LAAS-RIS - Équipe Robotique et InteractionS
LAAS - Laboratoire d'analyse et d'architecture des systèmes
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 β 2-adrenergic receptor.
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https://hal.laas.fr/hal-01986237
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Juan Cortés, Duc Thanh Le, Romain Iehl, Thierry Simeon. Simulating ligand-induced conformational changes in proteins using a mechanical disassembly method. Physical Chemistry Chemical Physics, Royal Society of Chemistry, 2010, 12 (29), pp.8268. ⟨hal-01986237⟩

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