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

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 mechan...

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Bibliographic Details
Published inPhysical chemistry chemical physics : PCCP Vol. 12; no. 29; pp. 8268 - 8276
Main Authors CORTES, Juan, THANH LE, Duc, IEHL, Romain, SIMEON, Thierry
Format Journal Article
LanguageEnglish
Published Cambridge Royal Society of Chemistry 01.01.2010
Subjects
Algorithms
Binding Sites
Bioinformatics
Chemical Sciences
Chemistry
Computer Science
Computer Simulation
Diffusion
Exact sciences and technology
General and physical chemistry
Hydrogen Bonding
Ligands
Membrane Transport Proteins - chemistry
or physical chemistry
Protein Structure, Tertiary
Receptors, Adrenergic, beta-2 - chemistry
Theoretical and
Motion
Lactose
Mechanical method
Simulation
Theoretical study
Models
Diffusion
Computing method
Mechanism
Protein
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Summary: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.
Bibliography:ObjectType-Article-1
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ISSN:1463-9076
1463-9084
DOI:10.1039/c002811h