Grand canonical Monte Carlo simulations of water in protein environments

The grand canonical simulation algorithm is considered as a general methodology to sample the configuration of water molecules confined within protein environments. First, the probability distribution of the number of water molecules and their configuration in a region of interest for biochemical si...

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Bibliographic Details
Published in:The Journal of chemical physics 2004-10, Vol.121 (13), p.6392-6400
Main Authors: Woo, Hyung-June, Dinner, Aaron R, Roux, Benoît
Format: Article
Language:English
Subjects:
Algorithms
Bacterial Proteins - chemistry
Bacterial Proteins - ultrastructure
Computer Simulation
Models, Chemical
Models, Molecular
Models, Statistical
Monte Carlo Method
Potassium Channels - chemistry
Potassium Channels - ultrastructure
Protein Conformation
Proteins - chemistry
Proteins - ultrastructure
Solvents - chemistry
Water - chemistry
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Summary:The grand canonical simulation algorithm is considered as a general methodology to sample the configuration of water molecules confined within protein environments. First, the probability distribution of the number of water molecules and their configuration in a region of interest for biochemical simulations, such as the active site of a protein, is derived by considering a finite subvolume in open equilibrium with a large system serving as a bulk reservoir. It is shown that the influence of the bulk reservoir can be represented as a many-body potential of mean force acting on the atoms located inside the subvolume. The grand canonical Monte Carlo (GCMC) algorithm, augmented by a number of technical advances to increase the acceptance of insertion attempts, is implemented, and tested for simple systems. In particular, the method is illustrated in the case of a pure water box with periodic boundary conditions. In addition, finite spherical systems of pure water and containing a dialanine peptide, are simulated with GCMC while the influence of the surrounding infinite bulk is incorporated using the generalized solvent boundary potential [W. Im, S. Berneche, and B. Roux, J. Chem. Phys. 114, 2924 (2001)]. As a last illustration of water confined in the interior of a protein, the hydration of the central cavity of the KcsA potassium channel is simulated.
ISSN:0021-9606
1089-7690
DOI:10.1063/1.1784436