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Simulation of peptide folding with explicit water—a mean solvation method

✍ Scribed by Xiong-Wu Wu; Shen-Shu Sung

Publisher
John Wiley and Sons
Year
1999
Tongue
English
Weight
137 KB
Volume
34
Category
Article
ISSN
0887-3585

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✦ Synopsis

A new approach to efficiently calculate solvent effect in computer simulation of macromolecular systems has been developed. Explicit solvent molecules are included in the simulation to provide a mean solvation force for the solute conformational search. Simulations of an alanine dipeptide in aqueous solution showed that the new approach is significantly more efficient than conventional molecular dynamics method in conformational search, mainly because the mean solvation force reduced the solvent damping effect. This approach allows the solute and solvent to be simulated separately with different methods. For the macromolecule, the rigid fragment constraint dynamics method we developed previously allows large time-steps. For the solvent, a combination of a modified force-bias Monte Carlo method and a preferential sampling can efficiently sample the conformational space. A folding simulation of a 16-residue peptide in water showed high efficiency of the new approach.

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