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Rapid Boundary Element Solvation Electrostatics

Summary: Rapid Boundary Element
Solvation Electrostatics
Calculations in Folding
Simulations: Successful
Folding of a 23-Residue
Maxim Totrov
Ruben Abagyan
Molsoft LLC,
3366 North Torrey Pines Ct.,
San Diego, CA 92037
Abstract: Solvation effects play a profound role in the energetics of protein folding. While a
continuum dielectric model of solvation may provide a sufficiently accurate estimate of the solvation
effects, until now this model was too computationally expensive and unstable for folding simula-
tions. Here we proposed a fast yet accurate and robust implementation of the boundary element
solution of the Poisson equation, the REBEL algorithm. Using our earlier double-energy scheme,
we included for the first time the mathematically rigorous continuous REBEL solvation term in our
Biased Probability Monte Carlo (BPMC) simulations of the peptide folding. The free energy of a
23-residue -peptide was then globally optimized with and without the solvation electrostatics
contribution. An ensemble of conformations was found at and near the global minimum of the


Source: Abagyan, Ruben - School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego


Collections: Biology and Medicine