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Pergamon Computers Chem. EnongVol.22.No. 6 pp. 765-788,1998 1998ElsevierScienceLtd

Summary: Pergamon Computers Chem. EnongVol.22.No. 6 pp. 765-788,1998
Printedin GreatBritain.Allrightsreserved
PII: S0098-1354(97)00258-5 0098-1354/98$19.00+ 0.00
Predicting solvated peptide conformations
via global minimization of energetic
atom-to-atom interactions
J.L. Klepeis, I.P. Androulakis, M.G. Ierapetritou and C.A. Floudas*
Department of Chemical Engineering, Princeton University, Princeton, N.J. 08544-5263 U.S.A.
A global optimization method is described for identifying the global minimum energy conformation, as well
as lower and upper bounds on the global minimum conformer of solvated peptides. Potential energy
contributions are calculated using the ECEPP/3 force field model. In considering the effects of hydration, two
implicit free energy models are compared. One method is based on the calculation of solvent-accessible surface
areas, while the other uses information on the solvent-accessible volume of hydration shells. Detailed informa-
tion on the potential and solvation energy contributions is presented for the terminally blocked single residue
peptides. In addition, based on a procedure that allows the exclusion of domains of the (q5,~) space, a number of
oligopeptide structure prediction problems are considered, and the role of the solvation model in defining
global minimum conformations is addressed. 1998 Elsevier Science Ltd. All rights reserved
Keywords: Protein folding; solvation; global optimization


Source: Androulakis, Ioannis (Yannis) - Biomedical Engineering Department & Department of Chemical and Biochemical Engineering, Rutgers University


Collections: Engineering; Biology and Medicine