ISSN:
1432-2234
Keywords:
Key words: Helical peptide
;
β-Hairpin
;
Random coil
;
Umbrella sampling
;
Multicanonical sampling
Source:
Springer Online Journal Archives 1860-2000
Topics:
Chemistry and Pharmacology
Notes:
Abstract. To compare different implicit solvent potentials, the folding thermodynamics of the helical peptide RN24 and the β-hairpin peptide BH8 are studied by molecular dynamics simulation with adaptive umbrella sampling. As the potential energy functions, the analytical continuum solvent (ACS) potential and three simplified variants, termed EPSR1, EPSR4, and EPSR10, are used. The ACS potential is a combination of the standard CHARMM force field for the internal energy (bonds, angles, dihedrals) and the van der Waals energy with the analytical continuum electrostatic (ACE) potential and a non-polar solvation potential. The EPSR potentials differ from the ACS potential by the use of Coulomb's law with a distance-dependent dielectric function to calculate the electrostatic energy. With the ACS potential, quantitative agreement with experiment is obtained for the helix propensity (RN24: 62% calculated vs 50–60% experiment) and the β-hairpin propensity (BH8: 33% calculated vs 19–37% experiment) of the peptides. During the simulations with the EPSR potentials, no significant formation of secondary structure is observed. It is shown that the preference for coil conformations over conformations with secondary structure by the EPSR potentials is due to an overestimation of the energy of salt bridge formation, independent of the magnitude of the Coulomb energy relative to the other energy terms. Possible improvements of the distance-dependent dielectric functions which may permit their application to the simulation of peptide folding, are discussed.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1007/s002140050429
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