The Structural Variation and Probability Redistribution in Alanine Dipeptide Conformers by the Hydration

The effects on structural variation and relative stability caused by hydration of alanine dipeptide in the C7eq, C7ax, C5, alpha(R) and P(II) conformations were investigated by the method of the SUMSL (secant-type unconstrained minimization solver) energy-minimization technique, using the empirical potential energy function of the solute and the ST2 water model. The binding sites of water molecules in the solute were selected from spherical interaction energy maps. As a function of the number of added water molecules, we traced the structural variations mainly in the (phi, psi) torsion angle space, and calculated the total internal energies of each solute-water system to evaluate the relative probabilities between those five conformers. The results indicate that the conformers having no intramolecular hydrogen bonds, such as alpha(R), C5 and P(II), shows larger structural variations than the C7ax and C7eq conformers which have intramolecular hydrogen bonds. The torsion angle, psi, fluctuated more than phi for all the examined conformers. The energetically dominant conformation is shifted from C7eq to alpha(R) as the hydration progresses.
Publisher
Elsevier Science Bv
Issue Date
1992
Language
ENG
Keywords

CONFORMATIONAL FREE-ENERGY; MOLECULAR-DYNAMICS; THERMODYNAMIC ANALYSIS; LIQUID WATER; MODEL; SIMULATION

Citation

JOURNAL OF MOLECULAR STRUCTURE, v.268, no.1-3, pp.169 - 179

ISSN
0022-2860
URI
http://hdl.handle.net/10203/57400
Appears in Collection
RIMS Journal Papers
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