Analysis on conformational stability of C-peptide of ribonuclease A in water using the reference interaction site model theory and Monte Carlo simulated annealing

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Abstract
Solvation structure and conformational stability of the C-peptide fragment of ribonuclease A in pure water have been analyzed using the full reference interaction site model (RISM) theory. The charged groups in the side chains of Lys -1 + , Glu -2 − , Lys -7 + , Arg -10 + , and His -12 + (in particular, the four like-charged groups) play substantial roles in stabilizing the conformations. The solvation free energy and the conformational energy are governed by the contribution from the electrostaticinteraction with water and the intramolecular Coulombic energy, respectively, and the conformational stability is determined by competition of these two factors. The contributions from the hydrophobic hydration and the van der Waals and torsion terms in the conformational energy are less important, which is in contrast to the result for Met-enkephalin. The Monte Carlo simulated annealing combined with the RISM theory has been applied to the C-peptide using an almost fully extended conformation as the initial one. The conformation first changes in the direction that the charged groups in the side chains are more exposed to water, and in particular, the positively charged groups are closer together. Thus, the solvation free energy decreases greatly in the initial stage. Although this leads to a significant increase in the intramolecular Coulombic repulsion energy, the decrease in the solvation free energy dominates. In the later stage, however, a further decrease in the solvation free energy gives rise to an even larger increase in the intramolecular Coulombic repulsion energy, and the conformational change is greatly decelerated. The conformations thus stabilized in four different runs of the combined program are quite similar. The peptide conformation in water is stabilized far more rapidly than in the gas phase.

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