Abstract
In order to investigate the role of the cis/trans isomerization of the X-Pro peptide bonds in the folding of ribonuclease T 1 (RNase T 1 ), conformational free energy calculations using an empirical potential ECEPP/2 and the hydration shell model were carried out on the terminally blocked tripeptides Ac-Tyr-Pro-His-NHMe, Ac-Ser-Pro-Tyr-NHMe, Ac-Trp-Pro-Ile-NHMe, and Ac-Ser-Pro-Gly-NHMe and on related dipeptides in the unhydrated and hydrated states. These tripeptides correspond to residues 38-40, 5456, 59-61, and 72-74 of native RNase T 1 , respectively. The conformational entropy computed using a harmonic method was included in the free energy of each minimum in both states
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