MOLECULAR-DYNAMICS SIMULATIONS OF CIS-TRANS ISOMERIZATION FOR A PROLINE-CONTAINING TRIPEPTIDE IN SOLUTION

The cis-trans isomerization of X-Pro (X is Pro or any other residue) o ften plays a rate-limiting role in protein folding. In order to study the dynamic properties of X-Pro in water, we have analyzed the traject ory data obtained from constrained molecular dynamics (MD) simulations of a tripeptide Phe-Pro-Ala in solution. Via calculation of autocorre lation functions and their corresponding spectral densities, we have f ound that the structural fluctuations of the solute are affected by th e motions of various degrees of freedom, and the solvent dynamic behav ior is bimodal rather than exponential or Gaussian. In addition, accor ding to the energy and torque analysis, we suggest that both the anti/ endo and the syn/endo could be the possible transition state for the c is-trans isomerization of the tripeptide.