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Abstract
Model tetrapeptide system was designed to investigate the cis/trans isomerization of peptidyl-prolyl imide bond of Ser–Pro motif. To establish the side-chain O-phosphorylation effect in regulating the peptides conformations, molecular dynamics (MD) simulations where carried out on the designed tetrapeptides and their corresponding phosphorylated forms by MD Insight II Discovery3 approach. The most stable configurations and the statistic cis/trans concentration distribution demonstrated that the phosphorylation evidently influences the peptidyl-prolyl imide bond isomerization and works as a key effect in regulating the peptide conformations. The charge state and the site provided for the charge of the phosphate moiety might be an important key. The results also demonstrated that phosphorylation changes the cis conformation ratio of the peptide and the maximum cis value is obtained when the phosphate group has no negative charge.
Acknowledgements
The authors would like to thank the financial supports from the National Natural Science Foundation of China (No.20272032, NSFCBIC20320130046), the Teaching and Research Award Program for Outstanding Young Teachers in Higher Education Institutions of MOE, P.R.C. (TRAPOYT), and the Specialized research Fund for the Doctoral Program of Higher Education (SRFDP) (No.20030003049). The authors also appreciate the useful comments by an anonymous reviewer.