Development and Testing of Force Field Parameters for Phenylalanine and Tyrosine Derivatives.

摘要: Theoretical analyses are valuable for the exploration of effects unnatural amino acids on enzyme functions; however, many necessary parameters remain lacking. In this study, we developed and tested force field compatible with Amber ff14SB 18 phenylalanine tyrosine derivatives. The charge were derived from ab initio calculations using RESP fitting approach then adjusted to reproduce benchmark relative energies (at MP2/TZ level) α- β-backbones each acid dipeptide. structures optimized under proposed dipeptides in both β-backbone forms good agreement their QM structures, as average RMSD was small 0.1 A. application seven proteins containing acids. RMSDs simulated configurations these approximately 1.0 A compared those crystal structures. vital interactions between five protein-ligand complexes also predicted MM/PBSA analysis, they largely consistent experimental observations. This work will provide theoretical aid drug design involving