Molecular dynamics study of a tripeptide Z-Ala-Ala-Leu-pNA

Abstract

Conformation of a substrate of subtilisin enzyme, N-benzyloxycarbonyl-L-alanyl-L-leucyl-p-nitroanilide have been explored using molecular dynamics simulation. The dynamic structure is characterized by overall extended and folded conformation of the peptide. Keywords: Molecular dynamics, tripeptide, protease-substrate, AAL.(first-order plus time delay) with a zero. It gives good resulst in all the simulation case studies considered. The effect of measurement noise and controller settings on the identification of transfer function model is studied.