**************** The 6th., Lab Seminar ****************************

Date: Thu, July 31, 2008  PM 2:30-

Place: No.616 Seminar room
　　　　　　 Graduate School of Information Science

Speaker: Norio Takenaka

Title: Modeling of serine protease prototype reactions
with the flexible effective fragment potential
quantum mechanical/molecular mechanical method

A. V. Nemukhin, B. L. Grigorenko, A. V. Rogov, 
I. A. Topol and S. K. Burt, Theor. Chem. Acc., 
111, 36 (2004). 

Abstract:
A complete cycle of chemical transformations for
the serine prototype reaction is modeled 
following calculations with the flexible 
effective QM/MM method. The molecular model is
based on the crystal structure of the trypcine-
bovine pancreatic trypcine inhibitor complex
including all atoms of the enzyme within 
15-18Å of the oxygen atom of the catalytic
serine residue. In the case of a model substrate
selected as a short peptide, the energy profile
for the acylation step shows too high activation
energy barriers. The energetics of this 
rate-limiting step is considerably improved,
if more realistic model for the substrate is
considered.

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