visualization of the differential transition state stabilization within the active site environment可视化的微分中的过渡态稳定活性部位的环境.pdfVIP

Int. J. Mol. Sci. 2004 , 5, 186–195 International Journal of Molecular Sciences ISSN 1422-0067 c 2004 by MDPI Visualization of the Differential Transition State Stabi- lization within the Active Site Environment Paweł K˛edzierski,a Paweł Wielgus,a Adrian Sikora,a W. Andrzej Sokalski,a ´ b and Jerzy Leszczynski a Molecular Modeling Laboratory, Institute of Physical and Theoretical Chemistry, Wroclaw University of Technology, ul. Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland, tel. +48 71 320 3200, fax +48 71 320 3364 b Dept. of Chemistry, Jackson State University Corresponding author: Paweł K˛edzierski, E-mail: P.Kedzierski@mml.ch.pwr.wroc.pl Received: 15 December 2003 Abstract: Increasing interest in the enzymatic reaction mechanisms and in the nature of catalytic effects in enzymes causes the need of appropriate visualization methods. A new in- teractive method to investigate catalytic effects using differential transition state stabilization approach (DTSS) [1, 2] is presented. The catalytic properties of the active site of cytidine deaminase (E.C. ) is visualized in the form of differential electrostatic properties. The visualization was implemented using scripting interface of VMD [3]. Cumulative Atomic Multipole Moments (CAMM) [4,5,6] were utilized for efficient yet accurate evaluation of the electrostatic properties. The implementation is efficient enough for interactive presentation of catalytic effects in the active site of t