Int. J. Mol. Sci. 2004, 5(4), 186-195; doi:10.3390/i5040186
Article

Visualization of the Differential Transition State Stabilization within the Active Site Environment

1 Molecular Modeling Laboratory, Institute of Physical and Theoretical Chemistry, Wroclaw University of Technology, ul. Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland 2 Dept. of Chemistry, Jackson State University, Jackson, Mississippi, USA
* Author to whom correspondence should be addressed.
Received: 15 December 2003; Published: 31 May 2004
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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 interactive 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. 3.5.4.5) 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 the enzyme due to transition state or substrate movement. This system of visualization of DTTS approach can be potentially used to validate hypotheses regarding the catalytic mechanism or to study binding properties of transition state analogues.
Keywords: Differential Transition State Stabilization; Catalytic properties; Visualization; Enzymatic catalysis; Molecular electrostatic potential; Molecular Electrostatic field; Multipole moments

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MDPI and ACS Style

Kedzierski, P.; Wielgus, P.; Sikora, A.; Sokalski, W.A.; Leszczynski, J. Visualization of the Differential Transition State Stabilization within the Active Site Environment. Int. J. Mol. Sci. 2004, 5, 186-195.

AMA Style

Kedzierski P, Wielgus P, Sikora A, Sokalski WA, Leszczynski J. Visualization of the Differential Transition State Stabilization within the Active Site Environment. International Journal of Molecular Sciences. 2004; 5(4):186-195.

Chicago/Turabian Style

Kedzierski, Pawel; Wielgus, Pawel; Sikora, Adrian; Sokalski, W. A.; Leszczynski, Jerzy. 2004. "Visualization of the Differential Transition State Stabilization within the Active Site Environment." Int. J. Mol. Sci. 5, no. 4: 186-195.

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