Chapter 35
Modeling the Citrate Synthase Reaction: QM/MM and Small Model Calculations 1
2
Adrian J . Mulholland and W. Graham Richards 1
School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom New Chemistry Laboratory, Oxford University, Oxford OX1 3QT, United Kingdom
Downloaded by UNIV MASSACHUSETTS AMHERST on August 7, 2012 | http://pubs.acs.org Publication Date: April 8, 1999 | doi: 10.1021/bk-1999-0721.ch035
2
In this chapter, we review calculations on the mechanism of the enzyme citrate synthase. Transition state and stable intermediate structures have been optimized for small models of the reaction, at semiempirical and ab initio levels. The reaction in the enzyme has been studied with combined quantum mechanical/molecular mechanical (QM/MM) methods. The first step of the reaction (deprotonation of acetyl-CoA by Asp-375), and the resulting nucleophilic intermediate, have been examined in detail. The results indicate that the enolate of acetyl-CoA is the likely intermediate, and that it is stabilized by normal hydrogen bonds from His-274 and a water molecule. The results do not support the proposal that a 'low -barrier' hydrogen bond stabilizes this intermediate in citrate synthase.
Achieving a deeper understanding of enzyme catalytic processes is a problem of great practical and fundamental significance. Computer simulations can make an important contribution by providing a description of enzyme mechanism at the molecular level (1-3). Calculations can be used to study unstable species, to evaluate possible alternative mechanisms, and to calculate energetic contributions to catalysis. These are central considerations in an enzyme-catalyzed reaction, which are difficult to address by experiment alone. A first step in the modeling process is the investigation of possible reaction intermediates and transition states (TSs), to identify basic features of the potential energy surface governing reaction. One approach is to perform supermolecule calculations on clusters of small molecular fragments representing functional groups of the enzyme and substrate (2,4) by standard quantum chemical techniques. TS and stable complex structures can then be optimized. By necessity, only a small portion of the enzyme can be treated (although recent advances allow single point semiempirical calculations on small proteins (5)).
