My research group, working at Argonne National Laboratory, has implemented a combined quantum (MOPAC-AM1) and molecular mechanics (CHARMM) method to study condensed phase chemical reactions. This method enables the study of electronic structure changes that occur for reactions in complex heterogeneous environments which includes enzyme reactions. We have applied our methods to the enzyme malate dehydrogenase (MDH) to determine the reaction mechanism and find the minimum energy pathway and transition state for the reaction. Our simulations suggest a sequential mechanism that consists of a proton transfer followed by a hydride transfer. Our calculations provide essential information about the mechanism of this enzyme, which is difficult to obtain from traditional experiments. These simulations and methods will be used in the next phase to explain the results of enzyme redesign experiments on lactate dehydrogenase (LDH) and MDH. Specifically, a single amino acid change in LDH has been shown to produce an effective MDH. However, an analogous change in MDH does not produce an effective LDH, even though the structures of the active sites of these two enzymes are essentially identical. We will use our methods to investigate the differneces in the catalytic properties of MDH, LDH, and their mutants. Our simulations of the mechanism of MDH produced a molecular dynamics trajectory that included the bond -making and -breaking events in the enzyme. Since we use a quantum mechanical method to treat the electronic structure changes, we obtained data for the electron density changes as well as the alterations in the coordinates of the atoms during the course of the enzyme reaction. We used the visualiztion and animation facilities at the Cornell Theory Center to produce an animation of the enzyme reaction in malate dehydrogenase. The resultant animation provided insights into the details of the dynamic and structural changes that occur during the enzyme reaction that are impossible to determine from the values of the energies produced by the simulation.
| Chiang, Chi-Tung; Shores, Kevin S; Freindorf, Marek et al. (2008) Size-restricted proton transfer within toluene-methanol cluster ions. J Phys Chem A 112:11559-65 |
| Kazmierkiewicz, Rajmund; Liwo, Adam; Scheraga, Harold A (2003) Addition of side chains to a known backbone with defined side-chain centroids. Biophys Chem 100:261-80 |
| Kazmierkiewicz, Rajmund; Liwo, Adam; Scheraga, Harold A (2002) Energy-based reconstruction of a protein backbone from its alpha-carbon trace by a Monte-Carlo method. J Comput Chem 23:715-23 |
| Liwo, Adam; Arlukowicz, Piotr; Czaplewski, Cezary et al. (2002) A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field. Proc Natl Acad Sci U S A 99:1937-42 |
| Scheraga, Harold A; Pillardy, Jaroslaw; Liwo, Adam et al. (2002) Evolution of physics-based methodology for exploring the conformational energy landscape of proteins. J Comput Chem 23:28-34 |
| Scheraga, Harold A; Vila, Jorge A; Ripoll, Daniel R (2002) Helix-coil transitions re-visited. Biophys Chem 101-102:255-65 |
| Pillardy, J; Arnautova, Y A; Czaplewski, C et al. (2001) Conformation-family Monte Carlo: a new method for crystal structure prediction. Proc Natl Acad Sci U S A 98:12351-6 |
| Vila, J A; Ripoll, D R; Scheraga, H A (2001) Influence of lysine content and pH on the stability of alanine-based copolypeptides. Biopolymers 58:235-46 |
| Pillardy, J; Czaplewski, C; Liwo, A et al. (2001) Recent improvements in prediction of protein structure by global optimization of a potential energy function. Proc Natl Acad Sci U S A 98:2329-33 |
| Czaplewski, C; Rodziewicz-Motowidlo, S; Liwo, A et al. (2000) Molecular simulation study of cooperativity in hydrophobic association. Protein Sci 9:1235-45 |
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