Freezing a Single Distal Motion in Dihydrofolate Reductase

• Published in: The journal of physical chemistry. B 2006-02, Vol.110 (5), p.2435-2441
• Main Authors: Sergi, Alessandro, Watney, James B, Wong, Kim F, Hammes-Schiffer, Sharon
• Format: Article
• Language: English
• Subjects: Biological Transport; Catalysis; Coenzymes - chemistry; Coenzymes - metabolism; Freezing; Kinetics; Models, Molecular; Protein Conformation; Quantum Theory; Substrate Specificity; Tetrahydrofolate Dehydrogenase - chemistry; Tetrahydrofolate Dehydrogenase - metabolism; Thermodynamics
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/jp056939u

Constraining a single motion between distal residues separated by ∼28 Å in hybrid quantum/classical molecular dynamics simulations is found to increase the free energy barrier for hydride transfer in dihydrofolate reductase by ∼3 kcal/mol. Our analysis indicates that a single distal constraint alters equilibrium motions throughout the enzyme on a wide range of time scales. This alteration of the conformational sampling of the entire system is sufficient to significantly increase the free energy barrier and decrease the rate of hydride transfer. Despite the changes in conformational sampling introduced by the constraint, the system assumes a similar transition state conformation with a donor−acceptor distance of ∼2.72 Å to enable the hydride transfer reaction. The modified thermal sampling leads to a substantial increase in the average donor−acceptor distance for the reactant state, however, thereby decreasing the probability of sampling the transition state conformations with the shorter distances required for hydride transfer. These simulations indicate that fast thermal fluctuations of the enzyme, substrate, and cofactor lead to conformational sampling of configurations that facilitate hydride transfer. The fast thermal motions are in equilibrium as the reaction progresses along the collective reaction coordinate, and the overall average equilibrium conformational changes occur on the slower time scale measured experimentally. Recent single molecule experiments suggest that at least some of these thermally averaged equilibrium conformational changes occur on the millisecond time scale of the hydride transfer reaction. Thus, introducing a constraint that modifies the conformational sampling of an enzyme could significantly impact its catalytic activity.