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Extra resources for Comprehensive Natural Products II: Chemistry and Biology: Enzymes and Enzyme Mechanisms
J. Benkovic; S. Hammes-Schiffer, Proc. Natl. Acad. Sci. A. 2002, 99, 2794–2799. in 11 residues had previously been shown to affect the rate of at least one of the first three steps in the catalytic cycle. Four of these residues line the active site, but seven are more remote. Notably, these seven residues occur in regions that are predicted to participate in anticorrelated motions. Agarwal et al. 75 The positions of several side chains in the vicinity of the active site changed as the transition state was approached and the distance between the NADPH and the acceptor carbon of dihydrofolate decreased (see Figure 24).
L. Radkiewicz; C. L. Brooks, III, J. Am. Chem. Soc. 2000, 122, 225–231. 34 Evolution and the Enzyme NADPH Asp122 DHF CA CD Gly15 H Phe31 Tyr100 Ile14 Figure 24 Coupled motions in DHFR are proposed to push NADPH toward dihydrofolate as the reaction proceeds. Reproduced with permission from P. K. Agarwal; S. R. Billeter; P. T. Rajagopalan; S. J. Benkovic; S. Hammes-Schiffer, Proc. Natl. Acad. Sci. A. 2002, 99, 2794–2799. in 11 residues had previously been shown to affect the rate of at least one of the first three steps in the catalytic cycle.
Below 30 C, both primary and secondary isotope effects increase, but the exponent decreases toward the semiclassical limit. These results suggest that protein fluctuations accelerate the rate at temperatures experienced by the microbe by facilitating tunneling. 6 kcal/mol. Thus, protein motions can have dramatic effects on the rate of the reaction. The role of protein motions in dihydrofolate reductase (DHFR) has been examined using molecular dynamics simulations as well as experimental studies of mutant enzymes.