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Calculation of a complete enzymic reaction surface: Reaction and activation free energies for hydride-ion transfer in dihyrofolate reductase

Cummins, Peter; Rostov, Ivan; Gready, Jill


We present a two-dimensional grid method for the calculation of complete free-energy surfaces for enzyme reactions using a hybrid quantum mechanical/molecular mechanical (QM/ MM) potential within the semiempirical (PM3) QM approximation. This implementation is novel in that parallel processing with multiple trajectories (replica-exchange molecular dynamics simulations) is used to sample configuration space. The free energies at each grid point are computed using the thermodynamic integration...[Show more]

CollectionsANU Research Publications
Date published: 2007
Type: Journal article
Source: Journal of Chemical Theory and Computation (JCTC)
DOI: 10.1021/ct600313b


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