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Large-Scale Density Functional Theory Transition State Searching in Enzymes

Lookup NU author(s): Dr Daniel Cole

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Abstract

Linear-scaling quantum mechanical density functional theory calculations have been applied to study the rearrangement of chorismate to prephenate in large-scale models of the Bacillus subtilis chorismate mutase enzyme. By treating up to 2000 atoms at a consistent quantum mechanical level of theory, we obtain an unbiased, almost parameter-free description of the transition state geometry and energetics. The activation energy barrier is calculated to be lowered by 10.5 kcal mol–1 in the enzyme, compared with the equivalent reaction in water, which is in good agreement with experiment. Natural bond orbital analysis identifies a number of active site residues that are important for transition state stabilization in chorismate mutase. This benchmark study demonstrates that linear-scaling density functional theory techniques are capable of simulating entire enzymes at the ab initio quantum mechanical level of accuracy.


Publication metadata

Author(s): Lever G, Cole DJ, Lonsdale R, Ranaghan KE, Wales DJ, Mulholland AJ, Skylaris C-K, Payne MC

Publication type: Article

Publication status: Published

Journal: Journal of Physical Chemistry Letters

Year: 2014

Volume: 5

Issue: 21

Pages: 3614-3619

Print publication date: 06/11/2014

Online publication date: 07/10/2014

Acceptance date: 07/10/2014

ISSN (print): 1089-5639

ISSN (electronic): 1948-7185

Publisher: American Chemical Society

URL: http://pubs.acs.org/doi/abs/10.1021/jz5018703

DOI: 10.1021/jz5018703


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