Umbrella sampling and double decoupling data for methanol binding to Candida antarctica lipase B

Markthaler, Daniel; Hansen, Niels

doi:10.1016/j.dib.2021.107618

Cited by 1 publication

(1 citation statement)

References 15 publications

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“…Shells A correspond to a productive binding site, while shells S correspond to nonspecific interactions with methanol. The binding free energy profiles were compared to the potential of mean force obtained from umbrella-sampling simulations of CALB–methanol at infinite dilution and 5.5 M and were found to be in close agreement. This points to the convergence of CALB–methanol interaction energetics irrespective of the employed simulation method.…”

Section: Resultsmentioning

confidence: 81%

Molecular Mechanism of Methanol Inhibition in CALB-Catalyzed Alcoholysis: Analyzing Molecular Dynamics Simulations by a Markov State Model

Carvalho

Ferrario

Pleiss

2021

J. Chem. Theory Comput.

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Lipases are widely used enzymes that catalyze hydrolysis and alcoholysis of fatty acid esters. At high concentrations of small alcohols such as methanol or ethanol, many lipases are inhibited by the substrate. The molecular basis of the inhibition of Candida antarctica lipase B (CALB) by methanol was investigated by unbiased molecular dynamics (MD) simulations, and the substrate binding kinetics was analyzed by Markov state models (MSMs). The modeled fluxes of productive methanol binding at concentrations between 50 mM and 5.5 M were in good agreement with the experimental activity profile of CALB, with a peak at 300 mM. The kinetic and structural analysis uncovered the molecular basis of CALB inhibition. Beyond 300 mM, the kinetic bottleneck results from crowding of methanol in the substrate access channel, which is caused by the gradual formation of methanol patches close to Leu140 (helix α5), Leu278, and Ile285 (helix α10) at a distance of 4–5 Å from the active site. Our findings demonstrate the usefulness of unbiased MD simulations to study enzyme–substrate interactions at realistic substrate concentrations and the feasibility of scale-bridging by an MSM analysis to derive kinetic information.

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Section: Resultsmentioning

confidence: 81%