Enzyme dynamics and tunneling enhanced by compression in the hydrogen abstraction catalyzed by soybean lipooxygenase-1
Article Abstract:
A fully microscopical simulation of the rate-limiting hydrogen abstraction catalyzed by soybean lipoxygenase-1 (SLO-1) was carried out and the rate constants and kinetic isotope effect (KIE) were calculated. The results show that the compression of the wild-type active site enzyme results in the huge contribution of tunneling to the rate of the hydrogen abstraction and the calculated KIE for the wild-type enzyme has an important dependence on the barrier width.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2006
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Reaction mechanism of the mandelate anion racemization catalyzed by mandate racemase enzyme: A QM/MM molecular dynamics free energy study
Article Abstract:
The reaction mechanism of the racemization of mandelate substrate by mandelate racemase enzyme is studied and a quantum mechanics/molecular mechanics (QM/MM) potential energy surface is used to compute the free energy profiles associated with the reaction. The results show that enzyme stabilized the reactants and the products through local hydrogen bond interactions and short and long range electrostatic contributions.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2005
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New insights into the reaction mechanism catalyzed by the glutamate racemase enzyme: pH titration curves and classical molecular dynamics simulations
Article Abstract:
Two mechanisms are proposed for the racemization reaction catalyzed by Aquifex pyrophillus glutamate racemase enzyme. The results have shown that the behavior of an enzyme depends on the ionization state of its active site residues and justifies the calculation of their ionization probabilities to understand the enzyme catalytic mechanism.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2007
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