The effect of MM polarization on the QM/MM transition state stabilization: application to chorismate mutase
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The effect of MM polarization on the QM/MM transition state stabilization: application to chorismate mutaseAutoria
Data de publicació
2008Editor
Taylor & FrancisISSN
0026-8976Cita bibliogràfica
Molecular Physics, 106, 12-13, p. 1511–1515Tipus de document
info:eu-repo/semantics/articleVersió de l'editorial
http://www.tandfonline.com/doi/abs/10.1080/00268970802077850#.Umd2jfVLZ6YVersió
info:eu-repo/semantics/publishedVersionParaules clau / Matèries
Resum
Hybrid quantum mechanics / molecular mechanics (QM/MM) calculations provide a
mechanism for studying enzyme catalysed reactions at the molecular level. Here, through
applications on the chorismate to prephenate ... [+]
Hybrid quantum mechanics / molecular mechanics (QM/MM) calculations provide a
mechanism for studying enzyme catalysed reactions at the molecular level. Here, through
applications on the chorismate to prephenate rearrangement within the enzyme chorismate
mutase, we have demonstrated the feasibility of including MM polarization into these
calculations using the method of induced charges. MM polarization is shown to be a shortrange
effect, such that 80% of the energy of MM polarization occurs within a 5 Å residuebased
cut-off of the substrate. MM polarization was shown to have a greater magnitude
within the enzyme catalysed reaction than in the aqueous reaction, indicating that MM
polarization may in principle have a significant effect on enzyme rate enhancement and
mechanism. In both the enzyme and the aqueous case, the percentage contribution of MM
polarization to the total stabilization energy was towards the upper end of the expected value.
For the specific structures studied here, MM polarization lowered the energy barrier for the
aqueous reaction, but the calculated contribution of MM polarization to both the reactant and
transition structure stability were similar. [-]
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