Linked Life Data

18069813

Source:http://linkedlifedata.com/resource/pubmed/id/18069813

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
19
pubmed:dateCreated
2008-5-8
pubmed:abstractText
The ability of using wave function propagation approaches to simulate isotope effects in enzymes is explored, focusing on the large H/D kinetic isotope effect of soybean lipoxygenase-1 (SLO-1). The H/D kinetic isotope effect (KIE) is calculated as the ratio of the rate constants for hydrogen and deuterium transfer. The rate constants are calculated from the time course of the H and D nuclear wave functions. The propagations are done using one-dimensional proton potentials generated as sections from the full multidimensional surface of the reacting system in the protein. The sections are obtained during a classical empirical valence bond (EVB) molecular dynamics simulation of SLO-1. Since the propagations require an extremely long time for treating realistic activation barriers, it is essential to use an effective biasing approach. Thus, we develop here an approach that uses the classical quantum path (QCP) method to evaluate the quantum free energy change associated with the biasing potential. This approach provides an interesting alternative to full QCP simulations and to other current approaches for simulating isotope effects in proteins. In particular, this approach can be used to evaluate the quantum mechanical transmission factor or other dynamical effects, while still obtaining reliable quantized activation free energies due to the QCP correction.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
May
pubmed:issn
1520-6106
pubmed:author
pubmed:issnType
Print
pubmed:day
15
pubmed:volume
112
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
5950-4
pubmed:meshHeading
pubmed:year
2008
pubmed:articleTitle
Simulation of tunneling in enzyme catalysis by combining a biased propagation approach and the quantum classical path method: application to lipoxygenase.
pubmed:affiliation
National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't, Research Support, N.I.H., Extramural