Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates
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Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates

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Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates

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dc.contributor.author García Meseguer, Rafael
dc.contributor.author Martí, Sergio
dc.contributor.author Ruiz Pernía, José Javier
dc.contributor.author Moliner, Vicent
dc.contributor.author Tuñón, Iñaki
dc.date.accessioned 2013-12-17T13:08:33Z
dc.date.available 2013-12-17T13:08:33Z
dc.date.issued 2013
dc.identifier.uri http://dx.doi.org/10.1038/nchem.1660
dc.identifier.uri http://hdl.handle.net/10550/32136
dc.description.abstract Conformational changes are known to be able to drive an enzyme through its catalytic cycle, allowing, for example, substrate binding or product release. However, the influence of protein motions on the chemical step is a controversial issue. One proposal is that the simple equilibrium fluctuations incorporated into transition-state theory are insufficient to account for the catalytic effect of enzymes and that protein motions should be treated dynamically. Here, we propose the use of free-energy surfaces, obtained as a function of both a chemical coordinate and an environmental coordinate, as an efficient way to elucidate the role of protein structure and motions during the reaction. We show that the structure of the protein provides an adequate environment for the progress of the reaction, although a certain degree of flexibility is needed to attain the full catalytic effect. However, these motions do not introduce significant dynamical corrections to the rate constant and can be described as equilibrium fluctuations.
dc.relation.ispartof Nature Chemistry, 2013, vol. 5, num. 7, p. 566-571
dc.rights.uri info:eu-repo/semantics/openAccess
dc.source García Meseguer, Rafael Martí, Sergio Ruiz Pernía, José Javier Moliner, Vicent Tuñón García de Vicuña, Ignacio 2013 Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates Nature Chemistry 5 7 566 571
dc.subject Proteïnes
dc.title Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates
dc.type info:eu-repo/semantics/article
dc.date.updated 2013-12-17T13:08:33Z
dc.identifier.doi http://dx.doi.org/10.1038/nchem.1660
dc.identifier.idgrec 089911

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