A dynamic view of enzyme catalysis |
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Authors: | Aurora Jiménez Pere Clapés Ramon Crehuet |
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Institution: | 1.Departament de Química de Pèptids i Prote?nes,Institut d′Investigacions Químiques i Ambientals de Barcelona (IIQAB–CSIC),Barcelona,Spain |
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Abstract: | Recent experimental advances have shown that enzymes are flexible molecules, and point to a direct link between dynamics and
catalysis. Movements span a wide time range, from nano- to milli-seconds. In this paper we introduce two aspects of enzyme
flexibility that are treated with two appropriate techniques. First, transition path sampling is used to obtain an unbiased
picture of the transition state ensemble in chorismate mutase, as well as its local flexibility and the energy flow during
the chemical step. Second, we consider the binding and release of substrates in L-rhamnulose-1-phosphate aldolase. We have calculated the normal modes of the enzyme with the elastic network model. The lowest
frequency modes generate active site deformations that change the coordination number of the catalytic zinc ion. The coordination
lability of zinc allows the binding and release of substrates. Substitution of zinc by magnesium blocks the exchange of ligands.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. |
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Keywords: | Enzyme catalysis Enzyme dynamics Transition path sampling Energy relaxation QM/MM Chorismate mutase Aldolase |
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