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Folding-Reaction Coupling in a Self-Cleaving Protein
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
2012 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 10, 3871-3879 p.Article in journal (Refereed) Published
Abstract [en]

Backbone torsional strain has been implicated as a cause of rate enhancement in a class of autoprocessing proteins performing proteolysis and protein splicing. In the autoproteolytic protein domain SEA, folding and proteolytic activity have experimentally been shown to be coupled with about 7 kcal/mol of folding free energy available for catalysis. Here, we have examined the catalytic strategy of SEA with molecular dynamics simulations, potential of mean force free energy profiles, and B3LYP/6-311G(d,p) density functional calculations. A quantitative estimate of the free energy stored as protein strain (about 8 kcal/mol), that is available for catalyzing the cleavage reaction, is obtained and found to be in excellent agreement with thermodynamic and kinetic data. It is further shown that there is strong coupling between folding and reaction coordinates leading to reactant state destabilization in the direction of folding and transition state stabilization along the reaction coordinate. This situation is different from the preorganized active site model in that the fully folded transition state stabilizing structure is not realized until the reaction barrier is surmounted.

Place, publisher, year, edition, pages
2012. Vol. 8, no 10, 3871-3879 p.
National Category
Natural Sciences
Identifiers
URN: urn:nbn:se:uu:diva-184642DOI: 10.1021/ct3001427ISI: 000309505600042OAI: oai:DiVA.org:uu-184642DiVA: diva2:567322
Available from: 2012-11-12 Created: 2012-11-12 Last updated: 2017-12-07Bibliographically approved

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Härd, TorleifÅqvist, Johan

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