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dc.contributor.authorMitternacht, Simoneng
dc.contributor.authorBerezovsky, Igor N.eng
dc.date.accessioned2012-02-20T10:12:40Z
dc.date.available2012-02-20T10:12:40Z
dc.date.issued2011-09-15eng
dc.identifier.citationPLoS Computational Biology 7(9): e1002148en
dc.identifier.issn1553-734Xeng
dc.identifier.urihttp://hdl.handle.net/1956/5617
dc.descriptionAllosteric protein regulation is the mechanism by which binding of a molecule to one site in a protein affects the activity at another site. Although the two classical phenomenological models, Monod-Wyman-Changeux (MWC) and Koshland-Némethy-Filmer (KNF), span from the case of hemoglobin to membrane receptors, they do not describe the intramolecular interactions involved. The coupling between two allosterically connected sites commonly takes place through coherent collective motion involving the whole protein. We therefore introduce a quantity called binding leverage to measure the strength of the coupling between particular binding sites and such motions. We show that high binding leverage is a characteristic of both allosteric sites and catalytic sites, emphasizing that both enzymatic function and allosteric regulation require a coupling between ligand binding and protein dynamics. We also consider the first known case of purely entropic allostery, where ligand binding only affects the amplitudes of fluctuations. We find that the binding site in this protein does not primarily connect to collective motions – instead the modulation of fluctuations is controlled from a deeply buried and highly connected site. Finally, sites with high binding leverage but no known biological function could be latent allosteric sites, and thus drug targets.en
dc.description.abstractAllosteric regulation involves conformational transitions or fluctuations between a few closely related states, caused by the binding of effector molecules. We introduce a quantity called binding leverage that measures the ability of a binding site to couple to the intrinsic motions of a protein. We use Monte Carlo simulations to generate potential binding sites and either normal modes or pairs of crystal structures to describe relevant motions. We analyze single catalytic domains and multimeric allosteric enzymes with complex regulation. For the majority of the analyzed proteins, we find that both catalytic and allosteric sites have high binding leverage. Furthermore, our analysis of the catabolite activator protein, which is allosteric without conformational change, shows that its regulation involves other types of motion than those modulated at sites with high binding leverage. Our results point to the importance of incorporating dynamic information when predicting functional sites. Because it is possible to calculate binding leverage from a single crystal structure it can be used for characterizing proteins of unknown function and predicting latent allosteric sites in any protein, with implications for drug design.en
dc.language.isoengeng
dc.publisherPublic Library of Scienceeng
dc.rightsAttribution CC BYeng
dc.rights.urihttp://creativecommons.org/licenses/by/2.5/eng
dc.subjectAllosteryeng
dc.subjectallosteric regulationeng
dc.subjectNormal mode analysiseng
dc.subjectdockingeng
dc.subjectEnzymeeng
dc.subjectProtein dynamicseng
dc.subjectProtein structureeng
dc.subjectproteinseng
dc.subjectbiophysicseng
dc.subjectbinding leverageeng
dc.titleBinding Leverage as a Molecular Basis for Allosteric Regulationeng
dc.typePeer reviewedeng
dc.typeJournal articleeng
dc.subject.nsiVDP::Mathematics and natural science: 400::Basic biosciences: 470eng
dc.rights.holderCopyright 2011 Mitternacht, Berezovsky
dc.type.versionpublishedVersioneng
bora.peerreviewedPeer reviewedeng
bibo.doihttp://dx.doi.org/10.1371/journal.pcbi.1002148eng
dc.identifier.doi10.1371/journal.pcbi.1002148


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