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Using Energy Landscape Theory to Uncover the Organization of Conformational Space of Proteins in Their Native States.

dc.contributor.advisorPapoian, Garegin Aen_US
dc.contributor.authorPotoyan, Daviten_US
dc.date.accessioned2012-07-06T11:15:44Z
dc.date.available2012-07-06T11:15:44Z
dc.date.issued2011en_US
dc.identifier.urihttp://hdl.handle.net/1903/12530
dc.description.abstractThe functional motions of proteins navigate on rugged energy landscapes. Hence, mapping of these multidimensional landscapes into lower dimensional manifolds is imperative for gaining deeper insights into the functional dynamics. In the present work we implement novel computational schemes and means of analysis to characterize the topography of conformational space of selected proteins and also to elucidate their functional implications. The present thesis is divided into two parts, where we focus on the case studies of the intrinsically disordered histone tails and the representative allosteric protein Adenlyate Kinase. In particular, analyzing the energy landscapes of histone tails, we find preferential clustering of transient secondary structural elements in the conformational ensembles, which have a dramatic impact on the chain statistics, conformational dynamics and the binding pathways. In the study of Adenylate Kinase we use a novel nonlinear order parameter to rigorously estimate the free energy difference between allosteric states and map out the plausible pathway of transition, which reveals important structural and thermodynamic insights about the mechanism of allostery in Adenylate Kinase. Taken together our findings indicate that the organization of conformational space of functional proteins is delicately crafted to ensure efficient functional regulation and robust response to external signals.en_US
dc.titleUsing Energy Landscape Theory to Uncover the Organization of Conformational Space of Proteins in Their Native States.en_US
dc.typeDissertationen_US
dc.contributor.publisherDigital Repository at the University of Marylanden_US
dc.contributor.publisherUniversity of Maryland (College Park, Md.)en_US
dc.contributor.departmentChemical Physicsen_US
dc.subject.pqcontrolledPhysical chemistryen_US
dc.subject.pqcontrolledBiophysicsen_US


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