Folding, Binding, Misfolding and Aggregation with AWSEM

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dc.contributor.advisorWolynes, Peter G.en_US
dc.contributor.committeeMemberOnuchic, Jose N.en_US
dc.contributor.committeeMemberClementi, Ceciliaen_US
dc.creatorSchafer, Nicholas Peteren_US
dc.date.accessioned2014-10-10T21:29:50Zen_US
dc.date.available2014-10-10T21:29:50Zen_US
dc.date.created2014-05en_US
dc.date.issued2014-04-23en_US
dc.date.submittedMay 2014en_US
dc.date.updated2014-10-10T21:29:50Zen_US
dc.description.abstractThis thesis discusses our recent results using the Associative-memory, Water-mediated, Structure and Energy Model (AWSEM), an optimized, coarse-grained molecular dynamics protein folding model, to fold, bind, and predict the misfolding behavior of proteins. AWSEM is capable of performing de novo structure prediction on small alpha-helical protein domains and predict the binding interfaces of homo- and hetero-dimers. More recent work demonstrates how the misfolding behavior of tandem constructs in AWSEM is consistent with crucial aspects of ensemble and single molecule experiments on the aggregation and misfolding of these constructs. The first chapter is a review of the energy landscape theory of protein folding as it applies to the problem of protein structure prediction, and more specifically how energy landscape theory and the principle of minimal frustration can be used to optimize parameters of coarse-grained protein folding simulation models. The subsequent four chapters are reports of novel research performed with one such model.en_US
dc.format.mimetypeapplication/pdfen_US
dc.identifier.citationSchafer, Nicholas Peter. "Folding, Binding, Misfolding and Aggregation with AWSEM." (2014) Diss., Rice University. <a href="https://hdl.handle.net/1911/77518">https://hdl.handle.net/1911/77518</a>.en_US
dc.identifier.urihttps://hdl.handle.net/1911/77518en_US
dc.language.isoengen_US
dc.rightsCopyright is held by the author, unless otherwise indicated. Permission to reuse, publish, or reproduce the work beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.en_US
dc.subjectProtein foldingen_US
dc.subjectCoarse-grained modelsen_US
dc.subjectOptimizationen_US
dc.subjectMisfoldingen_US
dc.subjectAggregationen_US
dc.subjectBinding interface predictionen_US
dc.subjectProtein structure predictionen_US
dc.titleFolding, Binding, Misfolding and Aggregation with AWSEMen_US
dc.typeThesisen_US
dc.type.materialTexten_US
thesis.degree.departmentPhysics and Astronomyen_US
thesis.degree.disciplineNatural Sciencesen_US
thesis.degree.grantorRice Universityen_US
thesis.degree.levelDoctoralen_US
thesis.degree.nameDoctor of Philosophyen_US
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