Folding, Binding, Misfolding and Aggregation with AWSEM

Simple item page
dc.contributor.advisorWolynes, Peter G.
dc.contributor.committeeMemberOnuchic, Jose N.
dc.contributor.committeeMemberClementi, Cecilia
dc.creatorSchafer, Nicholas Peter
dc.date.accessioned2014-10-10T21:29:50Z
dc.date.available2014-10-10T21:29:50Z
dc.date.created2014-05
dc.date.issued2014-04-23
dc.date.submittedMay 2014
dc.date.updated2014-10-10T21:29:50Z
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.
dc.format.mimetypeapplication/pdf
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>.
dc.identifier.urihttps://hdl.handle.net/1911/77518
dc.language.isoeng
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.
dc.subjectProtein folding
dc.subjectCoarse-grained models
dc.subjectOptimization
dc.subjectMisfolding
dc.subjectAggregation
dc.subjectBinding interface prediction
dc.subjectProtein structure prediction
dc.titleFolding, Binding, Misfolding and Aggregation with AWSEM
dc.typeThesis
dc.type.materialText
thesis.degree.departmentPhysics and Astronomy
thesis.degree.disciplineNatural Sciences
thesis.degree.grantorRice University
thesis.degree.levelDoctoral
thesis.degree.nameDoctor of Philosophy
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
SCHAFER-DOCUMENT-2014.pdf
Size:
23.13 MB
Format:
Adobe Portable Document Format
Download
License bundle
Now showing 1 - 2 of 2
No Thumbnail Available
Name:
LICENSE.txt
Size:
2.61 KB
Format:
Plain Text
Description:
Download
No Thumbnail Available
Name:
PROQUEST_LICENSE.txt
Size:
5.85 KB
Format:
Plain Text
Description:
Download
Collections
Rice University Electronic Theses and Dissertations