dc.creator | Lindert, Steffen | |
dc.date.accessioned | 2020-08-21T21:03:22Z | |
dc.date.available | 2011-09-09 | |
dc.date.issued | 2011-03-14 | |
dc.identifier.uri | https://etd.library.vanderbilt.edu/etd-02252011-123124 | |
dc.identifier.uri | http://hdl.handle.net/1803/10618 | |
dc.description.abstract | In the course of this dissertation a software EM-Fold was developed that combines de-novo protein structure prediction and medium resolution cryoEM density maps. It can be applied to proteins containing α-helices and β-strands if the density map has sufficient resolution to observe these secondary structure elements. EM-Fold was proven to be reliable over a large range of protein sizes in several benchmarks on simulated and experimental density maps. The software was used to predict a model for one of the capsid proteins of human Adenovirus, protein IIIa, for which there was no crystal structure available. EM-Fold in combination with Rosetta was be able to recover atomic detail information in several benchmark cases. A separate line of research dealt with the determination of a medium resolution density map of the Adenovirus-Integrin complex. The density was able to corroborate the extension model for integrin binding to a multivalent RGD ligand. | |
dc.format.mimetype | application/pdf | |
dc.subject | hybrid methods | |
dc.subject | de novo protein folding | |
dc.subject | cryoEM | |
dc.title | Cryo-EM guided de novo protein folding | |
dc.type | dissertation | |
dc.contributor.committeeMember | Charles Sanders | |
dc.contributor.committeeMember | Michael Stone | |
dc.contributor.committeeMember | Phoebe Stewart | |
dc.type.material | text | |
thesis.degree.name | PHD | |
thesis.degree.level | dissertation | |
thesis.degree.discipline | Chemical and Physical Biology | |
thesis.degree.grantor | Vanderbilt University | |
local.embargo.terms | 2011-09-09 | |
local.embargo.lift | 2011-09-09 | |
dc.contributor.committeeChair | Al Beth | |