dc.contributor.advisor | Tsai, Jerry W. | |
dc.creator | Fischer, Tiffany Brink | |
dc.date.accessioned | 2007-04-25T20:07:19Z | |
dc.date.available | 2007-04-25T20:07:19Z | |
dc.date.created | 2006-12 | |
dc.date.issued | 2007-04-25 | |
dc.identifier.uri | https://hdl.handle.net/1969.1/4775 | |
dc.description.abstract | Here, we present the program QContacts, which implements Voronoi polyhedra
to determine atomic and residue contacts across the interface of a protein-protein
interaction. While QContacts also describes hydrogen bonds, ionic pair and salt bridge
interactions, we focus on QContactsâ identification of atomic contacts in a protein
interface compared against the current methods. Initially, we investigated in detail the
differences between QContacts, radial cutoff and Change in Solvent Accessible Surface
Area (delta-SASA) methods in identifying pair-wise contacts across the binding interface.
The results were assessed based on a set of 71 double cycle mutants. QContacts
excelled at identifying knob-in-hole contacts. QContacts, closest atom radial cutoff and
the delta-SASA methods performed well at picking out direct contacts; however, QContacts
was the most accurate in excluding false positives. The significance of the differences
identified between QContacts and previous methods was assessed using pair-wise
contact frequencies in a broader set of 592 protein interfaces. The inaccuracies
introduced by commonly used radial cutoff methods were found to produce misleading
bias in the residue frequencies. This bias could compromise pair-wise potentials that are
based on such frequencies. Here we show that QContacts provides a more accurate description of protein interfaces at atomic resolution than other currently available
methods. QContacts is available in a web-based form at http://tsailab.tamu.edu/qcons
(Fischer et al., 2006). | en |
dc.format.extent | 3083444 bytes | en |
dc.format.medium | electronic | en |
dc.format.mimetype | application/pdf | |
dc.language.iso | en_US | |
dc.publisher | Texas A&M University | |
dc.subject | protein | en |
dc.subject | interaction | en |
dc.subject | Voronoi polyhedra | en |
dc.subject | solvent accessible surface area | en |
dc.title | A structural and energetic description of protein-protein interactions in atomic detail | en |
dc.type | Book | en |
dc.type | Thesis | en |
thesis.degree.department | Biochemistry and Biophysics | en |
thesis.degree.discipline | Biochemistry | en |
thesis.degree.grantor | Texas A&M University | en |
thesis.degree.name | Master of Science | en |
thesis.degree.level | Masters | en |
dc.contributor.committeeMember | Hu, James C. | |
dc.contributor.committeeMember | Ioerger, Thomas R. | |
dc.contributor.committeeMember | LiWang, Patricia J. | |
dc.type.genre | Electronic Thesis | en |
dc.type.material | text | en |
dc.format.digitalOrigin | born digital | en |