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dc.contributor.advisorTsai, Jerry W.en_US
dc.creatorFischer, Tiffany Brinken_US
dc.date.accessioned2007-04-25T20:07:19Z
dc.date.available2007-04-25T20:07:19Z
dc.date.created2006-12en_US
dc.date.issued2007-04-25
dc.identifier.urihttp://hdl.handle.net/1969.1/4775
dc.description.abstractHere, 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 QContacts’ 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_US
dc.format.extent3083444 bytes
dc.format.mediumelectronicen_US
dc.format.mimetypeapplication/pdf
dc.language.isoen_USen_US
dc.publisherTexas A&M Universityen_US
dc.subjectproteinen_US
dc.subjectinteractionen_US
dc.subjectVoronoi polyhedraen_US
dc.subjectsolvent accessible surface areaen_US
dc.titleA structural and energetic description of protein-protein interactions in atomic detailen_US
dc.typeBooken
dc.typeThesisen
thesis.degree.departmentBiochemistry and Biophysicsen_US
thesis.degree.disciplineBiochemistryen_US
thesis.degree.grantorTexas A&M Universityen_US
thesis.degree.nameMaster of Scienceen_US
thesis.degree.levelMastersen_US
dc.contributor.committeeMemberHu, James C.en_US
dc.contributor.committeeMemberIoerger, Thomas R.en_US
dc.contributor.committeeMemberLiWang, Patricia J.en_US
dc.type.genreElectronic Thesisen_US
dc.type.materialtexten_US
dc.format.digitalOriginborn digitalen_US


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