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).
| Identifer | oai:union.ndltd.org:tamu.edu/oai:repository.tamu.edu:1969.1/4775 |
| Date | 25 April 2007 |
| Creators | Fischer, Tiffany Brink |
| Contributors | Tsai, Jerry W. |
| Publisher | Texas A&M University |
| Source Sets | Texas A and M University |
| Language | en_US |
| Detected Language | English |
| Type | Book, Thesis, Electronic Thesis, text |
| Format | 3083444 bytes, electronic, application/pdf, born digital |
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