A structural and energetic description of protein-protein interactions in atomic detail
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).
Citation
Fischer, Tiffany Brink (2006). A structural and energetic description of protein-protein interactions in atomic detail. Master's thesis, Texas A&M University. Texas A&M University. Available electronically from https : / /hdl .handle .net /1969 .1 /4775.