An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes.
Hydrogen bonding is a key contributor to the specificity of intramolecular and intermolecular interactions in biological systems. Here, we develop an orientation-dependent hydrogen bonding potential based on the geometric characteristics of hydrogen bonds in high-resolution protein crystal structures, and evaluate it using four tests related to the prediction and design of protein structures and protein-protein complexes. The new potential is superior to the widely used Coulomb model of hydrogen bonding in prediction of the sequences of proteins and protein-protein interfaces from their structures, and improves discrimination of correctly docked protein-protein complexes from large sets of alternative structures.
Kortemme
Tanja
T
Howard Hughes Medical Institute and Department of Biochemistry, J-567 Health Sciences, Box 357350, University of Washington, Seattle, WA 98195-7350, USA.
Morozov
Alexandre V
AV
Baker
David
D
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D006860:Hydrogen Bonding; D008433:Mathematics; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism
D000596:Amino Acids; D011506:Proteins