New angle-dependent potential energy function for backbone-backbone hydrogen bond in protein-protein interactions.
Backbone-backbone hydrogen bonds (BBHBs) are one of the most abundant interactions at the interface of protein-protein complex. Here, we propose an angle-dependent potential energy function for BBHB based on density functional theory (DFT) calculations and the operation of a genetic algorithm to find the optimal parameters in the potential energy function. The angular part of the energy function is assumed to be the product of the power series of sine and cosine functions with respect to the two angles associated with BBHB. Two radial functions are taken into account in this study: Morse and Leonard-Jones 12-10 potential functions. Of these two functions under consideration, the former is found to be more accurate than the latter in terms of predicting the binding energies obtained from DFT calculations. The new HB potential function also compares well with the knowledge-based potential derived by applying Boltzmann statistics for a variety of protein-protein complexes in protein data bank.
Choi
Hwanho
H
Department of Bioscience and Biotechnology, Sejong University, 98, Kunja-Dong, Kwangjin-Ku, Seoul 143-747, Korea.
Kang
Hongsuk
H
Park
Hwangseo
H
D000465:Algorithms; D006860:Hydrogen Bonding; D008954:Models, Biological; D008958:Models, Molecular; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D011789:Quantum Theory; D013816:Thermodynamics
D011506:Proteins