Extended Morse function model for angle-dependent hydrogen bond in protein-protein interactions.
Backbone-backbone, backbone-asparagine, and serine-backbone hydrogen bonds (HBs) are the most abundant interactions at the interface of protein-protein complex. Here, we propose an angle-dependent potential energy function for these HBs constructed by the product of the radial and the angular Morse functions whose various parameters are optimized with high-level density functional theory (DFT) calculations. The new angular variables, the interatomic distance between the donor and the acceptor atoms (R(theta)) and that between the hydrogen and the base atom of the acceptor (R(phi)), are employed to define the angular Morse functions. The angular part in the new potential function is found to be comparable in the magnitude of energy values to the radial one, which is consistent with the significant angular dependence of HBs. The HB binding energies calculated with the new potential function compare well with those obtained by high-level DFT calculations with the associated squared correlation coefficients ranging from 0.82 to 0.85. This agreement indicates the suitability of the new energy functions as a potential function for HB in modeling the protein-protein interactions.
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
D003198:Computer Simulation; D006860:Hydrogen Bonding; D008956:Models, Chemical; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory
D011506:Proteins