GBr6NL: a generalized Born method for accurately reproducing solvation energy of the nonlinear Poisson-Boltzmann equation.
The nonlinear Poisson-Boltzmann (NLPB) equation can provide accurate modeling of electrostatic effects for nucleic acids and highly charged proteins. Generalized Born methods have been developed to mimic the linearized Poisson-Boltzmann (LPB) equation at substantially reduced cost. The computer time for solving the NLPB equation is approximately fivefold longer than for the LPB equation, thus presenting an even greater obstacle. Here we present the first generalized Born method, GBr(6)NL, for mimicking the NLPB equation. GBr(6)NL is adapted from GBr(6), a generalized Born method recently developed to reproduce the solvation energy of the LPB equation [Tjong and Zhou, J. Phys. Chem. B 111, 3055 (2007)]. Salt effects predicted by GBr(6)NL on 55 proteins overall deviate from NLPB counterparts by 0.5 kcal/mol from ionic strengths from 10 to 1000 mM, which is approximately 10% of the average magnitudes of the salt effects. GBr(6)NL predictions for the salts effects on the electrostatic interaction energies of two protein:RNA complexes are very promising.
Tjong
Harianto
H
Department of Physics and Institute of Molecular Biophysics, and School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA.
Zhou
Huan-Xiang
HX
D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D004735:Energy Transfer; D008956:Models, Chemical; D008958:Models, Molecular; D017711:Nonlinear Dynamics; D011485:Protein Binding; D012313:RNA / Q000737:chemistry* / Q000648:ultrastructure*; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D012492:Salts / Q000737:chemistry
D016601:RNA-Binding Proteins; D012492:Salts; D012313:RNA