Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method.
A fast stable finite difference Poisson-Boltzmann (FDPB) model for implicit solvation in molecular dynamics simulations was developed using the smooth permittivity FDPB method implemented in the OpenEye ZAP libraries. This was interfaced with two widely used molecular dynamics packages, AMBER and CHARMM. Using the CHARMM-ZAP software combination, the implicit solvent model was tested on eight proteins differing in size, structure, and cofactors: calmodulin, horseradish peroxidase (with and without substrate analogue bound), lipid carrier protein, flavodoxin, ubiquitin, cytochrome c, and a de novo designed 3-helix bundle. The stability and accuracy of the implicit solvent simulations was assessed by examining root-mean-squared deviations from crystal structure. This measure was compared with that of a standard explicit water solvent model. In addition we compared experimental and calculated NMR order parameters to obtain a residue level assessment of the accuracy of MD-ZAP for simulating dynamic quantities. Overall, the agreement of the implicit solvent model with experiment was as good as that of explicit water simulations. The implicit solvent method was up to eight times faster than the explicit water simulations, and approximately four times slower than a vacuum simulation (i.e., with no solvent treatment).
Prabhu
Ninad V
NV
Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, 37th and Hamilton Walk, Philadelphia, Pennsylvania 19104, USA.
Zhu
Peijuan
P
Sharp
Kim A
KA
D000465:Algorithms; D002147:Calmodulin / Q000737:chemistry; D002352:Carrier Proteins / Q000737:chemistry; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D045304:Cytochromes c / Q000737:chemistry; D005418:Flavodoxin / Q000737:chemistry; D006735:Horseradish Peroxidase / Q000737:chemistry; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics; D025801:Ubiquitin / Q000737:chemistry
D002147:Calmodulin; D002352:Carrier Proteins; D005418:Flavodoxin; D011506:Proteins; D025801:Ubiquitin; D045304:Cytochromes c; D006735:Horseradish Peroxidase