Protocol for MM/PBSA molecular dynamics simulations of proteins.
Continuum solvent models have been employed in past years for understanding processes such as protein folding or biomolecular association. In the last decade, several attempts have been made to merge atomic detail molecular dynamics simulations with solvent continuum models. Among continuum models, the Poisson-Boltzmann solvent accessible surface area model is one of the oldest and most fundamental. Notwithstanding its wide usage for simulation of biomolecular electrostatic potential, the Poisson-Boltzmann equation has been very seldom used to obtain solvation forces for molecular dynamics simulation. We propose here a fast and reliable methodology to implement continuum forces in standard molecular mechanics and dynamics algorithms. Results for a totally unrestrained 1 ns molecular dynamics simulation of a small protein are quantitatively similar to results obtained by explicit solvent molecular dynamics simulations.
Fogolari
Federico
F
Dipartimento Scientifico e Tecnologico, Università di Verona, 37134 Verona, Italy. fogolari@sci.univr.it
Brigo
Alessandro
A
Molinari
Henriette
H
D003198:Computer Simulation; D004735:Energy Transfer; D017408:Guidelines as Topic; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D009038:Motion; D028321:Plant Preparations / Q000737:chemistry; D010940:Plant Proteins; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D011786:Quality Control; D015203:Reproducibility of Results; D054790:Ribosome Inactivating Proteins, Type 2; D012680:Sensitivity and Specificity; D014118:Toxins, Biological / Q000737:chemistry
D028321:Plant Preparations; D010940:Plant Proteins; D011506:Proteins; D054790:Ribosome Inactivating Proteins, Type 2; D014118:Toxins, Biological; C009674:ribosome inactivating protein, Viscum