Combining a polarizable force-field and a coarse-grained polarizable solvent model: application to long dynamics simulations of bovine pancreatic trypsin inhibitor.
The dynamic coupling between a polarizable protein force field and a particle-based implicit solvent model is described. The polarizable force field, TCPEp, developed recently to simulate protein systems, is characterized by a reduced number of polarizable sites, with a substantial gain in efficiency for an equal chemical accuracy. The Polarizable Pseudo-Particle (PPP) solvent model represents the macroscopic solvent polarization by induced dipoles placed on mobile Lennard-Jones pseudo-particles. The solvent-induced dipoles are sensitive to the solute electric field, but not to each other, so that the computational cost of solvent-solvent interactions is basically negligible. The solute and solvent induced dipoles are determined self-consistently and the equations of motion are solved using an efficient iterative multiple time step procedure. The solvation cost with respect to vacuum simulations is shown to decrease with solute size: the estimated multiplicative factor is 2.5 for a protein containing about 1000 atoms, and as low as 1.15 for 8000 atoms. The model is tested for six 20 ns molecular dynamics trajectories of a traditional benchmark system: the hydrated Bovine Pancreatic Trypsin Inhibitor (BPTI). Even though the TCPEp parameters have not been refined to be used with the solvent PPP model, we observe a good conservation of the BPTI structure along the trajectories. Moreover, our approach is able to provide a description of the protein solvation thermodynamic at the same accuracy as the standard Poisson-Boltzman continuum methods. It provides in addition a good description of the microscopic structural aspects concerning the solute/solvent interaction.
Masella
Michel
M
Laboratoire de chimie du vivant, Service d'ingéniérie moléculaire des protéines, Institut de Biologie et de Technologies de Saclay, Commissariat à l'Energie Atomique, Centre de Saclay, 91191 Gif-sur-Yvette Cedex, France. michel.masella@cea.fr
Borgis
Daniel
D
Cuniasse
Philippe
P
D000818:Animals; D007611:Aprotinin / Q000737:chemistry*; D002417:Cattle; D008958:Models, Molecular; D012997:Solvents / Q000737:chemistry*
D012997:Solvents; D007611:Aprotinin