Solvent reaction field potential inside an uncharged globular protein: a bridge between implicit and explicit solvent models?
The solvent reaction field potential of an uncharged protein immersed in simple point charge/extended explicit solvent was computed over a series of molecular dynamics trajectories, in total 1560 ns of simulation time. A finite, positive potential of 13-24 kbTec(-1) (where T=300 K), dependent on the geometry of the solvent-accessible surface, was observed inside the biomolecule. The primary contribution to this potential arose from a layer of positive charge density 1.0 A from the solute surface, on average 0.008 ec/A3, which we found to be the product of a highly ordered first solvation shell. Significant second solvation shell effects, including additional layers of charge density and a slight decrease in the short-range solvent-solvent interaction strength, were also observed. The impact of these findings on implicit solvent models was assessed by running similar explicit solvent simulations on the fully charged protein system. When the energy due to the solvent reaction field in the uncharged system is accounted for, correlation between per-atom electrostatic energies for the explicit solvent model and a simple implicit (Poisson) calculation is 0.97, and correlation between per-atom energies for the explicit solvent model and a previously published, optimized Poisson model is 0.99.
Cerutti
David S
DS
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0365, USA. dcerutti@mccammon.ucsd.edu
Baker
Nathan A
NA
McCammon
J Andrew
JA
D002627:Chemistry, Physical / Q000379:methods; D003198:Computer Simulation; D008956:Models, Chemical; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D016012:Poisson Distribution; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry*; D055672:Static Electricity; D013997:Time Factors; D014867:Water / Q000737:chemistry
D011506:Proteins; D012997:Solvents; D014867:Water