Assessing the performance of implicit solvation models at a nucleic acid surface.
Implicit solvation models are popular alternatives to explicit solvent methods due to their ability to "pre-average" solvent behavior and thus reduce the need for computationally-expensive sampling. Previously, we have demonstrated that Poisson-Boltzmann models for polar solvation and integral-based models for nonpolar solvation can reproduce explicit solvation forces in a low-charge density protein system. In the present work, we examine the ability of these continuum models to describe solvation forces at the surface of a RNA hairpin. While these models do not completely describe all of the details of solvent behavior at this highly-charged biomolecular interface, they do provide a reasonable description of average solvation forces and therefore show significant promise for developing more robust implicit descriptions of solvent around nucleic acid systems for use in biomolecular simulation and modeling. Additionally, we observe fairly good transferability in the nonpolar model parameters optimized for protein systems, suggesting its robustness for modeling general nonpolar solvation phenomena in biomolecular systems.
Dong
Feng
F
Merck & Co. Inc., 770 Sumneytown Pike, West Point, PA 19486, USA. feng_dong@merck.com
Wagoner
Jason A
JA
Baker
Nathan A
NA
D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry
D012997:Solvents; D012313:RNA