What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules.
We have developed a version of our surface generalized Born (SGB) model that employs a Gaussian surface, as opposed to the van der Waals surface used previously. The Gaussian surface is smooth and its properties are analytically differentiable with respect to the positions of atoms. A significant advantage of a solvent model based on this analytically differentiable surface is the availability of analytical gradients of the surface and solvation forces. An efficient and robust algorithm is designed to construct and triangulate the Gaussian surface for large biomolecules with arbitrary shapes, and to compute the various terms required for energy gradients. The Gaussian surface is shown to better mimic the boundary between the solute and solvent by properly addressing solvent accessibility, as is demonstrated by comparisons with standard Poisson-Boltzmann calculations for proteins of different sizes. These results also demonstrate that surface definition is a dominant contribution to differences between GB and PB calculations, especially if the system is large. Application of the new surface to prediction of long loop regions is presented, and significant improvement in the energetics is seen compared with results obtained using the van der Waals surface, even in the absence of optimized empirical correction terms that were used in the latter calculations.
Yu
Zhiyun
Z
Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, NY 10027, USA.
Jacobson
Matthew P
MP
Friesner
Richard A
RA
D000465:Algorithms; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012997:Solvents; D055672:Static Electricity
D011506:Proteins; D012997:Solvents