"Solvent hydrogen-bond occlusion": A new model of polar desolvation for biomolecular energetics.
Water engages in two important types of interactions near biomolecules: it forms ordered "cages" around exposed hydrophobic regions, and it participates in hydrogen bonds with surface polar groups. Both types of interaction are critical to biomolecular structure and function, but explicitly including an appropriate number of solvent molecules makes many applications computationally intractable. A number of implicit solvent models have been developed to address this problem, many of which treat these two solvation effects separately. Here, we describe a new model to capture polar solvation effects, called SHO ("solvent hydrogen-bond occlusion"); our model aims to directly evaluate the energetic penalty associated with displacing discrete first-shell water molecules near each solute polar group. We have incorporated SHO into the Rosetta energy function, and find that scoring protein structures with SHO provides superior performance in loop modeling, virtual screening, and protein structure prediction benchmarks. These improvements stem from the fact that SHO accurately identifies and penalizes polar groups that do not participate in hydrogen bonds, either with solvent or with other solute atoms ("unsatisfied" polar groups). We expect that in future, SHO will enable higher-resolution predictions for a variety of molecular modeling applications. © 2017 Wiley Periodicals, Inc.
Center for Computational Biology, University of Kansas, 2030 Becker Dr, Lawrence, Kansas, 66045-7534.|Computational Chemical Biology Core, University of Kansas, 2030 Becker Dr, Lawrence, Kansas, 66045-7534.
Andrea
A
Bazzoli
Center for Computational Biology, University of Kansas, 2030 Becker Dr, Lawrence, Kansas, 66045-7534.|Department of Molecular Biosciences, University of Kansas, 2030 Becker Dr, Lawrence, Kansas, 66045-7534.|Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania, 19111-2497.
John
0000-0003-0300-726X
J
Karanicolas
D006859:Hydrogen / Q000737:chemistry*; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012996:Solutions / Q000737:chemistry; D012997:Solvents / Q000737:chemistry*; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D011506:Proteins; D012996:Solutions; D012997:Solvents; D014867:Water; D006859:Hydrogen
Rosetta energy function; hydration thermodynamics; implicit solvation