ArticleThe Journal of chemical physics2007
Solvent reaction field potential inside an uncharged globular protein: a bridge between implicit and explicit solvent models?
Article in The Journal of chemical physics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Electrostatic solvation and mobility in uniform and non-uniform electric fields: From simple ions to proteins.Biomicrofluidics · 2019Article
- Incorporating excluded solvent volume and physical dipoles for computing solvation free energy.Journal of molecular modeling · 2015Article
- Ionic strength independence of charge distributions in solvation of biomolecules.The Journal of chemical physics · 2014Article
- Effect of the Reaction Field on Molecular Forces and Torques Revealed by an Image-Charge Solvation Model.Communications in computational physics · 2013Article
- Biomolecular electrostatics and solvation: a computational perspective.Quarterly reviews of biophysics · 2012Review
- Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies.The Journal of chemical physics · 2012Article
- Predicting hydration free energies of polychlorinated aromatic compounds from the SAMPL-3 data set with FiSH and LIE models.Journal of computer-aided molecular design · 2012Article
- Alchemical prediction of hydration free energies for SAMPL.Journal of computer-aided molecular design · 2012Article
- Differential geometry based solvation model II: Lagrangian formulation.Journal of mathematical biology · 2011Article
- Dielectric Boundary Forces in Numerical Poisson-Boltzmann Methods: Theory and Numerical Strategies.Chemical physics letters · 2011Article
- Differential geometry based solvation model I: Eulerian formulation.Journal of computational physics · 2010Article
- Differential geometry based multiscale models.Bulletin of mathematical biology · 2010Article
- Geometric and potential driving formation and evolution of biomolecular surfaces.Journal of mathematical biology · 2009Article
- On the origin of the electrostatic potential difference at a liquid-vacuum interface.The Journal of chemical physics · 2008Article
- Simulations of a protein crystal: explicit treatment of crystallization conditions links theory and experiment in the streptavidin-biotin complex.Biochemistry · 2008Article
- Assessing the performance of implicit solvation models at a nucleic acid surface.Physical chemistry chemical physics : PCCP · 2008Article
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Authors and funding
3 authors.
Funding
Abstract
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.
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