Literature DB >> 18678891

Influence of nonlinear electrostatics on transfer energies between liquid phases: charge burial is far less expensive than Born model.

Haipeng Gong1, Glen Hocky, Karl F Freed.   

Abstract

The widely used Born model describes the electrostatic response of continuous media using static dielectric constants. However, when applied to a liquid environment, a comparison of Born model predictions with experimental values (e.g., transfer free energies and pK(a) shifts) found that agreement is only achieved by using physically unrealistic dielectric constants for proteins, lipids, etc., and/or equally unrealistic atomic radii. This leads to questions concerning the physical origins for this failure of the Born model. We partially resolve this question by applying the Langevin-Debye (LD) model of a continuous distribution of point, polarizable dipoles, a model that contains an added dependence of the electrostatic response on the solvent's optical dielectric constant and both gas- and liquid-phase dipole moments, features absent in the Born model to which the LD model reduces for weak fields. The LD model is applied to simple representations of three biologically relevant systems: (i) globular proteins, (ii) lipid bilayers, and (iii) membrane proteins. The linear Born treatment greatly overestimates both the self-energy and the transfer free energy from water to hydrophobic environments (e.g., a protein interior). By using the experimental dielectric constant, the energy cost of charge burial in either globular or membrane proteins of the Born model is reduced by almost 50% with the nonlinear theory as is the pK(a) shift, and the shifts agree well with experimental trends.

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Year:  2008        PMID: 18678891      PMCID: PMC2516240          DOI: 10.1073/pnas.0804506105

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  18 in total

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Authors:  L Sandberg; O Edholm
Journal:  Proteins       Date:  1999-09-01

Review 2.  What are the dielectric "constants" of proteins and how to validate electrostatic models?

Authors:  C N Schutz; A Warshel
Journal:  Proteins       Date:  2001-09-01

3.  Building native protein conformation from highly approximate backbone torsion angles.

Authors:  Haipeng Gong; Patrick J Fleming; George D Rose
Journal:  Proc Natl Acad Sci U S A       Date:  2005-10-26       Impact factor: 11.205

4.  Liquid-structure forces and electrostatic modulation of biomolecular interactions in solution.

Authors:  Sergio A Hassan
Journal:  J Phys Chem B       Date:  2007-01-11       Impact factor: 2.991

Review 5.  Modeling electrostatic effects in proteins.

Authors:  Arieh Warshel; Pankaz K Sharma; Mitsunori Kato; William W Parson
Journal:  Biochim Biophys Acta       Date:  2006-08-25

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Authors:  S Bone; R Pethig
Journal:  J Mol Biol       Date:  1985-01-20       Impact factor: 5.469

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Authors:  M K Gilson; B H Honig
Journal:  Biopolymers       Date:  1986-11       Impact factor: 2.505

8.  Dielectric studies of the binding of water to lysozyme.

Authors:  S Bone; R Pethig
Journal:  J Mol Biol       Date:  1982-05-25       Impact factor: 5.469

9.  High apparent dielectric constants in the interior of a protein reflect water penetration.

Authors:  J J Dwyer; A G Gittis; D A Karp; E E Lattman; D S Spencer; W E Stites; B García-Moreno E
Journal:  Biophys J       Date:  2000-09       Impact factor: 4.033

10.  Solvation effect on conformations of 1,2:dimethoxyethane: charge-dependent nonlinear response in implicit solvent models.

Authors:  Abhishek K Jha; Karl F Freed
Journal:  J Chem Phys       Date:  2008-01-21       Impact factor: 3.488

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  20 in total

1.  Histidine in continuum electrostatics protonation state calculations.

Authors:  Vernon Couch; Alexei Stuchebrukhov
Journal:  Proteins       Date:  2011-08-30

2.  Nonlocal Electrostatics in Spherical Geometries Using Eigenfunction Expansions of Boundary-Integral Operators.

Authors:  Jaydeep P Bardhan; Matthew G Knepley; Peter Brune
Journal:  Mol Based Math Biol       Date:  2015-01

3.  Water-exclusion and liquid-structure forces in implicit solvation.

Authors:  Sergio A Hassan; Peter J Steinbach
Journal:  J Phys Chem B       Date:  2011-11-15       Impact factor: 2.991

4.  Hydrophobe-water interactions: methane as a model.

Authors:  F Despa; R S Berry
Journal:  Biophys J       Date:  2008-08-01       Impact factor: 4.033

5.  A novel implicit solvent model for simulating the molecular dynamics of RNA.

Authors:  Yufeng Liu; Esmael Haddadian; Tobin R Sosnick; Karl F Freed; Haipeng Gong
Journal:  Biophys J       Date:  2013-09-03       Impact factor: 4.033

6.  Electrostatic solvation energy for two oppositely charged ions in a solvated protein system: salt bridges can stabilize proteins.

Authors:  Haipeng Gong; Karl F Freed
Journal:  Biophys J       Date:  2010-02-03       Impact factor: 4.033

7.  Ionic strength independence of charge distributions in solvation of biomolecules.

Authors:  J J Virtanen; T R Sosnick; K F Freed
Journal:  J Chem Phys       Date:  2014-12-14       Impact factor: 3.488

8.  A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations.

Authors:  Zongan Wang; John M Jumper; Sheng Wang; Karl F Freed; Tobin R Sosnick
Journal:  Biophys J       Date:  2018-10-23       Impact factor: 4.033

9.  Quantum cluster size and solvent polarity effects on the geometries and Mössbauer properties of the active site model for ribonucleotide reductase intermediate X: a density functional theory study.

Authors:  Wen-Ge Han; Louis Noodleman
Journal:  Theor Chem Acc       Date:  2010-03       Impact factor: 1.702

10.  Communication: modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions.

Authors:  Jaydeep P Bardhan; Matthew G Knepley
Journal:  J Chem Phys       Date:  2014-10-07       Impact factor: 3.488

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