Literature DB >> 18205504

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

Abhishek K Jha1, Karl F Freed.   

Abstract

The physical content of and, in particular, the nonlinear contributions from the Langevin-Debye model are illustrated using two applications. First, we provide an improvement in the Langevin-Debye model currently used in some implicit solvent models for computer simulations of solvation free energies of small organic molecules, as well as of biomolecular folding and binding. The analysis is based on the implementation of a charge-dependent Langevin-Debye (qLD) model that is modified by subsequent corrections due to Onsager and Kirkwood. Second, the physical content of the model is elucidated by discussing the general treatment within the LD model of the self-energy of a charge submerged in a dielectric medium for three different limiting conditions and by considering the nonlinear response of the medium. The modified qLD model is used to refine an implicit solvent model (previously applied to protein dynamics). The predictions of the modified implicit solvent model are compared with those from explicit solvent molecular dynamics simulations for the equilibrium conformational populations of 1,2-dimethoxyethane (DME), which is the shortest ether molecule to reproduce the local conformational properties of polyethylene oxide, a polymer with tremendous technological importance and a wide variety of applications. Because the conformational population preferences of DME change dramatically upon solvation, DME is a good test case to validate our modified qLD model. The present analysis of the modified qLD model provides the motivation and tools for studying a wide variety of other interesting systems with heterogeneous dielectric properties and spatial anisotropy.

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Year:  2008        PMID: 18205504      PMCID: PMC2717614          DOI: 10.1063/1.2815764

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  27 in total

1.  Effective energy function for proteins in solution.

Authors:  T Lazaridis; M Karplus
Journal:  Proteins       Date:  1999-05-01

Review 2.  Generalized born models of macromolecular solvation effects.

Authors:  D Bashford; D A Case
Journal:  Annu Rev Phys Chem       Date:  2000       Impact factor: 12.703

3.  Long time dynamics of Met-enkephalin: comparison of explicit and implicit solvent models.

Authors:  Min-yi Shen My; Karl F Freed
Journal:  Biophys J       Date:  2002-04       Impact factor: 4.033

4.  A critical analysis of continuum electrostatics: the screened Coulomb potential--implicit solvent model and the study of the alanine dipeptide and discrimination of misfolded structures of proteins.

Authors:  Sergio A Hassan; Ernest L Mehler
Journal:  Proteins       Date:  2002-04-01

5.  Distance and exposure dependent effective dielectric function.

Authors:  Buddhadeb Mallik; Artem Masunov; Themis Lazaridis
Journal:  J Comput Chem       Date:  2002-08       Impact factor: 3.376

6.  Kinetics of the coil-to-helix transition on a rough energy landscape.

Authors:  A Baumketner; J-E Shea
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2003-11-03

7.  Misfolded free energy surface of a peptide with alphabetabeta motif (1PSV) using the generalized Born solvation model.

Authors:  Youngshang Pak; Eunae Kim; Soonmin Jang
Journal:  J Chem Phys       Date:  2004-11-08       Impact factor: 3.488

Review 8.  Modeling protein folding: the beauty and power of simplicity.

Authors:  E I Shakhnovich
Journal:  Fold Des       Date:  1996

9.  Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides.

Authors:  T Ooi; M Oobatake; G Némethy; H A Scheraga
Journal:  Proc Natl Acad Sci U S A       Date:  1987-05       Impact factor: 11.205

10.  An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins.

Authors:  Wonpil Im; Michael Feig; Charles L Brooks
Journal:  Biophys J       Date:  2003-11       Impact factor: 4.033

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  11 in total

1.  Benchmarking implicit solvent folding simulations of the amyloid beta(10-35) fragment.

Authors:  Andrew Kent; Abhishek K Jha; James E Fitzgerald; Karl F Freed
Journal:  J Phys Chem B       Date:  2008-03-19       Impact factor: 2.991

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

Authors:  Haipeng Gong; Glen Hocky; Karl F Freed
Journal:  Proc Natl Acad Sci U S A       Date:  2008-08-04       Impact factor: 11.205

3.  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

4.  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

5.  Extended structures in RNA folding intermediates are due to nonnative interactions rather than electrostatic repulsion.

Authors:  Nathan J Baird; Haipeng Gong; Syed S Zaheer; Karl F Freed; Tao Pan; Tobin R Sosnick
Journal:  J Mol Biol       Date:  2010-02-23       Impact factor: 5.469

6.  Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations.

Authors:  Zhenli Xu; Wei Cai
Journal:  SIAM Rev Soc Ind Appl Math       Date:  2011-11-07       Impact factor: 10.780

7.  Image Charge Methods for a Three-Dielectric-Layer Hybrid Solvation Model of Biomolecules.

Authors:  Peihua Qin; Zhenli Xu; Wei Cai; Donald Jacobs
Journal:  Commun Comput Phys       Date:  2009-11       Impact factor: 3.246

8.  Computing ion solvation free energies using the dipolar Poisson model.

Authors:  Patrice Koehl; Henri Orland; Marc Delarue
Journal:  J Phys Chem B       Date:  2009-04-30       Impact factor: 2.991

9.  Quantifying the structural requirements of the folding transition state of protein A and other systems.

Authors:  Michael C Baxa; Karl F Freed; Tobin R Sosnick
Journal:  J Mol Biol       Date:  2008-07-01       Impact factor: 5.469

10.  Context and force field dependence of the loss of protein backbone entropy upon folding using realistic denatured and native state ensembles.

Authors:  Michael C Baxa; Esmael J Haddadian; Abhishek K Jha; Karl F Freed; Tobin R Sosnick
Journal:  J Am Chem Soc       Date:  2012-09-14       Impact factor: 15.419

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