Literature DB >> 21765968

Fast Calculations of Electrostatic Solvation Free Energy from Reconstructed Solvent Density using proximal Radial Distribution Functions.

Bin Lin1, Ka-Yiu Wong, Char Hu, Hironori Kokubo, B Montgomery Pettitt.   

Abstract

Although detailed atomic models may be applied for a full description of solvation, simpler phenomenological models are particularly useful to interpret the results for scanning many, large, complex systems where a full atomic model is too computationally expensive to use. Among the most costly are solvation free energy evaluations by simulation. Here we develop a fast way to calculate electrostatic solvation free energy while retaining much of the accuracy of explicit solvent free energy simulation. The basis of our method is to treat the solvent not as a structureless dielectric continuum, but as a structured medium by making use of universal proximal radial distribution functions. Using a deca-alanine peptide as a test case, we compare the use of our theory with free energy simulations and traditional continuum estimates of the electrostatic solvation free energy.

Entities:  

Year:  2011        PMID: 21765968      PMCID: PMC3134239          DOI: 10.1021/jz200609v

Source DB:  PubMed          Journal:  J Phys Chem Lett        ISSN: 1948-7185            Impact factor:   6.475


  30 in total

1.  Electrostatics of nanosystems: application to microtubules and the ribosome.

Authors:  N A Baker; D Sept; S Joseph; M J Holst; J A McCammon
Journal:  Proc Natl Acad Sci U S A       Date:  2001-08-21       Impact factor: 11.205

Review 2.  Virtual screening of chemical libraries.

Authors:  Brian K Shoichet
Journal:  Nature       Date:  2004-12-16       Impact factor: 49.962

3.  Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.

Authors:  Michael R Shirts; Vijay S Pande
Journal:  J Chem Phys       Date:  2005-04-01       Impact factor: 3.488

4.  Note: On the universality of proximal radial distribution functions of proteins.

Authors:  Bin Lin; B Montgomery Pettitt
Journal:  J Chem Phys       Date:  2011-03-14       Impact factor: 3.488

5.  Conformational studies of poly-L-alanine in water.

Authors:  R T Ingwall; H A Scheraga; N Lotan; A Berger; E Katchalski
Journal:  Biopolymers       Date:  1968       Impact factor: 2.505

6.  A global model of the protein-solvent interface.

Authors:  V Lounnas; B M Pettitt; G N Phillips
Journal:  Biophys J       Date:  1994-03       Impact factor: 4.033

7.  Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics (FEP/REMD).

Authors:  Wei Jiang; Milan Hodoscek; Benoît Roux
Journal:  J Chem Theory Comput       Date:  2009-10-01       Impact factor: 6.006

8.  Backbone additivity in the transfer model of protein solvation.

Authors:  Char Y Hu; Hironori Kokubo; Gillian C Lynch; D Wayne Bolen; B Montgomery Pettitt
Journal:  Protein Sci       Date:  2010-05       Impact factor: 6.725

9.  Tetracycline-tet repressor binding specificity: insights from experiments and simulations.

Authors:  Alexey Aleksandrov; Linda Schuldt; Winfried Hinrichs; Thomas Simonson
Journal:  Biophys J       Date:  2009-11-18       Impact factor: 4.033

10.  Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions.

Authors:  A Chakrabartty; T Kortemme; R L Baldwin
Journal:  Protein Sci       Date:  1994-05       Impact factor: 6.725

View more
  14 in total

1.  Proximal distributions from angular correlations: a measure of the onset of coarse-graining.

Authors:  Kippi M Dyer; B Montgomery Pettitt
Journal:  J Chem Phys       Date:  2013-12-07       Impact factor: 3.488

2.  Polymorphic Protein Crystal Growth: Influence of Hydration and Ions in Glucose Isomerase.

Authors:  C M Gillespie; D Asthagiri; A M Lenhoff
Journal:  Cryst Growth Des       Date:  2014-01-02       Impact factor: 4.076

3.  Solvation and cavity occupation in biomolecules.

Authors:  Gillian C Lynch; John S Perkyns; Bao Linh Nguyen; B Montgomery Pettitt
Journal:  Biochim Biophys Acta       Date:  2014-09-28

4.  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

5.  Free Energy Calculations Based on Coupling Proximal Distribution Functions and Thermodynamic Cycles.

Authors:  Shu-Ching Ou; B Montgomery Pettitt
Journal:  J Chem Theory Comput       Date:  2019-03-06       Impact factor: 6.006

6.  Electrostatic contribution from solvent in modulating single-walled carbon nanotube association.

Authors:  Shu-Ching Ou; Sandeep Patel
Journal:  J Chem Phys       Date:  2014-09-21       Impact factor: 3.488

7.  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

8.  The contribution of electrostatic interactions to the collapse of oligoglycine in water.

Authors:  D Karandur; B M Pettitt
Journal:  Condens Matter Phys       Date:  2016       Impact factor: 1.128

9.  Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins.

Authors:  Bao Linh Nguyen; B Montgomery Pettitt
Journal:  J Chem Theory Comput       Date:  2015-04-14       Impact factor: 6.006

10.  Solute-Solvent Energetics Based on Proximal Distribution Functions.

Authors:  Shu-Ching Ou; B Montgomery Pettitt
Journal:  J Phys Chem B       Date:  2016-05-04       Impact factor: 2.991

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.