Literature DB >> 11420443

A critical investigation of the Tanford-Kirkwood scheme by means of Monte Carlo simulations.

F L Da Silva1, B Jönsson, R Penfold.   

Abstract

Monte Carlo simulations are used to assess the adequacy of the Tanford-Kirkwood prescription for electrostatic interactions in macromolecules. Within a continuum dielectric framework, the approach accurately describes salt screening of electrostatic interactions for moderately charged systems consistent with common proteins at physiological conditions. The limitations of the Debye-Hückel theory, which forms the statistical mechanical basis for the Tanford-Kirkwood result, become apparent for highly charged systems. It is shown, both by an analysis of the Debye-Hückel theory and by numerical simulations, that the difference in dielectric permittivity between macromolecule and surrounding solvent does not play a significant role for salt effects if the macromolecule is highly charged. By comparison to experimental data, the continuum dielectric model (combined with either an approximate effective Hamiltonian as in the Tanford-Kirkwood treatment or with exact Monte Carlo simulations) satisfactorily predicts the effects of charge mutation on metal ion binding constants, but only if the macromolecule and solvent are assigned the same or similar permittivities.

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Year:  2001        PMID: 11420443      PMCID: PMC2374116          DOI: 10.1110/ps.42601

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  28 in total

1.  pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model.

Authors:  D Bashford; M Karplus
Journal:  Biochemistry       Date:  1990-11-06       Impact factor: 3.162

2.  Simplified methods for pKa and acid pH-dependent stability estimation in proteins: removing dielectric and counterion boundaries.

Authors:  J Warwicker
Journal:  Protein Sci       Date:  1999-02       Impact factor: 6.725

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Authors:  M Fushiki; B Svensson; B Jönsson; C E Woodward
Journal:  Biopolymers       Date:  1991-09       Impact factor: 2.505

4.  Electrostatic coupling to pH-titrating sites as a source of cooperativity in protein-ligand binding.

Authors:  V Spassov; D Bashford
Journal:  Protein Sci       Date:  1998-09       Impact factor: 6.725

5.  Calculation of the dielectric properties of a protein and its solvent: theory and a case study.

Authors:  G Löffler; H Schreiber; O Steinhauser
Journal:  J Mol Biol       Date:  1997-07-18       Impact factor: 5.469

6.  Electrostatic effects in myoglobin. Hydrogen ion equilibria in sperm whale ferrimyoglobin.

Authors:  S J Shire; G I Hanania; F R Gurd
Journal:  Biochemistry       Date:  1974-07-02       Impact factor: 3.162

7.  Interpretation of protein titration curves. Application to lysozyme.

Authors:  C Tanford; R Roxby
Journal:  Biochemistry       Date:  1972-05-23       Impact factor: 3.162

Review 8.  Classical electrostatics in biology and chemistry.

Authors:  B Honig; A Nicholls
Journal:  Science       Date:  1995-05-26       Impact factor: 47.728

9.  Calculation of the electric potential in the active site cleft due to alpha-helix dipoles.

Authors:  J Warwicker; H C Watson
Journal:  J Mol Biol       Date:  1982-06-05       Impact factor: 5.469

10.  Macroscopic models for studies of electrostatic interactions in proteins: limitations and applicability.

Authors:  A Warshel; S T Russell; A K Churg
Journal:  Proc Natl Acad Sci U S A       Date:  1984-08       Impact factor: 11.205

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  8 in total

1.  Calculating pH-dependent free energy of proteins by using Monte Carlo protonation probabilities of ionizable residues.

Authors:  Qiang Huang; Andreas Herrmann
Journal:  Protein Cell       Date:  2012-03-31       Impact factor: 14.870

2.  Coarse-grained dynamic RNA titration simulations.

Authors:  S Pasquali; E Frezza; F L Barroso da Silva
Journal:  Interface Focus       Date:  2019-04-19       Impact factor: 3.906

3.  pH Dependence of Charge Multipole Moments in Proteins.

Authors:  Anže Lošdorfer Božič; Rudolf Podgornik
Journal:  Biophys J       Date:  2017-10-03       Impact factor: 4.033

Review 4.  Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems.

Authors:  Fernando Luís Barroso daSilva; Luis Gustavo Dias
Journal:  Biophys Rev       Date:  2017-09-18

5.  Effects of pH and Salt Concentration on Stability of a Protein G Variant Using Coarse-Grained Models.

Authors:  Vinícius Martins de Oliveira; Vinícius de Godoi Contessoto; Fernando Bruno da Silva; Daniel Lucas Zago Caetano; Sidney Jurado de Carvalho; Vitor Barbanti Pereira Leite
Journal:  Biophys J       Date:  2018-01-09       Impact factor: 4.033

6.  The Role of Electrostatics and Folding Kinetics on the Thermostability of Homologous Cold Shock Proteins.

Authors:  Paulo Henrique Borges Ferreira; Frederico Campos Freitas; Michelle E McCully; Gabriel Gouvêa Slade; Ronaldo Junio de Oliveira
Journal:  J Chem Inf Model       Date:  2020-01-17       Impact factor: 4.956

7.  Salt enhances calmodulin-target interaction.

Authors:  Ingemar André; Tõnu Kesvatera; Bo Jönsson; Sara Linse
Journal:  Biophys J       Date:  2006-01-20       Impact factor: 4.033

8.  Sulfate anion stabilization of native ribonuclease A both by anion binding and by the Hofmeister effect.

Authors:  Carlos H I Ramos; Robert L Baldwin
Journal:  Protein Sci       Date:  2002-07       Impact factor: 6.725

  8 in total

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