Literature DB >> 22072521

Histidine in continuum electrostatics protonation state calculations.

Vernon Couch1, Alexei Stuchebrukhov.   

Abstract

A modification to the standard continuum electrostatics approach to calculate protein pK(a)s, which allows for the decoupling of histidine tautomers within a two-state model, is presented. Histidine with four intrinsically coupled protonation states cannot be easily incorporated into a two-state formalism, because the interaction between the two protonatable sites of the imidazole ring is not purely electrostatic. The presented treatment, based on a single approximation of the interrelation between histidine's charge states, allows for a natural separation of the two protonatable sites associated with the imidazole ring as well as the inclusion of all protonation states within the calculation.
Copyright © 2011 Wiley-Liss, Inc.

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Year:  2011        PMID: 22072521      PMCID: PMC4229071          DOI: 10.1002/prot.23114

Source DB:  PubMed          Journal:  Proteins        ISSN: 0887-3585


  46 in total

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Journal:  Eur Biophys J       Date:  1999       Impact factor: 1.733

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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

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

4.  Optimizing pKa computation in proteins with pH adapted conformations.

Authors:  Gernot Kieseritzky; Ernst-Walter Knapp
Journal:  Proteins       Date:  2008-05-15

5.  Electrostatic interactions between FeS clusters in NADH:ubiquinone oxidoreductase (Complex I) from Escherichia coli.

Authors:  Liliya Euro; Dmitry A Bloch; Mårten Wikström; Michael I Verkhovsky; Marina Verkhovskaya
Journal:  Biochemistry       Date:  2008-02-13       Impact factor: 3.162

6.  Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility.

Authors:  T J You; D Bashford
Journal:  Biophys J       Date:  1995-11       Impact factor: 4.033

7.  CuZn Superoxide Dismutase Geometry Optimization, Energetics, and Redox Potential Calculations by Density Functional and Electrostatic Methods.

Authors:  Robert Konecny; Jian Li; Cindy L. Fisher; Valerie Dillet; Donald Bashford; Louis Noodleman
Journal:  Inorg Chem       Date:  1999-03-08       Impact factor: 5.165

8.  Electrostatics of the FeS clusters in respiratory complex I.

Authors:  Vernon A Couch; Emile S Medvedev; Alexei A Stuchebrukhov
Journal:  Biochim Biophys Acta       Date:  2009-05-13

9.  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

10.  Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus.

Authors:  Leonid A Sazanov; Philip Hinchliffe
Journal:  Science       Date:  2006-02-09       Impact factor: 47.728

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  4 in total

Review 1.  The pKa Cooperative: a collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins.

Authors:  Jens E Nielsen; M R Gunner; Bertrand E García-Moreno
Journal:  Proteins       Date:  2011-10-15

Review 2.  Proteins as strongly correlated protonic systems.

Authors:  Vernon Couch; Alexei Stuchebrukhov
Journal:  FEBS Lett       Date:  2011-10-05       Impact factor: 4.124

3.  Energy Minimization of Discrete Protein Titration State Models Using Graph Theory.

Authors:  Emilie Purvine; Kyle Monson; Elizabeth Jurrus; Keith Star; Nathan A Baker
Journal:  J Phys Chem B       Date:  2016-05-03       Impact factor: 2.991

4.  A comprehensive analysis of the computed tautomer fractions of the imidazole ring of histidines in Loligo vulgaris.

Authors:  Yury N Vorobjev; Harold A Scheraga; Jorge A Vila
Journal:  J Biomol Struct Dyn       Date:  2017-09-25
  4 in total

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