Literature DB >> 7479686

A simple algorithm for the calculation of multiple site titration curves.

A Karshikoff1.   

Abstract

A simple algorithm for the calculation of multiple site titration curves is proposed. It is based on a hybridization of two computational techniques: (i) a modified Tanford-Roxby iterative procedure [Tanford and Roxby (1972) Biochemistry, 11, 2193-2198] and (ii) the Boltzmann statistics. The sites characterized by strong electrostatic coupling were selected for statistical mechanical treatment, whereas all other sites were treated by means of the modified Tanford-Roxby procedure. The selection of the two sets was made on the basis of a criterion related to the interaction energy between the titratable sites in the protein molecule. The algorithm was tested for bovine pancreatic trypsin inhibitor and the pK values calculated were discussed in the light of experimental data and theoretical results obtained by other authors. The algorithm can easily be coded and incorporated into any program package for the calculation of electrostatic interactions in proteins.

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Year:  1995        PMID: 7479686     DOI: 10.1093/protein/8.3.243

Source DB:  PubMed          Journal:  Protein Eng        ISSN: 0269-2139


  13 in total

1.  On the evaluation and optimization of protein X-ray structures for pKa calculations.

Authors:  Jens Erik Nielsen; J Andrew McCammon
Journal:  Protein Sci       Date:  2003-02       Impact factor: 6.725

2.  Improved 3D continuum calculations of ion flux through membrane channels.

Authors:  Assen Koumanov; Ulrich Zachariae; Harald Engelhardt; Andrey Karshikoff
Journal:  Eur Biophys J       Date:  2003-07-18       Impact factor: 1.733

3.  Calculating pKa values in enzyme active sites.

Authors:  Jens Erik Nielsen; J Andrew McCammon
Journal:  Protein Sci       Date:  2003-09       Impact factor: 6.725

Review 4.  Progress in the prediction of pKa values in proteins.

Authors:  Emil Alexov; Ernest L Mehler; Nathan Baker; António M Baptista; Yong Huang; Francesca Milletti; Jens Erik Nielsen; Damien Farrell; Tommy Carstensen; Mats H M Olsson; Jana K Shen; Jim Warwicker; Sarah Williams; J Michael Word
Journal:  Proteins       Date:  2011-10-15

5.  Redesigning protein pKa values.

Authors:  Barbara Mary Tynan-Connolly; Jens Erik Nielsen
Journal:  Protein Sci       Date:  2006-12-22       Impact factor: 6.725

6.  Protein dielectric constants determined from NMR chemical shift perturbations.

Authors:  Predrag Kukic; Damien Farrell; Lawrence P McIntosh; Bertrand García-Moreno E; Kristine Steen Jensen; Zigmantas Toleikis; Kaare Teilum; Jens Erik Nielsen
Journal:  J Am Chem Soc       Date:  2013-10-31       Impact factor: 15.419

7.  Optimization of the electrostatic interactions between ionized groups and peptide dipoles in proteins.

Authors:  V Z Spassov; R Ladenstein; A D Karshikoff
Journal:  Protein Sci       Date:  1997-06       Impact factor: 6.725

8.  Electrostatic properties of the anion selective porin Omp32 from Delftia acidovorans and of the arginine cluster of bacterial porins.

Authors:  Ulrich Zachariae; Assen Koumanov; Harald Engelhardt; Andrey Karshikoff
Journal:  Protein Sci       Date:  2002-06       Impact factor: 6.725

9.  Explicit solvent models in protein pKa calculations.

Authors:  C J Gibas; S Subramaniam
Journal:  Biophys J       Date:  1996-07       Impact factor: 4.033

10.  Ionization states of residues in OmpF and mutants: effects of dielectric constant and interactions between residues.

Authors:  Sameer Varma; Eric Jakobsson
Journal:  Biophys J       Date:  2004-02       Impact factor: 4.033

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