Literature DB >> 11969577

Charge optimization leads to favorable electrostatic binding free energy.

E Kangas1, B Tidor.   

Abstract

Variational optimization of molecular electrostatic charge distributions is a tool for the study of association reactions of molecules in solution. In principle, this method can be used in drug design and protein folding to analyze and improve molecular interactions and to provide electrostatic templates for molecular design. This optimization problem reduces to an inverse source problem in classical electrostatics, where the sources are determined by a combination of external and self-polarization potentials. In this paper, we show that the electrostatic portion of the free energy of association for electrostatically optimized molecules has an upper bound of zero in many situations of physical interest. That is, variational optimization provides a ligand-charge distribution that contributes favorably to the energetics of binding, even in a strongly polar medium. This stabilizing effect on association reactions is contrary to the usual role of electrostatics in aqueous complexes, in which desolvation effects generally dominate. We also show the existence and nonuniqueness of the variational solution and make a connection to the electrostatic image charge problem.

Mesh:

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Year:  1999        PMID: 11969577     DOI: 10.1103/physreve.59.5958

Source DB:  PubMed          Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics        ISSN: 1063-651X


  18 in total

1.  Optimization of binding electrostatics: charge complementarity in the barnase-barstar protein complex.

Authors:  L P Lee; B Tidor
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2.  Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase.

Authors:  Aaron T Fafarman; Paul A Sigala; Jason P Schwans; Timothy D Fenn; Daniel Herschlag; Steven G Boxer
Journal:  Proc Natl Acad Sci U S A       Date:  2012-01-17       Impact factor: 11.205

3.  Electrostatic properties of protein-protein complexes.

Authors:  Petras J Kundrotas; Emil Alexov
Journal:  Biophys J       Date:  2006-06-16       Impact factor: 4.033

4.  Electrostatic evaluation of isosteric analogues.

Authors:  Roger Sayle; Anthony Nicholls
Journal:  J Comput Aided Mol Des       Date:  2006-07-15       Impact factor: 3.686

5.  Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease.

Authors:  Michael D Altman; Ellen A Nalivaika; Moses Prabu-Jeyabalan; Celia A Schiffer; Bruce Tidor
Journal:  Proteins       Date:  2008-02-15

6.  Optimal drug cocktail design: methods for targeting molecular ensembles and insights from theoretical model systems.

Authors:  Mala L Radhakrishnan; Bruce Tidor
Journal:  J Chem Inf Model       Date:  2008-05-27       Impact factor: 4.956

7.  HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants.

Authors:  Michael D Altman; Akbar Ali; G S Kiran Kumar Reddy; Madhavi N L Nalam; Saima Ghafoor Anjum; Hong Cao; Sripriya Chellappan; Visvaldas Kairys; Miguel X Fernandes; Michael K Gilson; Celia A Schiffer; Tariq M Rana; Bruce Tidor
Journal:  J Am Chem Soc       Date:  2008-04-16       Impact factor: 15.419

8.  Novel method for probing the specificity binding profile of ligands: applications to HIV protease.

Authors:  Woody Sherman; Bruce Tidor
Journal:  Chem Biol Drug Des       Date:  2008-03-31       Impact factor: 2.817

9.  A "Reverse-Schur" Approach to Optimization With Linear PDE Constraints: Application to Biomolecule Analysis and Design.

Authors:  Jaydeep P Bardhan; Michael D Altman; B Tidor; Jacob K White
Journal:  J Chem Theory Comput       Date:  2009       Impact factor: 6.006

10.  Proteomic identification of 14-3-3zeta as a mitogen-activated protein kinase-activated protein kinase 2 substrate: role in dimer formation and ligand binding.

Authors:  David W Powell; Madhavi J Rane; Brian A Joughin; Ralitsa Kalmukova; Jeong-Ho Hong; Bruce Tidor; William L Dean; William M Pierce; Jon B Klein; Michael B Yaffe; Kenneth R McLeish
Journal:  Mol Cell Biol       Date:  2003-08       Impact factor: 4.272

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