Literature DB >> 19843443

On the utilization of energy minimization to the study of ion selectivity.

Haibo Yu, Benoît Roux.   

Abstract

The major pitfalls in studying ion selectivity in binding site models using energy minimization based methods are examined and discussed. It is shown that the properties derived from energy minimization are strongly configuration-dependent and that the results should be interpreted with caution. It is concluded that computational studies of ion selectivity must include thermal fluctuations and entropic effects.

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Year:  2009        PMID： 19843443      PMCID： PMC2764064          DOI： 10.1016/j.bpj.2009.08.005

Source DB:  PubMed          Journal:  Biophys J        ISSN： 0006-3495            Impact factor:   4.033


  17 in total

1.  Energetics of ion conduction through the K+ channel.

Authors:  S Bernèche; B Roux
Journal:  Nature       Date:  2001-11-01       Impact factor: 49.962

2.  On the potential functions used in molecular dynamics simulations of ion channels.

Authors:  Benoît Roux; Simon Bernèche
Journal:  Biophys J       Date:  2002-03       Impact factor: 4.033

Review 3.  Ion selectivity in potassium channels.

Authors:  Sergei Yu Noskov; Benoît Roux
Journal:  Biophys Chem       Date:  2006-06-18       Impact factor: 2.352

Review 4.  Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels.

Authors:  Sergei Yu Noskov; Benoît Roux
Journal:  J Gen Physiol       Date:  2007-01-16       Impact factor: 4.086

5.  The predominant role of coordination number in potassium channel selectivity.

Authors:  Michael Thomas; Dylan Jayatilaka; Ben Corry
Journal:  Biophys J       Date:  2007-06-15       Impact factor: 4.033

6.  Conformational changes in the selectivity filter of the open-state KcsA channel: an energy minimization study.

Authors:  Gennady V Miloshevsky; Peter C Jordan
Journal:  Biophys J       Date:  2008-07-11       Impact factor: 4.033

7.  Ion selectivity in the KcsA potassium channel from the perspective of the ion binding site.

Authors:  Purushottam D Dixit; Safir Merchant; D Asthagiri
Journal:  Biophys J       Date:  2009-03-18       Impact factor: 4.033

8.  Control of ion selectivity in LeuT: two Na+ binding sites with two different mechanisms.

Authors:  Sergei Y Noskov; Benoît Roux
Journal:  J Mol Biol       Date:  2008-01-15       Impact factor: 5.469

9.  All-atom empirical potential for molecular modeling and dynamics studies of proteins.

Authors:  A D MacKerell; D Bashford; M Bellott; R L Dunbrack; J D Evanseck; M J Field; S Fischer; J Gao; H Guo; S Ha; D Joseph-McCarthy; L Kuchnir; K Kuczera; F T Lau; C Mattos; S Michnick; T Ngo; D T Nguyen; B Prodhom; W E Reiher; B Roux; M Schlenkrich; J C Smith; R Stote; J Straub; M Watanabe; J Wiórkiewicz-Kuczera; D Yin; M Karplus
Journal:  J Phys Chem B       Date:  1998-04-30       Impact factor: 2.991

10.  Ionic selectivity in L-type calcium channels by electrostatics and hard-core repulsion.

Authors:  Dezso Boda; Mónika Valiskó; Douglas Henderson; Bob Eisenberg; Dirk Gillespie; Wolfgang Nonner
Journal:  J Gen Physiol       Date:  2009-05       Impact factor: 4.086
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  8 in total

1.  Exploring the ion selectivity properties of a large number of simplified binding site models.

Authors:  Benoît Roux
Journal:  Biophys J       Date:  2010-06-16       Impact factor: 4.033

2.  Assessing the accuracy of approximate treatments of ion hydration based on primitive quasichemical theory.

Authors:  Benoît Roux; Haibo Yu
Journal:  J Chem Phys       Date:  2010-06-21       Impact factor: 3.488

3.  Probing the thermodynamics of competitive ion binding using minimum energy structures.

Authors:  David M Rogers; Susan B Rempe
Journal:  J Phys Chem B       Date:  2011-07-01       Impact factor: 2.991

4.  Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field.

Authors:  Haibo Yu; Troy W Whitfield; Edward Harder; Guillaume Lamoureux; Igor Vorobyov; Victor M Anisimov; Alexander D Mackerell; Benoît Roux
Journal:  J Chem Theory Comput       Date:  2010       Impact factor: 6.006

5.  Selective complexation of K+ and Na+ in simple polarizable ion-ligating systems.

Authors:  David L Bostick; Charles L Brooks
Journal:  J Am Chem Soc       Date:  2010-09-29       Impact factor: 15.419

6.  Ion binding sites and their representations by reduced models.

Authors:  Benoît Roux
Journal:  J Phys Chem B       Date:  2012-04-30       Impact factor: 2.991

Review 7.  Ion selectivity in channels and transporters.

Authors:  Benoît Roux; Simon Bernèche; Bernhard Egwolf; Bogdan Lev; Sergei Y Noskov; Christopher N Rowley; Haibo Yu
Journal:  J Gen Physiol       Date:  2011-05       Impact factor: 4.086

8.  Perspectives on: ion selectivity: design principles for K+ selectivity in membrane transport.

Authors:  Sameer Varma; David M Rogers; Lawrence R Pratt; Susan B Rempe
Journal:  J Gen Physiol       Date:  2011-06       Impact factor: 4.086
  8 in total

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