Literature DB >> 17429993

Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations.

Jessica M J Swanson1, C Mark Maupin, Hanning Chen, Matt K Petersen, Jiancong Xu, Yujie Wu, Gregory A Voth.   

Abstract

The excess proton in aqueous media plays a pivotal role in many fundamental chemical (e.g., acid-base chemistry) and biological (e.g., bioenergetics and enzyme catalysis) processes. Understanding the hydrated proton is, therefore, crucial for chemistry, biology, and materials sciences. Although well studied for over 200 years, excess proton solvation and transport remains to this day mysterious, surprising, and perhaps even misunderstood. In this feature article, various efforts to address this problem through computer modeling and simulation will be described. Applications of computer simulations to a number of important and interesting systems will be presented, highlighting the roles of charge delocalization and Grotthuss shuttling, a phenomenon unique in many ways to the excess proton in water.

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Year:  2007        PMID: 17429993      PMCID: PMC2548316          DOI: 10.1021/jp070104x

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  102 in total

1.  Negligible effect of ions on the hydrogen-bond structure in liquid water.

Authors:  Anne Willem Omta; Michel F Kropman; Sander Woutersen; Huib J Bakker
Journal:  Science       Date:  2003-07-18       Impact factor: 47.728

Review 2.  Quantum-classical simulation methods for hydrogen transfer in enzymes: a case study of dihydrofolate reductase.

Authors:  Sharon Hammes-Schiffer
Journal:  Curr Opin Struct Biol       Date:  2004-04       Impact factor: 6.809

3.  A computational study of the closed and open states of the influenza a M2 proton channel.

Authors:  Yujie Wu; Gregory A Voth
Journal:  Biophys J       Date:  2005-07-22       Impact factor: 4.033

4.  Nuclear transport of influenza virus ribonucleoproteins: the viral matrix protein (M1) promotes export and inhibits import.

Authors:  K Martin; A Helenius
Journal:  Cell       Date:  1991-10-04       Impact factor: 41.582

5.  Evidence for an enhanced hydronium concentration at the liquid water surface.

Authors:  Poul B Petersen; Richard J Saykally
Journal:  J Phys Chem B       Date:  2005-04-28       Impact factor: 2.991

6.  DFT/electrostatic calculations of pK(a) values in cytochrome c oxidase.

Authors:  Dragan M Popović; Jason Quenneville; Alexei A Stuchebrukhov
Journal:  J Phys Chem B       Date:  2005-03-03       Impact factor: 2.991

Review 7.  Computer simulation of proton solvation and transport in aqueous and biomolecular systems.

Authors:  Gregory A Voth
Journal:  Acc Chem Res       Date:  2006-02       Impact factor: 22.384

8.  Ab initio molecular dynamics simulation of the structure and proton transport dynamics of methanol-water solutions.

Authors:  Joseph A Morrone; Kiryn E Haslinger; Mark E Tuckerman
Journal:  J Phys Chem B       Date:  2006-03-02       Impact factor: 2.991

9.  Structure of native and apo carbonic anhydrase II and structure of some of its anion-ligand complexes.

Authors:  K Håkansson; M Carlsson; L A Svensson; A Liljas
Journal:  J Mol Biol       Date:  1992-10-20       Impact factor: 5.469

10.  Molecular dynamics simulations of human carbonic anhydrase II: insight into experimental results and the role of solvation.

Authors:  D Lu; G A Voth
Journal:  Proteins       Date:  1998-10-01
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  64 in total

Review 1.  Solid-state 2H NMR spectroscopy of retinal proteins in aligned membranes.

Authors:  Michael F Brown; Maarten P Heyn; Constantin Job; Suhkmann Kim; Stephan Moltke; Koji Nakanishi; Alexander A Nevzorov; Andrey V Struts; Gilmar F J Salgado; Ingrid Wallat
Journal:  Biochim Biophys Acta       Date:  2007-10-23

2.  Modeling negative ion defect migration through the gramicidin A channel.

Authors:  Alexander V Nemukhin; Ilya A Kaliman; Alexander A Moskovsky
Journal:  J Mol Model       Date:  2009-02-07       Impact factor: 1.810

3.  Introducing titratable water to all-atom molecular dynamics at constant pH.

Authors:  Wei Chen; Jason A Wallace; Zhi Yue; Jana K Shen
Journal:  Biophys J       Date:  2013-08-20       Impact factor: 4.033

4.  Density functional tight binding: values of semi-empirical methods in an ab initio era.

Authors:  Qiang Cui; Marcus Elstner
Journal:  Phys Chem Chem Phys       Date:  2014-07-28       Impact factor: 3.676

Review 5.  Theory of coupled electron and proton transfer reactions.

Authors:  Sharon Hammes-Schiffer; Alexei A Stuchebrukhov
Journal:  Chem Rev       Date:  2010-11-04       Impact factor: 60.622

Review 6.  Uncovering channels in photosystem II by computer modelling: current progress, future prospects, and lessons from analogous systems.

Authors:  Felix M Ho
Journal:  Photosynth Res       Date:  2008-09-17       Impact factor: 3.573

7.  A theory for the proton transport of the influenza virus M2 protein: extensive test against conductance data.

Authors:  Huan-Xiang Zhou
Journal:  Biophys J       Date:  2011-02-16       Impact factor: 4.033

8.  Many-body energies during proton transfer in an aqueous system.

Authors:  Ajay Chaudhari; Gul Afroz Meraj; Shyi-Long Lee
Journal:  J Mol Model       Date:  2010-02-27       Impact factor: 1.810

9.  Redox-coupled proton pumping in cytochrome c oxidase: further insights from computer simulation.

Authors:  Jiancong Xu; Gregory A Voth
Journal:  Biochim Biophys Acta       Date:  2007-12-04

10.  Origins of enhanced proton transport in the Y7F mutant of human carbonic anhydrase II.

Authors:  C Mark Maupin; Marissa G Saunders; Ian F Thorpe; Robert McKenna; David N Silverman; Gregory A Voth
Journal:  J Am Chem Soc       Date:  2008-07-31       Impact factor: 15.419

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