@article {539, title = {Enhancement of Proton Conductance by Mutations of the Selectivity Filter of Aquaporin-1}, journal = {J. Mol. Biol.}, volume = {407}, year = {2011}, pages = {607{\textendash}620}, doi = {10.1016/j.jmb.2011.01.036}, author = {Li, H. and Chen, H. and Zeuthen, T. and Conrad, C. and Wu, B. and Beitz, E. and G. A. Voth} } @article {423, title = {An Efficient Multi-State Reactive Molecular Dynamics Approach Based on Short-Ranged Effective Potentials}, journal = {J. Chem. Theor. Comp.}, volume = {6}, year = {2010}, pages = {3039{\textendash}3047}, doi = {10.1021/ct100318f}, author = {Chen, H. and Liu, P. and G. A. Voth} } @article {424, title = {The Kinetics of Proton Migration in Liquid Water}, journal = {J. Phys. Chem. B}, volume = {114}, year = {2010}, pages = {333{\textendash}339}, doi = {10.1021/jp908126a}, author = {Chen, H. and G. A. Voth} } @article {428, title = {A Computer Simulation Model for Proton Transport in Liquid Imidazole}, journal = {J. Phys. Chem. A}, volume = {113}, year = {2009}, pages = {4507-4517}, doi = {10.1021/jp811156r}, author = {Chen, H. and T. Yan and G. A. Voth} } @article {467, title = {The Hydrated Excess Proton at Water-Hydrophobic Interfaces}, journal = {J. Phys. Chem. B}, volume = {113}, year = {2009}, pages = {4017-4030}, doi = {10.1021/jp805304j}, author = {Iuchi, S. and Chen, H. and Paesani, F. and G. A. Voth} } @article {427, title = {Unusual Hydrophobic Interactions in Acidic Aqueous Solutions}, journal = {J. Phys. Chem. B}, volume = {113}, year = {2009}, pages = {7291-7297}, doi = {10.1021/jp9025909}, author = {Chen, H. and Xu, J. and G. A. Voth} } @article {704, title = {An Improved Multistate Empirical Valence Bond Model for Aqueous Proton Solvation and Transport}, journal = {J. Phys. Chem. B}, volume = {112}, year = {2008}, pages = {467-482}, doi = {10.1021/jp076658h}, author = {Y. Wu and Chen, H. and Wang, F. and Paesani, F. and G. A. Voth} } @article {560, title = {Special Pair Dance and Partner Selection: Elementary Steps in Proton Transport in Liquid Water}, journal = {J. Phys. Chem. B}, volume = {112}, year = {2008}, pages = {9456-9466}, doi = {10.1021/jp804018y}, author = {Markovitch, O. and Chen, H. and Izvekov, S. and Paesani, F. and G. A. Voth and Agmon, N.} } @article {422, title = {Charge Delocalization in Proton Channels, I: the Aquaporin Channels and Proton Blockage}, journal = {Biophys J}, volume = {92}, number = {1}, year = {2007}, note = {Chen, Hanning Ilan, Boaz Wu, Yujie Zhu, Fangqiang Schulten, Klaus Voth, Gregory A 2 P41 RR05969/RR/NCRR NIH HHS/United States R01 GM067887/GM/NIGMS NIH HHS/United States R01-GM53148/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States Biophysical journal Biophys J. 2007 Jan 1;92(1):46-60. Epub 2006 Oct 20.}, pages = {46-60}, abstract = {

The explicit contribution to the free energy barrier and proton conductance from the delocalized nature of the excess proton is examined in aquaporin channels using an accurate all-atom molecular dynamics computer simulation model. In particular, the channel permeation free energy profiles are calculated and compared for both a delocalized (fully Grotthuss shuttling) proton and a classical (nonshuttling) hydronium ion along two aquaporin channels, Aqp1 and GlpF. To elucidate the effects of the bipolar field thought to arise from two alpha-helical macrodipoles on proton blockage, free energy profiles were also calculated for computational mutants of the two channels where the bipolar field was eliminated by artificially discharging the backbone atoms. Comparison of the free energy profiles between the proton and hydronium cases indicates that the magnitude of the free energy barrier and position of the barrier peak for the fully delocalized and shuttling proton are somewhat different from the case of the (localized) classical hydronium. The proton conductance through the two aquaporin channels is also estimated using Poisson-Nernst-Planck theory for both the Grotthuss shuttling excess proton and the classical hydronium cation.

}, keywords = {Aquaporin 1/*chemistry Aquaporins/*chemistry Biological Transport Biophysics/*methods Escherichia coli Proteins/*chemistry Ions Models, Chemical Models, Molecular Models, Secondary Protons Thermodynamics, Statistical Mutation Oxygen/chemistry Protein Structure}, doi = {10.1529/biophysj.106.091934}, author = {Chen, H. and B. Ilan and Y. Wu and Zhu, F. and K. Schulten and G. A. Voth} } @article {659, title = {Proton Solvation and Transport in Aqueous and Biomolecular Systems: Insights from Computer Simulations}, journal = {J Phys Chem B}, volume = {111}, number = {17}, year = {2007}, note = {Swanson, Jessica M J Maupin, C Mark Chen, Hanning Petersen, Matt K Xu, Jiancong Wu, Yujie Voth, Gregory A R01 GM053148-12/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. Review United States The journal of physical chemistry. B J Phys Chem B. 2007 May 3;111(17):4300-14. Epub 2007 Apr 13.}, pages = {4300-14}, 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.

}, keywords = {Biological Transport *Computer Simulation *Protons Solubility Solvents/*chemistry Water/chemistry}, doi = {10.1021/jp070104x}, author = {Swanson, J. M. and Maupin, C. M. and Chen, H. and Petersen, M. K. and Xu, J. and Y. Wu and G. A. Voth} } @article {426, title = {Proton Transport Behavior Through the Influenza A M2 Channel: Insights from Molecular Simulation}, journal = {Biophys. J.}, volume = {93}, year = {2007}, pages = {3470-3479}, doi = {10.1529/biophysj.107.105742}, author = {Chen, H. and Y. Wu and G. A. Voth} } @article {425, title = {Origins of Proton Transport Behavior from Selectivity Domain Mutations of the Aquaporin-1 Channel}, journal = {Biophys J}, volume = {90}, number = {10}, year = {2006}, note = {Chen, Hanning Wu, Yujie Voth, Gregory A R01-GM53148/GM/NIGMS NIH HHS/United States Letter Research Support, N.I.H., Extramural United States Biophysical journal Biophys J. 2006 May 15;90(10):L73-5. Epub 2006 Mar 31.}, pages = {L73-5}, abstract = {

The permeation free-energy profile and maximum ion conductance of proton transport along the channel of three aquaporin-1 (AQP1) mutants (H180A/R195V, H180A, and R195V) are calculated via molecular dynamics simulations and Poisson-Nernst-Planck theory. The proton dynamics was described by the multistate empirical valence bond (MS-EVB) model. The results reveal three major contributions to the overall free-energy barrier for proton transport in AQP1: 1), the bipolar field, 2), the electrostatic repulsion due to the Arg-195 residue, and 3), the dehydration penalty due to the narrow channel pore. The double mutation (H180A/R195V) drastically drops the overall free-energy barrier by roughly 20 kcal/mol via simultaneously relaxing the direct electrostatic interaction (by R195V) and dehydration effect (by H180A).

}, keywords = {Amino Acid Substitution Aquaporin 1/*chemistry/genetics Cell Membrane/*chemistry Computer Simulation *Ion Channel Gating *Models, Chemical *Models, Molecular Mutagenesis, Site-Directed Porosity Protein Conformation Protein Structure, Tertiary *Protons Structure-Activity Relationship}, doi = {10.1529/biophysj.106.084061}, author = {Chen, H. and Y. Wu and G. A. Voth} }