Simulations of the alternating access mechanism of the sodium symporter Mhp1.

[1]  Jonathan A. Javitch,et al.  Substrate-modulated gating dynamics in a Na+-coupled neurotransmitter transporter homolog , 2011, Nature.

[2]  L. Chong,et al.  Efficient Explicit-Solvent Molecular Dynamics Simulations of Molecular Association Kinetics: Methane/Methane, Na(+)/Cl(-), Methane/Benzene, and K(+)/18-Crown-6 Ether. , 2011, Journal of chemical theory and computation.

[3]  L. Forrest,et al.  The structural basis of secondary active transport mechanisms. , 2011, Biochimica et biophysica acta.

[4]  Michael Grabe,et al.  The mechanism of sodium and substrate release from the binding pocket of vSGLT , 2010, Nature.

[5]  J. Rosenberg,et al.  Water permeation through the sodium-dependent galactose cotransporter vSGLT. , 2010, Biophysical journal.

[6]  Emad Tajkhorshid,et al.  Modeling and Dynamics of the Inward-Facing State of a Na+/Cl− Dependent Neurotransmitter Transporter Homologue , 2010, PLoS Comput. Biol..

[7]  Harel Weinstein,et al.  Ion/substrate-dependent conformational dynamics of a bacterial homolog of neurotransmitter:sodium symporters , 2010, Nature Structural &Molecular Biology.

[8]  S. Iwata,et al.  Molecular Basis of Alternating Access Membrane Transport by the Sodium-Hydantoin Transporter Mhp1 , 2010, Science.

[9]  Pu Liu,et al.  Fast determination of the optimal rotational matrix for macromolecular superpositions , 2009, J. Comput. Chem..

[10]  Bin W. Zhang,et al.  Steady-state simulations using weighted ensemble path sampling. , 2009, The Journal of chemical physics.

[11]  Daniel M Zuckerman,et al.  The "weighted ensemble" path sampling method is statistically exact for a broad class of stochastic processes and binning procedures. , 2008, The Journal of chemical physics.

[12]  Vijay S. Pande,et al.  Efficient nonbonded interactions for molecular dynamics on a graphics processing unit , 2010, J. Comput. Chem..

[13]  J. Onuchic,et al.  Robustness and generalization of structure‐based models for protein folding and function , 2009, Proteins.

[14]  L. Forrest,et al.  The rocking bundle: a mechanism for ion-coupled solute flux by symmetrical transporters. , 2009, Physiology.

[15]  E. Wright,et al.  Structure and function of Na(+)-symporters with inverted repeats. , 2009, Current opinion in structural biology.

[16]  Harini Krishnamurthy,et al.  Unlocking the molecular secrets of sodium-coupled transporters , 2009, Nature.

[17]  Vijay S. Pande,et al.  Accelerating molecular dynamic simulation on graphics processing units , 2009, J. Comput. Chem..

[18]  C. Vonrhein,et al.  Molecular basis of transport and regulation in the Na+/betaine symporter BetP , 2009, Nature.

[19]  J. P. Garrahan,et al.  The limited role of nonnative contacts in the folding pathways of a lattice protein. , 2008, Journal of molecular biology.

[20]  Shunsuke Yajima,et al.  Structure and Molecular Mechanism of a Nucleobase–Cation–Symport-1 Family Transporter , 2008, Science.

[21]  László Csanády,et al.  The twain shall meet: channels, transporters and things between , 2008, EMBO reports.

[22]  D. Cascio,et al.  The Crystal Structure of a Sodium Galactose Transporter Reveals Mechanistic Insights into Na+/Sugar Symport , 2008, Science.

[23]  Li Xie,et al.  Mechanism for alternating access in neurotransmitter transporters , 2008, Proceedings of the National Academy of Sciences.

[24]  Harel Weinstein,et al.  The mechanism of a neurotransmitter:sodium symporter--inward release of Na+ and substrate is triggered by substrate in a second binding site. , 2008, Molecular cell.

[25]  Benoît Roux,et al.  Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms , 2008, PLoS Comput. Biol..

[26]  Macoto Kikuchi,et al.  Structural change and nucleotide dissociation of Myosin motor domain: dual go model simulation. , 2007, Biophysical journal.

[27]  Bin W. Zhang,et al.  Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin , 2007, Proceedings of the National Academy of Sciences.

[28]  Aaron R Dinner,et al.  Umbrella sampling for nonequilibrium processes. , 2007, The Journal of chemical physics.

[29]  William H. Press,et al.  Numerical Recipes 3rd Edition: The Art of Scientific Computing , 2007 .

[30]  D. Loo,et al.  Conformational Dynamics of hSGLT1 during Na+/Glucose Cotransport , 2006, The Journal of general physiology.

[31]  J. Onuchic,et al.  Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations , 2006, Proceedings of the National Academy of Sciences.

[32]  P. Henderson,et al.  The Hydantoin Transport Protein from Microbacterium liquefaciens , 2006, Journal of bacteriology.

[33]  D. Frenkel,et al.  Simulating rare events in equilibrium or nonequilibrium stochastic systems. , 2005, The Journal of chemical physics.

[34]  Eric Gouaux,et al.  Crystal structure of a bacterial homologue of Na+/Cl--dependent neurotransmitter transporters , 2005, Nature.

[35]  D. Theobald short communications Acta Crystallographica Section A Foundations of , 2005 .

[36]  R. Elber,et al.  Computing time scales from reaction coordinates by milestoning. , 2004, The Journal of chemical physics.

[37]  Daniel M. Zuckerman,et al.  Simulation of an Ensemble of Conformational Transitions in a United-Residue Model of Calmodulin , 2004 .

[38]  P. Bolhuis,et al.  A novel path sampling method for the calculation of rate constants , 2002, cond-mat/0210614.

[39]  David Chandler,et al.  Transition path sampling: throwing ropes over rough mountain passes, in the dark. , 2002, Annual review of physical chemistry.

[40]  J. Onuchic,et al.  Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. , 2000, Journal of molecular biology.

[41]  H. Jung,et al.  Unidirectional reconstitution and characterization of purified Na+/proline transporter of Escherichia coli. , 1998, Biochemistry.

[42]  Gerhard Hummer,et al.  Multistate Gaussian Model for Electrostatic Solvation Free Energies , 1997 .

[43]  H. Lester,et al.  H+ Permeation and pH Regulation at a Mammalian Serotonin Transporter , 1997, The Journal of Neuroscience.

[44]  D. Loo,et al.  Cotransport of water by the Na+/glucose cotransporter. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[45]  D. Loo,et al.  Mechanisms of the Human Intestinal H-coupled Oligopeptide Transporter hPEPT1 (*) , 1996, The Journal of Biological Chemistry.

[46]  G. Huber,et al.  Weighted-ensemble Brownian dynamics simulations for protein association reactions. , 1996, Biophysical journal.

[47]  D. Loo,et al.  Protons drive sugar transport through the Na+/glucose cotransporter (SGLT1). , 1994, The Journal of biological chemistry.

[48]  N. Go,et al.  Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions. , 2009 .

[49]  O. Jardetzky,et al.  Simple Allosteric Model for Membrane Pumps , 1966, Nature.