Simulations of the alternating access mechanism of the sodium symporter Mhp1.
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Divesh Bhatt | Joshua L Adelman | Michael Grabe | Daniel M Zuckerman | Lillian T Chong | Matthew C Zwier | L. Chong | D. Bhatt | D. Zuckerman | M. Zwier | J. Adelman | M. Grabe | Amy L Dale | A. Dale
[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.