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Huan Rui, Ph.D. - Publications

Affiliations: 
2013 Biochemistry and Molecular Biology University of Kansas, Lawrence, KS, United States 
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45 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Artigas P, Meyer DJ, Young VC, Spontarelli K, Eastman J, Strandquist E, Rui H, Roux B, Birk MA, Nakanishi H, Abe K, Gatto C. A Na pump with reduced stoichiometry is up-regulated by brine shrimp in extreme salinities. Proceedings of the National Academy of Sciences of the United States of America. 120: e2313999120. PMID 38079564 DOI: 10.1073/pnas.2313999120  0.394
2021 Thirman J, Rui H, Roux B. Elusive Intermediate State Key in the Conversion of ATP Hydrolysis into Useful Work Driving the Ca Pump SERCA. The Journal of Physical Chemistry. B. PMID 33720716 DOI: 10.1021/acs.jpcb.1c00558  0.458
2020 Rohaim A, Gong L, Li J, Rui H, Blachowicz L, Roux B. Barium blockade of the KcsA channel in open and closed conformation datasets. Data in Brief. 32: 106135. PMID 32904340 DOI: 10.1016/J.Dib.2020.106135  0.534
2020 Rohaim A, Gong L, Li J, Rui H, Blachowicz L, Roux B. Open and closed structures of a barium-blocked potassium channel. Journal of Molecular Biology. PMID 32615129 DOI: 10.1016/J.Jmb.2020.06.012  0.517
2019 Ellis-Guardiola K, Rui H, Beckner RL, Srivastava P, Sukumar N, Roux B, Lewis JC. Crystal Structure and Conformational Dynamics of Pyrococcus furiosus Prolyl Oligopeptidase. Biochemistry. PMID 30786206 DOI: 10.1021/Acs.Biochem.9B00031  0.538
2018 Rui H, Das A, Nakamoto R, Roux B. Proton Countertransport and Coupled Gating in the Sarcoplasmic Reticulum Calcium Pump. Journal of Molecular Biology. 430: 5050-5065. PMID 30539761 DOI: 10.1016/J.Jmb.2018.10.014  0.523
2018 Rui H, Das A, Roux B. The Allosteric Coupling of the Cytoplasmic Phosphorylation and Transmembrane Domain Deocclusion in the Ca2+ SERCA Pump Elucidated by Free Energy Simulations Biophysical Journal. 114: 148a. DOI: 10.1016/J.Bpj.2017.11.829  0.467
2018 Rohaim A, Gong L, Li J, Rui H, Roux B. A Structural and Computational Study of Barium Blockade in the KcsA Channel Biophysical Journal. 114: 237a. DOI: 10.1016/J.Bpj.2017.11.1321  0.465
2017 Li J, Ostmeyer J, Boulanger E, Rui H, Perozo E, Roux B. Chemical substitutions in the selectivity filter of potassium channels do not rule out constricted-like conformations for C-type inactivation. Proceedings of the National Academy of Sciences of the United States of America. PMID 28973956 DOI: 10.1073/Pnas.1706983114  0.516
2017 Beaven AH, Maer AM, Sodt AJ, Rui H, Pastor RW, Andersen OS, Im W. Gramicidin A Channel Formation Induces Local Lipid Redistribution I: Experiment and Simulation. Biophysical Journal. 112: 1185-1197. PMID 28355546 DOI: 10.1016/J.Bpj.2017.01.028  0.492
2017 Das A, Rui H, Nakamoto R, Roux B. Conformational transitions and alternating-access mechanism in the sarcoplasmic reticulum calcium pump. Journal of Molecular Biology. PMID 28093226 DOI: 10.1016/J.Jmb.2017.01.007  0.539
2017 Sánchez-Rodríguez JE, Rui H, Roux B, Holmgren M, Bezanilla F. Tuning Voltage Dependent Transitions during the Extracellular Na + Binding/Release of the Na + /K + -ATPase by External Protons Biophysical Journal. 112: 569a-570a. DOI: 10.1016/J.Bpj.2016.11.3068  0.48
2017 Rui H, Sanchez-Rodriguez J, Holmgren M, Bezanilla F, Roux B. Ion Binding and Charge Movements in the Function of the Na/K-Pump Biophysical Journal. 112: 569a. DOI: 10.1016/J.Bpj.2016.11.3067  0.481
2017 Meyer DJ, Eastman J, Rui H, Stanley K, Roux B, Gatto C, Artigas P. A Na/K Pump with Altered Stoichiometry Contributes to Brine Shrimp Adaptation to High Salinity Biophysical Journal. 112: 569a. DOI: 10.1016/J.Bpj.2016.11.3065  0.455
2016 Jo S, Cheng X, Lee J, Kim S, Park SJ, Patel DS, Beaven AH, Lee KI, Rui H, Park S, Lee HS, Roux B, MacKerell AD, Klauda JB, Qi Y, et al. CHARMM-GUI 10 years for biomolecular modeling and simulation. Journal of Computational Chemistry. PMID 27862047 DOI: 10.1002/Jcc.24660  0.705
2016 Dhakshnamoorthy B, Rohaim A, Rui H, Blachowicz L, Roux B. Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola. Nature Communications. 7: 12753. PMID 27678077 DOI: 10.1038/Ncomms12753  0.519
2016 Rui H, Artigas P, Roux B. The selectivity of the Na(+)/K(+)-pump is controlled by binding site protonation and self-correcting occlusion. Elife. 5. PMID 27490484 DOI: 10.7554/Elife.16616  0.553
2016 Rui H, Artigas P, Roux B. Author response: The selectivity of the Na+/K+-pump is controlled by binding site protonation and self-correcting occlusion Elife. DOI: 10.7554/Elife.16616.017  0.463
2016 Meyer DJ, Eastman J, Rui H, Stanley K, Gatto C, Roux B, Artigas P. Molecular Mechanism by which Two Lysine Substitutions Alter Na/K-Pump Stoichiometry to Confer High-Salinity Adaptation in Brine Shrimp Biophysical Journal. 110: 629a. DOI: 10.1016/J.Bpj.2015.11.3371  0.512
2016 Rui H, Roux B. Binding Site Protonation and Uphill Occlusion Control the Na+/K+-Pump Selectivity Biophysical Journal. 110: 629a. DOI: 10.1016/J.Bpj.2015.11.3368  0.534
2015 Castillo JP, Rui H, Basilio D, Das A, Roux B, Latorre R, Bezanilla F, Holmgren M. Mechanism of potassium ion uptake by the Na(+)/K(+)-ATPase. Nature Communications. 6: 7622. PMID 26205423 DOI: 10.1038/Ncomms8622  0.53
2015 Roux B, Rui H, Das A. 49 Structure and energetics of the pumping mechanism of membrane ATPase. Journal of Biomolecular Structure & Dynamics. 33: 33-4. PMID 26103258 DOI: 10.1080/07391102.2015.1032598  0.512
2015 Yao H, Rui H, Kumar R, Eshelman K, Lovell S, Battaile KP, Im W, Rivera M. Concerted motions networking pores and distant ferroxidase centers enable bacterioferritin function and iron traffic. Biochemistry. 54: 1611-27. PMID 25640193 DOI: 10.1021/Bi501255R  0.508
2015 Rui H, Das A, Roux B. Na+/K+-ATPase Pumping Mechanism: Insights from Simulations Biophysical Journal. 108: 144a. DOI: 10.1016/J.Bpj.2014.11.796  0.533
2014 Jo S, Cheng X, Islam SM, Huang L, Rui H, Zhu A, Lee HS, Qi Y, Han W, Vanommeslaeghe K, MacKerell AD, Roux B, Im W. CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues. Advances in Protein Chemistry and Structural Biology. 96: 235-65. PMID 25443960 DOI: 10.1016/Bs.Apcsb.2014.06.002  0.685
2014 Wu EL, Cheng X, Jo S, Rui H, Song KC, Dávila-Contreras EM, Qi Y, Lee J, Monje-Galvan V, Venable RM, Klauda JB, Im W. CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. Journal of Computational Chemistry. 35: 1997-2004. PMID 25130509 DOI: 10.1002/Jcc.23702  0.668
2014 Venable RM, Sodt AJ, Rogaski B, Rui H, Hatcher E, MacKerell AD, Pastor RW, Klauda JB. CHARMM all-atom additive force field for sphingomyelin: elucidation of hydrogen bonding and of positive curvature. Biophysical Journal. 107: 134-45. PMID 24988348 DOI: 10.1016/J.Bpj.2014.05.034  0.317
2014 Rui H, Root KT, Lee J, Glover KJ, Im W. Probing the U-shaped conformation of caveolin-1 in a bilayer. Biophysical Journal. 106: 1371-80. PMID 24655512 DOI: 10.1016/J.Bpj.2014.02.005  0.572
2014 Rui H, Root KT, Lee J, Glover KJ, Im W. Caveolin in Bilayers: Can the Intramembrane U-Shaped Conformation Really Exist Biophysical Journal. 106: 641a. DOI: 10.1016/J.Bpj.2013.11.3547  0.568
2013 Rui H, Kossiakoff AA, Im W. Structural Modeling of Human Growth Hormone Receptor using Computational Simulations and NMR Spectroscopy Biophysical Journal. 104: 117a-118a. DOI: 10.1016/J.Bpj.2012.11.678  0.532
2013 Rui H, Jebrell Glover K, Im W. Molecular Dynamics Simulations of Caveolin-1 in Membrane Bilayers Biophysical Journal. 104: 410a. DOI: 10.1016/J.Bpj.2012.11.2287  0.549
2012 Rui H, Rivera M, Im W. Protein dynamics and ion traffic in bacterioferritin. Biochemistry. 51: 9900-10. PMID 23167635 DOI: 10.1021/Bi3013388  0.507
2012 Lee KI, Jo S, Rui H, Egwolf B, Roux B, Pastor RW, Im W. Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel pores. Journal of Computational Chemistry. 33: 331-9. PMID 22102176 DOI: 10.1002/Jcc.21952  0.712
2012 Rui H, Im W. Turning on the Human Growth Hormone Receptor: A Computational Study on its Structure and Activation Mechanism Biophysical Journal. 102: 667a. DOI: 10.1016/J.Bpj.2011.11.3635  0.511
2011 Rui H, Kumar R, Im W. Membrane tension, lipid adaptation, conformational changes, and energetics in MscL gating. Biophysical Journal. 101: 671-9. PMID 21806935 DOI: 10.1016/J.Bpj.2011.06.029  0.542
2011 Lee KI, Rui H, Pastor RW, Im W. Brownian dynamics simulations of ion transport through the VDAC. Biophysical Journal. 100: 611-9. PMID 21281575 DOI: 10.1016/J.Bpj.2010.12.3708  0.582
2011 Rui H, Lee KI, Pastor RW, Im W. Molecular dynamics studies of ion permeation in VDAC. Biophysical Journal. 100: 602-10. PMID 21281574 DOI: 10.1016/J.Bpj.2010.12.3711  0.58
2011 Lee KI, Jo S, Rui H, Im W. Web-Based Interface for Brownian Dynamics Simulation of Ion Channels and Its Application to Vdac Biophysical Journal. 100: 156a. DOI: 10.1016/J.Bpj.2010.12.1068  0.692
2010 Jo S, Rui H, Lim JB, Klauda JB, Im W. Cholesterol flip-flop: insights from free energy simulation studies. The Journal of Physical Chemistry. B. 114: 13342-8. PMID 20923227 DOI: 10.1021/Jp108166K  0.63
2010 Rui H, Im W. Protegrin-1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations. Journal of Computational Chemistry. 31: 2859-67. PMID 20589740 DOI: 10.1002/Jcc.21580  0.538
2010 Jepkorir G, Rodríguez JC, Rui H, Im W, Lovell S, Battaile KP, Alontaga AY, Yukl ET, Moënne-Loccoz P, Rivera M. Structural, NMR spectroscopic, and computational investigation of hemin loading in the hemophore HasAp from Pseudomonas aeruginosa. Journal of the American Chemical Society. 132: 9857-72. PMID 20572666 DOI: 10.1021/Ja103498Z  0.528
2010 Rui H, Im W. Protegrin-1 Orientation in Membrane Bilayers: Insights from Potential of Mean Force Calculations as A Function of Its Tilt and Rotation Angles Biophysical Journal. 98: 218a. DOI: 10.1016/J.Bpj.2009.12.1177  0.531
2009 Rui H, Lee J, Im W. Comparative molecular dynamics simulation studies of protegrin-1 monomer and dimer in two different lipid bilayers. Biophysical Journal. 97: 787-95. PMID 19651037 DOI: 10.1016/J.Bpj.2009.05.029  0.572
2009 Im W, Lee J, Kim T, Rui H. Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function. Journal of Computational Chemistry. 30: 1622-33. PMID 19496166 DOI: 10.1002/Jcc.21320  0.599
2009 Rui H, Lee J, Im W. PG-1 Orientation in Lipid Bilayers: Insights from Molecular Dynamics Simulations and Calculations of Potentials of Mean Force as a Function of Its Tilt Angle Biophysical Journal. 96: 153a. DOI: 10.1016/J.Bpj.2008.12.693  0.561
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