Items where Division is "05 Faculty of Science > Departement Biozentrum > Former Organization Units Biozentrum > Computational Biophysics (Bernèche)"

Article

Roy, Sophie and Johner, Niklaus and Trendafilov, Viktor and Gautschi, Ivan and Bignucolo, Olivier and Molton, Ophélie and Bernèche, Simon and Kellenberger, Stephan. (2022) Calcium regulates acid-sensing ion channel 3 activation by competing with protons in the channel pore and at an allosteric binding site. Open biology, 12 (12). p. 220243.

Bignucolo, Olivier and Bernèche, Simon. (2020) The Voltage-Dependent Deactivation of the KvAP Channel Involves the Breakage of Its S4 Helix. Frontiers in molecular biosciences, 7. p. 162.

Leisle, Lilia and Xu, Yanyan and Fortea, Eva and Lee, Sangyun and Galpin, Jason D. and Vien, Malvin and Ahern, Christopher A. and Accardi, Alessio and Bernèche, Simon. (2020) Divergent Cl; -; and H; +; pathways underlie transport coupling and gating in CLC exchangers and channels. eLife, 9. e51224.

Heer, Florian T. and Posson, David J. and Wojtas-Niziurski, Wojciech and Nimigean, Crina M. and Bernèche, Simon. (2017) Mechanism of activation at the selectivity filter of the KcsA K(+) channel. eLife, 6. e25844.

Koegel, Sally and Mieulet, Delphine and Baday, Sefer and Chatagnier, Odile and Lehmann, Moritz F. and Wiemken, Andres and Boller, Thomas and Wipf, Daniel and Bernèche, Simon and Guiderdoni, Emmanuel and Courty, Pierre-Emmanuel. (2017) Phylogenetic, structural, and functional characterization of AMT3;1, an ammonium transporter induced by mycorrhization among model grasses. Mycorrhiza, 27 (7). pp. 695-708.

Starek, Greg and Freites, J. Alfredo and Bernèche, Simon and Tobias, Douglas J.. (2017) Gating energetics of a voltage-dependent K(+) channel pore domain. Journal of Computational Chemistry, 38 (16). pp. 1472-1478.

Vullo, Sabrina and Bonifacio, Gaetano and Roy, Sophie and Johner, Niklaus and Bernèche, Simon and Kellenberger, Stephan. (2017) Conformational dynamics and role of the acidic pocket in ASIC pH-dependent gating. Proceedings of the National Academy of Sciences of the United States of America, 114 (14). pp. 3768-3773.

Xu, Yanyan and Egido, Estefanía and Li-Blatter, Xiaochun and Müller, Rita and Merino, Gracia and Bernèche, Simon and Seelig, Anna. (2015) Allocrite Sensing and Binding by the Breast Cancer Resistance Protein (ABCG2) and P-Glycoprotein (ABCB1). Biochemistry, 54 (40). pp. 6195-6206.

Ramming, Thomas and Okumura, Masaki and Kanemura, Shingo and Baday, Sefer and Birk, Julia and Moes, Suzette and Spiess, Martin and Jenö, Paul and Bernèche, Simon and Inaba, Kenji and Appenzeller-Herzog, Christian. (2015) A PDI-catalyzed thiol-disulfide switch regulates the production of hydrogen peroxide by human Ero1. Free radical biology & medicine, 83. pp. 361-372.

Baday, Sefer and Orabi, Esam A. and Wang, Shihao and Lamoureux, Guillaume and Bernèche, Simon. (2015) Mechanism of NH4(+) Recruitment and NH3 Transport in Rh Proteins. Structure: with folding and design, Vol. 23, H. 8. pp. 1550-1557.

Bignucolo, Olivier and Leung, Hoi Tik Alvin and Grzesiek, Stephan and Bernèche, Simon. (2015) Backbone hydration determines the folding signature of amino acid residues. Journal of the American Chemical Society, Vol. 137, H. 13. pp. 4300-4303.

Thomson, Andrew S. and Heer, Florian T. and Smith, Frank J. and Hendron, Eunan and Bernèche, Simon and Rothberg, Brad S.. (2014) Initial steps of inactivation at the K+ channel selectivity filter. Proceedings of the National Academy of Sciences of the United States of America, Vol. 111, H. 17 , E1713-E1722.

Baday, Sefer and Wang, Shihao and Lamoureux, Guillaume and Bernèche, Simon. (2013) Different Hydration Patterns in the Pores of AmtB and RhCG Could Determine Their Transport Mechanisms. Biochemistry, Vol. 52, H. 40 , S. 7091–7098.

Roy, Sophie and Boiteux, Céline and Alijevic, Omar and Liang, Chungwen and Bernèche, Simon and Kellenberger, Stephan. (2013) Molecular determinants of desensitization in an ENaC/degenerin channel. The FASEB journal, Vol. 27, H. 12. pp. 5034-5045.

Wojtas-Niziurski, Wojciech and Meng, Yilin and Roux, Benoit and Bernèche, Simon. (2013) Self-Learning Adaptive Umbrella Sampling Method for the Determination of Free Energy Landscapes in Multiple Dimensions. Journal of chemical theory and computation, Vol. 9, H. 4. pp. 1885-1895.

Faure, Elise and Starek, Greg and McGuire, Hugo and Bernèche, Simon and Blunck, Rikard. (2012) A limited 4 a radial displacement of the s4-s5 linker is sufficient for internal gate closing in kv channels. Journal of biological chemistry, Vol. 287, H. 47. pp. 40091-40098.

Picollo, Alessandra and Xu, Yanyan and Johner, Niklaus and Bernèche, Simon and Accardi, Alessio. (2012) Synergistic substrate binding determines the stoichiometry of transport of a prokaryotic H(+)/Cl(-) exchanger. Nature structural & molecular biology, Vol. 19, no. 5. pp. 525-531.

Silván, Unai and Boiteux, Céline and Sütterlin, Rosmarie and Schroeder, Ulrich and Mannherz, Hans Georg and Jockusch, Brigitte M. and Bernèche, Simon and Aebi, Ueli and Schoenenberger, Cora-Ann. (2012) An antiparallel actin dimer is associated with the endocytic pathway in mammalian cells. Journal of structural biology, Vol. 177, H. 1. pp. 70-80.

Wang, Shihao and Orabi, Esam A. and Baday, Sefer and Bernèche, Simon and Lamoureux, Guillaume. (2012) Ammonium Transporters Achieve Charge Transfer by Fragmenting Their Substrate. Journal of the American Chemical Society, Vol. 134, H. 25. pp. 10419-10427.

Boiteux, C. and Bernèche, S.. (2011) Absence of ion-binding affinity in the putatively inactivated low-[K+] structure of the KcsA potassium channel. Structure, Vol. 19, H. 1. pp. 70-79.

Roux, B. and Berneche, S. and Egwolf, B. and Lev, B. and Noskov, S. Y. and Rowley, C. N. and Yu, H.. (2011) Ion selectivity in channels and transporters. Journal of general physiology, Vol. 137, H. 5. pp. 415-426.

Lamoureux, G. and Javelle, A. and Baday, S. and Wang, S. and Bernèche, S.. (2010) Transport mechanisms in the ammonium transporter family. Transfusion clinique et biologique, Vol. 17, H. 3. pp. 168-175.

Liechti, L. A. and Bernèche, S. and Bargeton, B. and Iwaszkiewicz, J. and Roy, S. and Michielin, O. and Kellenberger, S.. (2010) A combined computational and functional approach identifies new residues involved in pH-dependent gating of ASIC1a. Journal of biological chemistry, Vol. 285, H. 21. pp. 16315-16329.

Lamoureux, Guillaume and Klein, Michael L. and Bernèche, Simon. (2007) A stable water chain in the hydrophobic pore of the AmtB ammonium transporter. Biophysical journal, Vol. 92, H. 9 , L82-L84.

Philippsen, A. and Schenk, A. D. and Signorell, G. A. and Mariani, V. and Berneche, S. and Engel, A.. (2007) Collaborative EM image processing with the IPLT image processing library and toolbox. Journal of structural biology, Vol. 157, H. 1. pp. 28-37.

Bernèche, Simon and Roux, Benoît. (2005) A gate in the selectivity filter of potassium channels. Structure: with folding and design, Vol. 13, H. 4. pp. 591-600.

Noskov, Sergei Yu and Bernèche, Simon and Roux, Benoît. (2004) Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature, Vol. 431. pp. 830-834.

Roux, Benoît and Allen, Toby and Bernèche, Simon and Im, Wonpil. (2004) Theoretical and computational models of biological ion channels. Quarterly Reviews of Biophysics, 37 (1). pp. 15-103.

Zheng, Lei and Kostrewa, Dirk and Bernèche, Simon and Winkler, Fritz K. and Li, Xiao-Dan. (2004) The mechanism of ammonia transport based on the crystal structure of AmtB of Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 49. pp. 17090-17095.

Bernèche, Simon and Roux, Benoît. (2003) A microscopic view of ion conduction through the K+ channel. Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 15. pp. 8644-8648.

Bernèche, Simon and Roux, Benoît. (2002) The ionization state and the conformation of Glu-71 in the KcsA K(+) channel. Biophysical journal, Vol. 82, H. 2. pp. 772-780.

Roux, Benoît and Bernèche, Simon. (2002) On the potential functions used in molecular dynamics simulations of ion channels. Biophysical journal, Vol. 82, H. 3. pp. 1681-1684.

Bernèche, S. and Roux, B.. (2001) Energetics of ion conduction through the K+ channel. Nature, Vol. 414 No. 6859. pp. 73-77.

Crouzy, S. and Bernèche, S. and Roux, B.. (2001) Extracellular blockade of K(+) channels by TEA : results from molecular dynamics simulations of the KcsA channel. Journal of general physiology, Vol. 118, H. 2. pp. 207-218.

Bernèche, S. and Roux, B.. (2000) Molecular dynamics of the KcsA K(+) channel in a bilayer membrane. Biophysical journal, Vol. 78, H. 6. pp. 2900-2917.

Nina, M. and Bernèche, S. and Roux, B.. (2000) Anchoring of a monotopic membrane protein : the binding of prostaglandin H2 synthase-1 to the surface of a phospholipid bilayer. European biophysics journal, Vol. 29 , H. 6. pp. 439-454.

Roux, B. and Bernèche, S. and Im, W.. (2000) Ion channels, permeation, and electrostatics : insight into the function of KcsA. Biochemistry, Vol. 39, H. 44. pp. 13295-13306.

Bernèche, S. and Nina, M. and Roux, B.. (1998) Molecular dynamics simulation of melittin in a dimyristoylphosphatidylcholine bilayer membrane. Biophysical journal, Vol. 75, H. 4. pp. 1603-1618.

Assad, M. and Lombardi, S. and Bernèche, S. and Desrosiers, E. A. and Yahia, L. H. and Rivard, C. H.. (1994) [Assays of cytotoxicity of the Nickel-Titanium shape memory alloy]. Annales de chirurgie, Vol. 48, no. 8. pp. 731-736.

Book Section

Bernèche, S. and Roux, B.. (2008) Modeling and simulation of ion channels. In: Computational structural biology. London, pp. 325-361.

Thesis

Baday, Sefer. Computational investigation of function of membrane proteins : Amt/Rh Ammonium transporters and SecY translocon. 2014, Doctoral Thesis, University of Basel, Faculty of Science.

Starek, Greg. Molecular mechanisms of the coupling of gating to voltage sensing in transmembrane proteins. 2014, Doctoral Thesis, University of Basel, Faculty of Science.

Other

Berneche, Simon. (2018) Regulation of ion permeation in K channels: From kinetic models to atomistic simulations and back. Abstracts of Papers of the American Chemical Society, 256. Washington, DC.

Johner, Niklaus B. and Berneche, Simon. (2017) Effect of Membrane Composition on Ion Conduction in a Voltage-Gated Potassium Channel. Biophysical Journal, 112 (3, Supplement 1). 542A.

Xu, Yanyan and Vien, Malvin and Liang, Chungwen and Accardi, Alessio and Berneche, Simon. (2017) Molecular Mechanism of Cl-/H+ Coupling in a CLC Antiporter. Biophysical Journal, 112 (3, Supplement 1). 336A.