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1

Phylogenetic, structural, and functional characterization of AMT3;1, an ammonium transporter induced by mycorrhization among model grasses

Koegel, Sally, Mieulet, Delphine, Baday, Sefer, Chatagnier, Odile, Lehmann, Moritz F., Wiemken, Andres, Boller, Thomas, Wipf, Daniel, Bernèche, Simon, Guiderdoni, Emmanuel, Courty, Pierre-Emmanuel

Journal:

Year:

2017

Language:

english

File:

PDF, 1.58 MB

english, 2017

2

Anchoring of a monotopic membrane protein: the binding of prostaglandin H2synthase-1 to the surface of a phospholipid bilayer

Mafalda Nina, Simon Bernèche, Benoît Roux

Journal:

European Biophysics Journal

Year:

2000

Language:

english

File:

PDF, 889 KB

english, 2000

3

10.1038/35102067

Bernèche, Simon, Roux, Benoît

Journal:

Year:

2001

Language:

english

File:

PDF, 551 KB

english, 2001

4

Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands

Noskov, Sergei Yu., Bernèche, Simon, Roux, Benoît

Journal:

Year:

2004

Language:

english

File:

PDF, 261 KB

english, 2004

5

A Gate in the Selectivity Filter of Potassium Channels

Simon Bernèche, Benoît Roux

Journal:

Year:

2005

Language:

english

File:

PDF, 341 KB

english, 2005

6

Absence of Ion-Binding Affinity in the Putatively Inactivated Low-[K+] Structure of the KcsA Potassium Channel

Céline Boiteux, Simon Bernèche

Journal:

Year:

2011

Language:

english

File:

PDF, 1.84 MB

english, 2011

7

NanC Crystal Structure, a Model for Outer-Membrane Channels of the Acidic Sugar-Specific KdgM Porin Family

Christophe Wirth, Guy Condemine, Céline Boiteux, Simon Bernèche, Tilman Schirmer, Caroline M. Peneff

Journal:

Journal of Molecular Biology

Year:

2009

Language:

english

File:

PDF, 1.19 MB

english, 2009

8

Collaborative EM image processing with the IPLT image processing library and toolbox

Ansgar Philippsen, Andreas D. Schenk, Gian A. Signorell, Valerio Mariani, Simon Berneche, Andreas Engel

Journal:

Journal of Structural Biology

Year:

2007

Language:

english

File:

PDF, 1.15 MB

english, 2007

9

An antiparallel actin dimer is associated with the endocytic pathway in mammalian cells

Unai Silván, Céline Boiteux, Rosmarie Sütterlin, Ulrich Schroeder, Hans Georg Mannherz, Brigitte M. Jockusch, Simon Bernèche, Ueli Aebi, Cora-Ann Schoenenberger

Journal:

Journal of Structural Biology

Year:

2012

Language:

english

File:

PDF, 2.65 MB

english, 2012

10

Molecular Dynamics of the KcsA K+ Channel in a Bilayer Membrane

Bernèche, Simon, Roux, Benoît

Journal:

Biophysical Journal

Year:

2000

Language:

english

File:

PDF, 1.55 MB

english, 2000

11

The Ionization State and the Conformation of Glu-71 in the KcsA K+ Channel

Bernèche, Simon, Roux, Benoît

Journal:

Biophysical Journal

Year:

2002

Language:

english

File:

PDF, 515 KB

english, 2002

12

On the Potential Functions used in Molecular Dynamics Simulations of Ion Channels

Roux, Benoît, Bernèche, Simon

Journal:

Biophysical Journal

Year:

2002

Language:

english

File:

PDF, 78 KB

english, 2002

13

Molecular Dynamics Simulation of Melittin in a Dimyristoylphosphatidylcholine Bilayer Membrane

Bernèche, Simon, Nina, Mafalda, Roux, Benoît

Journal:

Biophysical Journal

Year:

1998

Language:

english

File:

PDF, 1.74 MB

english, 1998

14

A Stable Water Chain in the Hydrophobic Pore of the AmtB Ammonium Transporter

Lamoureux, Guillaume, Klein, Michael L., Bernèche, Simon

Journal:

Biophysical Journal

Year:

2007

Language:

english

File:

PDF, 240 KB

english, 2007

15

Self-Learning Adaptive Umbrella Sampling Method for the Determination of Free Energy Landscapes in Multiple Dimensions

Wojtas-Niziurski, Wojciech, Meng, Yilin, Roux, Benoı̂t, Bernèche, Simon

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 2.10 MB

english, 2013

16

Ammonium Transporters Achieve Charge Transfer by Fragmenting Their Substrate

Wang, Shihao, Orabi, Esam A., Baday, Sefer, Bernèche, Simon, Lamoureux, Guillaume

Journal:

Journal of the American Chemical Society

Year:

2012

Language:

english

File:

PDF, 2.42 MB

english, 2012

17

Different Hydration Patterns in the Pores of AmtB and RhCG Could Determine Their Transport Mechanisms

Baday, Sefer, Wang, Shihao, Lamoureux, Guillaume, Bernèche, Simon

Journal:

Year:

2013

Language:

english

File:

PDF, 3.34 MB

english, 2013

18

Two Distinct Transport Mechanisms in AmtB and RhCG Proteins

Baday, Sefer, Wang, Shihao, Lamoureux, Guillaume, Bernèche, Simon

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 41 KB

english, 2013

19

Obituary.

Baday, Sefer, Wang, Shihao, Lamoureux, Guillaume, Bernèche, Simon

Journal:

Year:

1857

Language:

english

File:

PDF, 401 KB

english, 1857

20

Computational Investigation of Charge Transfer Mechanisms in Ammonium Transporters

Wang, Shihao, Orabi, Esam A., Baday, Sefer, Bernèche, Simon, Lamoureux, Guillaume

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 41 KB

english, 2013

21

Permeation Mechanism in the AmtB Ammonium Transporter: Putative Electrogenic Co-Transport of NH3 and H+

Wang, Shihao, Baday, Sefer, Orabi, Esam A., Bernèche, Simon, Lamoureux, Guillaume

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 44 KB

english, 2011

22

Molecular Dynamics Study of Structural Elements Relevant to Gating of Kv Channels

Starek, Greg, Bernèche, Simon

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 35 KB

english, 2011

23

International symposium on advanced evoked potentials and related techniques in clinical neurophysiology: basic principles and special applications

Starek, Greg, Bernèche, Simon

Journal:

Clinical Neurology and Neurosurgery

Year:

1988

Language:

english

File:

PDF, 52 KB

english, 1988

24

Mechanisms of Fast Blockade and Gating of the MthK Channel Pore by Divalent Cations

Thomson, Andrew S., Heer, Florian, Berneche, Simon, Rothberg, Brad S.

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 40 KB

english, 2013

25

Aromatic Amino Acids Confer Folding Propensities to a Nine-Residue Peptide

Bignucolo, Olivier, Grzesiek, Stephan, Bernèche, Simon

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 52 KB

english, 2013

26

Conformational Changes Required for Chloride Ion Permeation in the CLC-ec1 Exchanger

Xu, Yanyan, Liang, Chungwen, Basilio, Daniel, Accardi, Alessio, Bernèche, Simon

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 65 KB

english, 2014

27

A Molecular Mechanics Model of a Closed Voltage-Gated Potassium Channel Generated from S4-S5 Linker LRET Measurements

Starek, Greg, Faure, Élise, McGuire, Hugo, Blunck, Rikard, Bernèche, Simon

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 39 KB

english, 2013

28

Ion Permeation in the MthK Potassium Channel

Heer, Florian, Bernèche, Simon

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 36 KB

english, 2012

29

Molecular Mechanics Investigation on the Mechanism of Multidrug Resistance

Xu, Yanyan, Seelig, Anna, Bernèche, Simon

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 37 KB

english, 2012

30

Investigating Co-Transport Mechanisms in the AmtB Ammonium Transporter using QM/MM Molecular Dynamics

Wang, Shihao, Baday, Sefer, Bernèche, Simon, Lamoureux, Guillaume

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 58 KB

english, 2011

31

Initial Steps of Inactivation at the K+ Channel Selectivity Filter

Thomson, Andrew S., Heer, Florian T., Smith, Frank J., Berneche, Simon, Rothberg, Brad S.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 42 KB

english, 2014

32

Transport Mechanism in CLC H+/C- Exchangers

Liang, Chungwen, Xu, YanYan, Bernèche, Simon

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 44 KB

english, 2014

33

Investigating Ammonium Transport Mechanisms in AmtB and RhCG by Molecular Dynamics Simulations

Baday, Sefer, Wang, Shihao, Lamoureux, Guillaume, Bernèche, Simon

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 44 KB

english, 2011

34

Aromatic Amino Acids Promote Peptide Folding by Reducing Backbone Hydration

Bignucolo, Olivier, Grzesiek, Stephan, Berneche, Simon

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 36 KB

english, 2014

35

Regulation of ion Permeation in the Selectivity Filter of Potassium Channels

Berneche, Simon, Wojtas-Niziurski, Wojciech, Heer, Florian

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 42 KB

english, 2014

36

Inactivation and Voltage-Dependent Rectification Mechanisms in the KcsA Potassium Channel

Boiteux, Celine, Bernèche, Simon

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 33 KB

english, 2011

37

Ion Channels, Permeation, and Electrostatics: Insight into the Function of KcsA

Roux, Benoît, Bernèche, Simon, Im, Wonpil

Journal:

Year:

2000

Language:

english

File:

PDF, 220 KB

english, 2000

38

Synergistic substrate binding determines the stoichiometry of transport of a prokaryotic H+/Cl− exchanger

Picollo, Alessandra, Xu, Yanyan, Johner, Niklaus, Bernèche, Simon, Accardi, Alessio

Journal:

Nature Structural and Molecular Biology

Year:

2012

Language:

english

File:

PDF, 998 KB

english, 2012

39

A PDI-catalyzed thiol–disulfide switch regulates the production of hydrogen peroxide by human Ero1

Ramming, Thomas, Okumura, Masaki, Kanemura, Shingo, Baday, Sefer, Birk, Julia, Moes, Suzette, Spiess, Martin, Jenö, Paul, Bernèche, Simon, Inaba, Kenji, Appenzeller-Herzog, Christian

Journal:

Free Radical Biology and Medicine

Year:

2015

Language:

english

File:

PDF, 2.32 MB

english, 2015

40

Backbone Hydration Determines the Folding Signature of Amino Acid Residues

Bignucolo, Olivier, Leung, Hoi Tik Alvin, Grzesiek, Stephan, Bernèche, Simon

Journal:

Journal of the American Chemical Society

Year:

2015

Language:

english

File:

PDF, 647 KB

english, 2015

41

Mechanism of NH4+ Recruitment and NH3 Transport in Rh Proteins

Baday, Sefer, Orabi, Esam A., Wang, Shihao, Lamoureux, Guillaume, Bernèche, Simon

Journal:

Year:

2015

Language:

english

File:

PDF, 2.30 MB

english, 2015

42

Allocrite Sensing and Binding by the Breast Cancer Resistance Protein (ABCG2) and P-Glycoprotein (ABCB1)

Xu, Yanyan, Egido, Estefania, Li-Blatter, Xiaochun, Müller, Rita, Merino, Gracia, Bernèche, Simon, Seelig, Anna

Journal:

Year:

2015

Language:

english

File:

PDF, 896 KB

english, 2015

43

A rigorous and efficient method to reweight very large conformational ensembles using average experimental data and to determine their relative information content

Leung, Hoi Tik Alvin, Bignucolo, Olivier, Aregger, Regula, Dames, Sonja, Bernèche, Simon, Grzesiek, Stephan

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 1.00 MB

english, 2015

44

Catch-bond mechanism of the bacterial adhesin FimH

Sauer, Maximilian M., Jakob, Roman P., Eras, Jonathan, Baday, Sefer, Eriş, Deniz, Navarra, Giulio, Bernèche, Simon, Ernst, Beat, Maier, Timm, Glockshuber, Rudi

Journal:

Nature Communications

Year:

2016

Language:

english

File:

PDF, 1.82 MB

english, 2016

45

Gating energetics of a voltage-dependent K + channel pore domain

Starek, Greg, Freites, J. Alfredo, Bernèche, Simon, Tobias, Douglas J.

Journal:

Journal of Computational Chemistry

Year:

2017

Language:

english

File:

PDF, 765 KB

english, 2017

46

Conformational dynamics and role of the acidic pocket in ASIC pH-dependent gating

Vullo, Sabrina, Bonifacio, Gaetano, Roy, Sophie, Johner, Niklaus, Bernèche, Simon, Kellenberger, Stephan

Journal:

Proceedings of the National Academy of Sciences

Year:

2017

Language:

english

File:

PDF, 3.31 MB

english, 2017

47

Molecular Mechanism of Cl − /H + Coupling in a CLC Antiporter

Xu, Yanyan, Vien, Malvin, Liang, Chungwen, Accardi, Alessio, Bernèche, Simon

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 50 KB

english, 2017

48

Effect of Membrane Composition on Ion Conduction in a Voltage-Gated Potassium Channel

Johner, Niklaus B., Berneche, Simon

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 46 KB

english, 2017

49

Unidirectional Transport Mechanism in an ATP Dependent Exporter

Xu, Yanyan, Seelig, Anna, Bernèche, Simon

Journal:

ACS Central Science

Year:

2017

Language:

english

File:

PDF, 3.69 MB

english, 2017

50

A bas les barrières… d’énergie dans les canaux potassiques !

Parent, Lucie, Sauvé, Rémy, Bernèche, Simon, Roux, Benoît

Journal:

médecine/sciences

Year:

2002

Language:

french

File:

PDF, 84 KB

french, 2002