A. Stock, V. Robinson, and P. Goudreau, Two-Component Signal Transduction, Annual Review of Biochemistry, vol.69, issue.1, pp.183-215, 2000.
DOI : 10.1146/annurev.biochem.69.1.183

J. Parkinson, Signaling Mechanisms of HAMP Domains in Chemoreceptors and Sensor Kinases, Annual Review of Microbiology, vol.64, issue.1, pp.101-122, 2010.
DOI : 10.1146/annurev.micro.112408.134215

L. Aravind and C. Ponting, The cytoplasmic helical linker domain of receptor histidine kinase and methyl-accepting proteins is common to many prokaryotic signalling proteins, FEMS Microbiology Letters, vol.176, issue.1, pp.111-116, 1999.
DOI : 10.1111/j.1574-6968.1999.tb13650.x

S. Williams and V. Stewart, MicroReview: Functional similarities among twocomponent sensors and methyl-accepting chemotaxis proteins suggest a role for linker region amphipathic helices in transmembrane signal transduction, Molecular Microbiology, vol.33, 1999.

M. Hulko, F. Berndt, M. Gruber, J. Linder, and V. Truffault, The HAMP Domain Structure Implies Helix Rotation in Transmembrane Signaling, Cell, vol.126, issue.5, 2006.
DOI : 10.1016/j.cell.2006.06.058

M. Airola, K. Watts, A. Bilwes, and B. Crane, Structure of Concatenated HAMP Domains Provides a Mechanism for Signal Transduction, Structure, vol.18, issue.4, pp.436-448, 2010.
DOI : 10.1016/j.str.2010.01.013

P. Ames, Q. Zhou, and J. Parkinson, Mutational Analysis of the Connector Segment in the HAMP Domain of Tsr, the Escherichia coli Serine Chemoreceptor, Journal of Bacteriology, vol.190, issue.20, pp.6676-6685, 2008.
DOI : 10.1128/JB.00750-08

Q. Zhou, P. Ames, and J. Parkinson, Mutational analyses of HAMP helices suggest a dynamic bundle model of input-output signalling in chemoreceptors, Molecular Microbiology, vol.232, issue.5, pp.801-814, 2009.
DOI : 10.1111/j.1365-2958.2009.06819.x

M. Airola, K. Watts, A. Bilwes, and B. Crane, Structure of Concatenated HAMP Domains Provides a Mechanism for Signal Transduction, Structure, vol.18, issue.4, pp.436-448, 2010.
DOI : 10.1016/j.str.2010.01.013

K. Watts, M. Johnson, and B. Taylor, Structure-Function Relationships in the HAMP and Proximal Signaling Domains of the Aerotaxis Receptor Aer, Journal of Bacteriology, vol.190, issue.6, pp.2118-2127, 2008.
DOI : 10.1128/JB.01858-07

M. Etzkorn, K. Seidel, L. Li, S. Martell, and M. Geyer, Complex Formation and Light Activation in Membrane-Embedded Sensory Rhodopsin II as Seen by Solid-State NMR Spectroscopy, Structure, vol.18, issue.3, 2010.
DOI : 10.1016/j.str.2010.01.011

URL : http://doi.org/10.1016/j.str.2010.01.011

E. Bordignon, J. Klare, M. Doebber, A. Wegener, and S. Martell, Structural Analysis of a HAMP Domain: THE LINKER REGION OF THE PHOTOTRANSDUCER IN COMPLEX WITH SENSORY RHODOPSIN II, Journal of Biological Chemistry, vol.280, issue.46, pp.38767-38775, 2005.
DOI : 10.1074/jbc.M509391200

M. Doebber, E. Bordignon, J. Klare, J. Holterhues, and S. Martell, Salt-driven Equilibrium between Two Conformations in the HAMP Domain from Natronomonas pharaonis: THE LANGUAGE OF SIGNAL TRANSFER?, Journal of Biological Chemistry, vol.283, issue.42, pp.28691-28701, 2008.
DOI : 10.1074/jbc.M801931200

J. Wang, J. Sasaki, A. Tsai, and J. Spudich, HAMP Domain Signal Relay Mechanism in a Sensory Rhodopsin-Transducer Complex, Journal of Biological Chemistry, vol.287, issue.25, pp.21316-21325, 2012.
DOI : 10.1074/jbc.M112.344622

J. Appleman and V. Stewart, Mutational Analysis of a Conserved Signal-Transducing Element: the HAMP Linker of the Escherichia coli Nitrate Sensor NarX, Journal of Bacteriology, vol.185, issue.1, pp.89-97, 2003.
DOI : 10.1128/JB.185.1.89-97.2003

R. Kishii, L. Falzon, T. Yoshida, H. Kobayashi, and M. Inouye, Structural and Functional Studies of the HAMP Domain of EnvZ, an Osmosensing Transmembrane Histidine Kinase in Escherichia coli, Journal of Biological Chemistry, vol.282, issue.36, pp.26401-26408, 2007.
DOI : 10.1074/jbc.M701342200

H. Ferris, S. Dunin-horkawicz, N. Hornig, M. Hulko, and J. Martin, Mechanism of Regulation of Receptor Histidine Kinases, Structure, vol.20, issue.1, pp.56-66, 2012.
DOI : 10.1016/j.str.2011.11.014

H. Ferris, S. Dunin-horkawicz, L. Mondéjar, M. Hulko, and K. Hantke, The Mechanisms of HAMP-Mediated Signaling in Transmembrane Receptors, Structure, vol.19, issue.3, pp.378-385, 2011.
DOI : 10.1016/j.str.2011.01.006

J. Cheung and W. Hendrickson, Structural Analysis of Ligand Stimulation of the Histidine Kinase NarX, Structure, vol.17, issue.2, pp.190-201, 2009.
DOI : 10.1016/j.str.2008.12.013

J. Falke and A. Erbse, The Piston Rises Again, Structure, vol.17, issue.9, pp.1149-1151, 2009.
DOI : 10.1016/j.str.2009.08.005

S. Chervitz and J. Falke, Molecular mechanism of transmembrane signaling by the aspartate receptor: a model., Proceedings of the National Academy of Sciences, vol.93, issue.6, pp.2545-2550, 1996.
DOI : 10.1073/pnas.93.6.2545

Q. Zhou, P. Ames, and J. Parkinson, Biphasic control logic of HAMP domain signalling in the Escherichia coli serine chemoreceptor, Molecular Microbiology, vol.73, issue.3, pp.596-611, 2011.
DOI : 10.1111/j.1365-2958.2011.07577.x

I. Gushchin, V. Gordeliy, and S. Grudinin, Role of the HAMP Domain Region of Sensory Rhodopsin Transducers in Signal Transduction, Biochemistry, vol.50, issue.4, pp.574-580, 2011.
DOI : 10.1021/bi101032a

URL : https://hal.archives-ouvertes.fr/hal-00784550

K. Nishikata, S. Fuchigami, M. Ikeguchi, and A. Kidera, Molecular modeling of the HAMP domain of sensory rhodopsin II transducer from Natronomonas pharaonis, BIOPHYSICS, vol.6, pp.27-36, 2010.
DOI : 10.2142/biophysics.6.27

M. Etzkorn, K. Seidel, L. Li, S. Martell, and M. Geyer, Complex Formation and Light Activation in Membrane-Embedded Sensory Rhodopsin II as Seen by Solid-State NMR Spectroscopy, Structure, vol.18, issue.3, 2010.
DOI : 10.1016/j.str.2010.01.011

K. Nishikata, M. Ikeguchi, and A. Kidera, Comparative Simulations of the Ground State and the M-Intermediate State of the Sensory Rhodopsin II???Transducer Complex with a HAMP Domain Model, Biochemistry, vol.51, issue.30, pp.5958-5966, 2012.
DOI : 10.1021/bi300696b

H. Park, W. Im, and C. Seok, Transmembrane Signaling of Chemotaxis Receptor Tar: Insights from Molecular Dynamics Simulation Studies, Biophysical Journal, vol.100, issue.12, pp.2955-2963, 2011.
DOI : 10.1016/j.bpj.2011.05.030

B. Hall, J. Armitage, and M. Sansom, Transmembrane Helix Dynamics of Bacterial Chemoreceptors Supports a Piston Model of Signalling, PLoS Computational Biology, vol.7, issue.10, 2011.
DOI : 10.1371/journal.pcbi.1002204.s004

T. Lemmin, C. Soto, G. Clinthorne, W. Degrado, D. Peraro et al., Assembly of the Transmembrane Domain of E. coli PhoQ Histidine Kinase: Implications for Signal Transduction from Molecular Simulations, PLoS Computational Biology, vol.10, issue.1, 2013.
DOI : 10.1371/journal.pcbi.1002878.s007

B. Hall, J. Armitage, and M. Sansom, Mechanism of Bacterial Signal Transduction Revealed by Molecular Dynamics of Tsr Dimers and Trimers of Dimers in Lipid Vesicles, PLoS Computational Biology, vol.8, issue.9, 2012.
DOI : 10.1371/journal.pcbi.1002685.t001

A. Kitao and N. Go, Investigating protein dynamics in collective coordinate space, Current Opinion in Structural Biology, vol.9, issue.2, pp.164-169, 1999.
DOI : 10.1016/S0959-440X(99)80023-2

K. Lindorff-larsen, P. Maragakis, S. Piana, M. Eastwood, and R. Dror, Systematic Validation of Protein Force Fields against Experimental Data, PLoS ONE, vol.7, 2012.

K. Beauchamp, Y. Lin, R. Das, and V. Pande, Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements, Journal of Chemical Theory and Computation, vol.8, issue.4, pp.1409-1414, 2012.
DOI : 10.1021/ct2007814

F. Kiefer, K. Arnold, M. Kunzli, L. Bordoli, and T. Schwede, The SWISS-MODEL Repository and associated resources, Nucleic Acids Research, vol.37, issue.Database, pp.387-392, 2009.
DOI : 10.1093/nar/gkn750

B. Hess, C. Kutzner, D. Van-der-spoel, and E. Lindahl, GROMACS 4:?? Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation, Journal of Chemical Theory and Computation, vol.4, issue.3, pp.435-447, 2008.
DOI : 10.1021/ct700301q

A. Mackerell, M. Feig, and C. Brooks, Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations, Journal of Computational Chemistry, vol.44, issue.Pt 6 Pt 1, pp.1400-1415, 2004.
DOI : 10.1002/jcc.20065

V. Hornak, R. Abel, A. Okur, B. Strockbine, and A. Roitberg, Comparison of multiple Amber force fields and development of improved protein backbone parameters, Proteins: Structure, Function, and Bioinformatics, vol.43, issue.3, pp.712-725, 2006.
DOI : 10.1002/prot.21123

K. Lindorff-larsen, S. Piana, K. Palmo, P. Maragakis, and J. Klepeis, Improved side-chain torsion potentials for the Amber ff99SB protein force field, Proteins: Structure, Function, and Bioinformatics, vol.105, pp.1950-1958, 2010.
DOI : 10.1002/prot.22711

A. Barducci, G. Bussi, and M. Parrinello, Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method, Physical Review Letters, vol.100, issue.2, 2008.
DOI : 10.1103/PhysRevLett.100.020603

M. Parrinello and A. Rahman, Polymorphic transitions in single crystals: A new molecular dynamics method, Journal of Applied Physics, vol.52, issue.12, pp.7182-7190, 1981.
DOI : 10.1063/1.328693

S. Hovmöller, T. Zhou, and T. Ohlson, Conformations of amino acids in proteins, Acta Crystallographica Section D Biological Crystallography, vol.58, issue.5, pp.768-776, 2002.
DOI : 10.1107/S0907444902003359