A. Kessel and N. Ben, Introduction to proteins: Structure, function, and motion, 2011.
DOI : 10.1201/b10456

E. Buxbaum, Fundamentals of protein structure and function, 2015.
DOI : 10.1007/978-3-319-19920-7

G. A. Petsko and D. Ringe, Protein structure and function, 2004.

R. E. Dickerson and I. Geis, The structure and action of proteins, 1969.

J. A. Mccommon, Protein dynamics, Reports on Progress in Physics, vol.47, issue.1, pp.1-46, 1984.
DOI : 10.1088/0034-4885/47/1/001

S. Hay and N. S. Scrutton, Good vibrations in enzyme-catalysed reactions, Nature Chemistry, vol.276, issue.3, pp.161-168, 2012.
DOI : 10.1038/nchem.1223

P. K. Agarwal, Enzymes: An integrated view of structure, dynamics and function, Microb. Cell Fact, vol.5, pp.1-12, 2006.

N. Boekelheide, R. Salomón-ferrer, T. F. Miller, and I. , Dynamics and dissipation in enzyme catalysis, Proceedings of the National Academy of Sciences, vol.123, issue.19, pp.16159-16163, 2011.
DOI : 10.1063/1.2372496

K. A. Henzler-wildman, M. Lei, V. Thai, S. J. Kerns, M. Karplus et al., A hierarchy of timescales in protein dynamics is linked to enzyme catalysis, Nature, vol.21, issue.7171, pp.913-916, 2007.
DOI : 10.1038/nature06407

D. O. Freund, V. Alonso, A. R. Daggett, and . Fersht, The complete folding pathway of a protein from nanoseconds to microseconds, Nature, vol.421, pp.863-867, 2003.

M. Seo, J. Park, E. Kim, S. Hohng, and H. Kim, Protein conformational dynamics dictate the binding affinity for a ligand, Nature Communications, vol.78, pp.3724-3725, 2014.
DOI : 10.1038/nature06232

E. Kim, S. Lee, A. Jeon, J. M. Choi, H. Lee et al., A single-molecule dissection of ligand binding to a protein with intrinsic dynamics, Nature Chemical Biology, vol.269, issue.5, pp.313-318, 2013.
DOI : 10.1002/prot.22223

K. Henzler-wildman and D. Kern, Dynamic personalities of proteins, Nature, vol.124, issue.7172, pp.964-972, 2007.
DOI : 10.1038/nature06522

H. Frauenfelder, F. Parak, and R. D. Young, Conformational Substates in Proteins, Annual Review of Biophysics and Biophysical Chemistry, vol.17, issue.1
DOI : 10.1146/annurev.bb.17.060188.002315

A. Ramanathan, A. J. Savol, C. J. Langmead, P. K. Agarwal, and C. S. Chennubhotla, Discovering Conformational Sub-States Relevant to Protein Function, PLoS ONE, vol.86, issue.1, p.15827, 2011.
DOI : 10.1371/journal.pone.0015827.s016
URL : http://doi.org/10.1016/j.bpj.2010.12.1162

H. Frauenfelder, S. G. Sligar, and P. G. Wolynes, The energy landscapes and motions of proteins, Science, vol.254, issue.5038, pp.1598-1603, 1991.
DOI : 10.1126/science.1749933

M. Lagi, P. Baglioni, and S. Chen, Logarithmic Decay in Single-Particle Relaxation of Hydrated Lysozyme Powder, Physical Review Letters, vol.103, issue.10, pp.108102-108103, 2009.
DOI : 10.1103/PhysRevLett.103.108102

R. D. Young, The physics of proteins: An introduction to biological physics and molecular biophysics, 2010.

J. A. Rupley, E. Gratton, and G. Careri, Water and globular proteins, Trends in Biochemical Sciences, vol.8, issue.1, pp.18-22, 1983.
DOI : 10.1016/0968-0004(83)90063-4
URL : http://www.escholarship.org/uc/item/5378t9rk

J. A. Rupley and G. Careri, Protein Hydration and Function, Adv. Protein Chem, vol.41, p.37, 1991.
DOI : 10.1016/S0065-3233(08)60197-7

M. Tarek and D. J. Tobias, The Dynamics of Protein Hydration Water: A Quantitative Comparison of Molecular Dynamics Simulations and Neutron-scattering Experiments, Biophysical Journal, vol.79, issue.6, pp.3244-3257, 2000.
DOI : 10.1016/S0006-3495(00)76557-X

X. Chu, M. Gajapathy, K. L. Weiss, E. Mamontov, J. D. Ng et al., Dynamic Behavior of Oligomeric Inorganic Pyrophosphatase Explored by Quasielastic Neutron Scattering, The Journal of Physical Chemistry B, vol.116, issue.33, pp.9917-9921, 2012.
DOI : 10.1021/jp303127w

U. R. Shrestha, D. Bhowmik, J. R. Copley, M. Tyagi, J. B. Leão et al., Effects of pressure on the dynamics of an oligomeric protein from deep-sea hyperthermophile, Proceedings of the National Academy of Sciences, vol.3, issue.3, pp.13886-13891, 2015.
DOI : 10.1038/337754a0

X. Chu, E. Mamontov, H. O. Neill, and Q. Zhang, Temperature Dependence of Logarithmic-like Relaxational Dynamics of Hydrated tRNA, The Journal of Physical Chemistry Letters, vol.4, issue.6, pp.936-942, 2013.
DOI : 10.1021/jz400128u

F. Gabel, Protein dynamics in solution and powder measured by incoherent elastic neutron scattering: the influence of Q-range and energy resolution, European Biophysics Journal, vol.41, issue.1, pp.1-12, 2005.
DOI : 10.1007/s00249-004-0433-0

S. Magazù, G. Maisano, F. Migliardo, and C. Mondelli, Mean-Square Displacement Relationship in Bioprotectant Systems by Elastic Neutron Scattering, Biophysical Journal, vol.86, issue.5, pp.3241-3249, 2004.
DOI : 10.1016/S0006-3495(04)74372-6

J. D. Nickels, H. O. Neill, L. Hong, M. Tyagi, G. Ehlers et al., Dynamics of Protein and its Hydration Water: Neutron Scattering Studies on Fully Deuterated GFP, Biophysical Journal, vol.103, issue.7, pp.1566-1575, 2012.
DOI : 10.1016/j.bpj.2012.08.046

P. W. Fenimore, H. Frauenfelder, B. H. Mcmahon, and F. G. Parak, Slaving: Solvent fluctuations dominate protein dynamics and functions, Proceedings of the National Academy of Sciences, vol.346, issue.5, pp.16047-16051, 2002.
DOI : 10.1016/0167-4838(89)90273-2
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC138562

H. Frauenfelder, P. W. Fenimore, G. Chen, and B. H. Mcmahon, Protein folding is slaved to solvent motions, Proceedings of the National Academy of Sciences, vol.425, issue.6953, pp.15469-15472, 2006.
DOI : 10.1038/425027a
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1592535

E. Mamontov, H. O. Neill, and Q. Zhang, Mean-squared atomic displacements in hydrated lysozyme, native and denatured, Journal of Biological Physics, vol.79, issue.3, pp.291-297, 2010.
DOI : 10.1007/s10867-009-9184-6
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2868976

A. P. Briber and . Sokolov, Dynamics of biological macromolecules: Not a simple slaving by hydration water, Biophys. J, vol.98, pp.1321-1326, 2010.

A. P. Sokolov, J. H. Roh, E. Mamontov, V. García, and . Sakai, Role of hydration water in dynamics of biological macromolecules, Chemical Physics, vol.345, issue.2-3, pp.212-218, 2008.
DOI : 10.1016/j.chemphys.2007.07.013

S. Khodadadi and A. P. Sokolov, Protein dynamics: from rattling in a cage to structural relaxation, Soft Matter, vol.1, issue.25, pp.4984-4998, 2015.
DOI : 10.1039/C5SM00636H

W. Doster, S. Cusack, and W. Petry, Dynamical transition of myoglobin revealed by inelastic neutron scattering, Nature, vol.337, issue.6209, pp.754-756, 1989.
DOI : 10.1038/337754a0

A. P. Gregory and . Sokolov, Influence of hydration on the dynamics of lysozyme, Biophys. J, vol.91, pp.2573-2588, 2006.

. Sokolov, Onsets of anharmonicity in protein dynamics, Phys. Rev. Lett, vol.95, pp.38101-38102, 2005.

G. Zacca¨?zacca¨?, How Soft Is a Protein? A Protein Dynamics Force Constant Measured by Neutron Scattering, Science, vol.288, issue.5471, pp.1604-1607, 2000.
DOI : 10.1126/science.288.5471.1604

G. L. Squires, Introduction to the theory of thermal neutron scattering, 2012.

M. Bée, Quasielastic neutron scattering: Principles and applications in solid state chemistry, biology, and materials science, 1988.

P. Lindner, . Th, and . Zemb, Neutron, X-ray and light scattering : Introduction to an investigative tool for colloidal and polymeric systems, 1991.

. Th, P. Zemb, and . Lindner, Neutron, X-rays and light. Scattering methods applied to soft condensed matter, 2002.

C. E. Blanchet and D. I. Svergun, Small-Angle X-Ray Scattering on Biological Macromolecules and Nanocomposites in Solution, Annual Review of Physical Chemistry, vol.64, issue.1, pp.37-54, 2013.
DOI : 10.1146/annurev-physchem-040412-110132

L. A. Feigin and D. I. Svergun, Structure analysis by small-angle X-ray and neutron scattering, 1987.
DOI : 10.1007/978-1-4757-6624-0

T. Brückel, G. Heger, D. Richter, G. Roth, and R. Zorn, Neutron scattering. Lectures of the JCNS laboratory course held at Forschungszentrum Jülich and the research reactor FRM II of TU Munich in cooperation with, Forschungszentrum Jülich GmbH, vol.39, 2012.

F. Gabel, D. Bicout, U. Lehnert, M. Tehei, M. Weik et al., Protein dynamics studied by neutron scattering, Quarterly Reviews of Biophysics, vol.35, issue.4, pp.327-367, 2002.
DOI : 10.1017/S0033583502003840

M. Tehei, R. Daniel, and G. Zacca¨?zacca¨?, Fundamental and biotechnological applications of neutron scattering measurements for macromolecular dynamics, European Biophysics Journal, vol.40, issue.Pt 2, pp.551-558, 2006.
DOI : 10.1007/s00249-006-0082-6

T. A. Harroun, G. D. Wignall, and J. Katsaras, Neutron Scattering for Biology, pp.1-18, 2006.
DOI : 10.1007/3-540-29111-3_1

A. Berthaud, J. Manzi, J. Pérez, and S. Mangenot, Modeling Detergent Organization around Aquaporin-0 Using Small-Angle X-ray Scattering, Journal of the American Chemical Society, vol.134, issue.24, pp.10080-10088, 2012.
DOI : 10.1021/ja301667n

U. R. Shrestha, D. Bhowmik, S. M. Perera, U. Chawla, A. V. Struts et al., Small Angle Neutron and X-Ray Scattering Reveal Conformational Differences in Detergents Affecting Rhodopsin Activation, Biophysical Journal, vol.108, issue.2, p.39, 2015.
DOI : 10.1016/j.bpj.2014.11.240
URL : http://doi.org/10.1016/j.bpj.2014.11.240

C. Sardet, A. Tardieu, and V. Luzzati, Shape and size of bovine rhodopsin: A small-angle X-ray scattering study of a rhodopsin-detergent complex, Journal of Molecular Biology, vol.105, issue.3, pp.383-407, 1976.
DOI : 10.1016/0022-2836(76)90100-5

H. B. Osborne, C. Sardet, M. Michel-villaz, and M. Chabre, Structural study of rhodopsin in detergent micelles by small-angle neutron scattering, Journal of Molecular Biology, vol.123, issue.2, pp.177-206, 1978.
DOI : 10.1016/0022-2836(78)90320-0
URL : https://hal.archives-ouvertes.fr/hal-00293444

A. J. Jackson, Introduction to small-angle neutron scattering and neutron reflectometry, NIST Center for Neutron Research, 2008.

D. A. Jacques and J. Trewhella, Small-angle scattering for structural biology-Expanding the frontier while avoiding the pitfalls, Protein Science, vol.394, issue.4, pp.642-657, 2010.
DOI : 10.1002/pro.351

M. H. Koch, P. Vachette, and D. I. Svergun, Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution, Quarterly Reviews of Biophysics, vol.36, issue.2
DOI : 10.1017/S0033583503003871

D. I. Svergun and M. H. Koch, Small-angle scattering studies of biological macromolecules in solution, Reports on Progress in Physics, vol.66, issue.10, p.1735, 2003.
DOI : 10.1088/0034-4885/66/10/R05

C. Neylon, Small angle neutron and X-ray scattering in structural biology: recent examples from the literature, European Biophysics Journal, vol.15, issue.386, pp.531-541, 2008.
DOI : 10.1007/s00249-008-0259-2

J. R. Copley and J. C. Cook, The Disk Chopper Spectrometer at NIST: a new instrument for quasielastic neutron scattering studies, Chemical Physics, vol.292, issue.2-3, pp.477-485, 2003.
DOI : 10.1016/S0301-0104(03)00124-1

E. Mamontov and K. W. Herwig, A time-of-flight backscattering spectrometer at the Spallation Neutron Source, BASIS, Review of Scientific Instruments, vol.11, issue.8, pp.85109-85110, 2011.
DOI : 10.1103/PhysRevLett.102.016405

A. Meyer, R. M. Dimeo, P. M. Gehring, and D. A. Neumann, The high-flux backscattering spectrometer at the NIST Center for Neutron Research, Review of Scientific Instruments, vol.311, issue.5, pp.2759-2777, 2003.
DOI : 10.1063/1.462505

C. A. Orengo, A. E. Todd, and J. M. Thornton, From protein structure to function, Current Opinion in Structural Biology, vol.9, issue.3
DOI : 10.1016/S0959-440X(99)80051-7

F. G. Parak and E. W. Knapp, A consistent picture of protein dynamics., Proc.Natl
DOI : 10.1073/pnas.81.22.7088

H. Frauenfelder and D. T. Leeson, The energy landscape in non-biological and biological molecules, Nature Structural Biology, vol.4, issue.9, pp.757-759, 1998.
DOI : 10.1146/annurev.physchem.48.1.545

R. H. Austin, K. W. Beeson, L. Eisenstein, H. Frauenfelder, and I. C. Gunsalus, Dynamics of ligand binding to myoglobin, Biochemistry, vol.14, issue.24, pp.5355-5373, 1975.
DOI : 10.1021/bi00695a021

J. N. Onuchic, Z. Luthey-schulten, and P. G. Wolynes, THEORY OF PROTEIN FOLDING: The Energy Landscape Perspective, Annual Review of Physical Chemistry, vol.48, issue.1, pp.545-600, 1997.
DOI : 10.1146/annurev.physchem.48.1.545

C. Hofmann, T. J. Aartsma, H. Michel, and J. Köhler, Direct observation of tiers in the energy landscape of a chromoprotein: A single-molecule study, Proc. Natl. Acad
DOI : 10.1038/355848a0

A. Kitao, S. Hayward, and N. Go, Energy landscape of a native protein: Jumping-among-minima model, Proteins: Structure, Function, and Genetics, vol.107, issue.4, pp.496-517, 1998.
DOI : 10.1002/(SICI)1097-0134(19981201)33:4<496::AID-PROT4>3.0.CO;2-1

L. Milanesi, J. P. Waltho, C. A. Hunter, D. J. Shaw, G. S. Beddard et al., Measurement of energy landscape roughness of folded and unfolded proteins, Proceedings of the National Academy of Sciences, vol.405, issue.6782, pp.19563-19568, 2012.
DOI : 10.1038/35011000

X. Q. Chu, M. Lagi, E. Mamontov, E. Fratini, P. Baglioni et al., Experimental evidence of logarithmic relaxation in single-particle dynamics of hydrated protein molecules, Soft Matter, vol.78, issue.12, pp.2623-2627, 2010.
DOI : 10.1039/c002602f

V. Calandrini and G. R. Kneller, Influence of pressure on the slow and fast fractional relaxation dynamics in lysozyme: A simulation study, The Journal of Chemical Physics, vol.128, issue.6, pp.65102-65103, 2008.
DOI : 10.1002/jcc.10243

X. Chu, A. Faraone, C. Kim, E. Fratini, P. Baglioni et al., Proteins Remain Soft at Lower Temperatures under Pressure, The Journal of Physical Chemistry B, vol.113, issue.15, pp.5001-5006, 2009.
DOI : 10.1021/jp900557w

A. Filabozzi, A. Deriu, M. T. Di-bari, D. Russo, S. Croci et al., Elastic incoherent neutron scattering as a probe of high pressure induced changes in protein flexibility, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, vol.1804, issue.1, pp.63-67, 2010.
DOI : 10.1016/j.bbapap.2009.08.025

K. Heremans and L. Smeller, Protien structure and dynamics at high pressure

E. Mamontov, H. O. Neill, Q. Zhang, and S. M. Chathoth, Temperature dependence of the internal dynamics of a protein in an aqueous solvent: Decoupling from the solvent viscosity, Chemical Physics, vol.424, pp.12-19, 2013.
DOI : 10.1016/j.chemphys.2013.02.026

R. F. Tilton-jr, Effects of temperature on protein structure and dynamics: x-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320K, Biochemistry, vol.31, issue.9, pp.2469-2481, 1992.
DOI : 10.1021/bi00124a006

G. K. Dhindsa, M. Tyagi, and X. Chu, Temperature-dependent dynamics of dry and hydrated beta-casein studied by quasielastic neutron scattering, J. Phys. Chem
DOI : 10.1021/jp504548w

R. Day, B. J. Bennion, S. Ham, and V. Daggett, Increasing Temperature Accelerates Protein Unfolding Without Changing the Pathway of Unfolding, Journal of Molecular Biology, vol.322, issue.1, pp.189-203, 2002.
DOI : 10.1016/S0022-2836(02)00672-1

N. N. Khechinashvili, J. Janin, and F. Rodier, Thermodynamics of the temperature-induced unfolding of globular proteins, Protein Science, vol.193, issue.7, pp.1315-1324, 1995.
DOI : 10.1002/pro.5560040707

F. Meersman, C. Atilgan, A. J. Miles, R. Bader, W. Shang et al., Consistent Picture of the Reversible Thermal Unfolding of Hen Egg-White Lysozyme from Experiment and Molecular Dynamics, Biophysical Journal, vol.99, issue.7, pp.2255-2263, 2010.
DOI : 10.1016/j.bpj.2010.07.060

I. E. Hong, J. B. Iben, S. Johnson, M. C. Luck, J. R. Marden et al., Proteins and pressure, J. Phys. Chem, vol.94, pp.1024-1037, 1990.

V. V. Mozhaev, K. Heremans, J. Frank, P. Masson, and C. Balny, High pressure effects on protein structure and function, Proteins: Structure, Function, and Genetics, vol.68, issue.1, pp.81-91, 1996.
DOI : 10.1002/(SICI)1097-0134(199601)24:1<81::AID-PROT6>3.0.CO;2-R

M. Gross and R. Jaenicke, Proteins under pressure. The influence of high hydrostatic pressure on structure, function and assembly of proteins and protein complexes, European Journal of Biochemistry, vol.57, issue.2, pp.617-630, 1994.
DOI : 10.1016/0968-0004(86)90178-7

H. Li, H. Yamada, and K. Akasaka, Effect of Pressure on the Tertiary Structure and Dynamics of Folded Basic Pancreatic Trypsin Inhibitor, Biophysical Journal, vol.77, issue.5, pp.2801-2812, 1999.
DOI : 10.1016/S0006-3495(99)77112-2

B. B. Boonyaratanakornkit, C. B. Park, and D. S. Clark, Pressure effects on intra- and intermolecular interactions within proteins, Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, vol.1595, issue.1-2, pp.235-249, 2002.
DOI : 10.1016/S0167-4838(01)00347-8

J. Roche, J. A. Caro, D. R. Norberto, P. Barthe, C. Roumestand et al., Cavities determine the pressure unfolding of proteins, Proceedings of the National Academy of Sciences, vol.92, issue.6, pp.6945-6950, 2012.
DOI : 10.1529/biophysj.106.090266

N. Hillson, J. N. Onuchic, and A. E. García, Pressure-induced protein-folding/unfolding kinetics, Proceedings of the National Academy of Sciences, vol.32, issue.2, pp.14848-14853, 1999.
DOI : 10.1002/(SICI)1097-0134(19980801)32:2<136::AID-PROT2>3.0.CO;2-J
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC24736/pdf

I. Daniel, P. Oger, and R. Winter, Origins of life and biochemistry under high-pressure conditions, Chemical Society Reviews, vol.50, issue.10, pp.858-875, 2006.
DOI : 10.1039/b517766a
URL : https://hal.archives-ouvertes.fr/hal-00341807

K. O. Stetter, Hyperthermophiles in the history of life, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.2, issue.12, pp.1837-1843, 2006.
DOI : 10.1073/pnas.87.12.4576

R. C. Hughes, L. Coates, M. P. Blakeley, S. J. Tomanicek, P. Langan et al., Inorganic pyrophosphatase crystals from Thermococcus thioreducens for X-ray and neutron diffraction, Acta Crystallogr. Sect
DOI : 10.1107/s1744309112032447
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3509969

M. L. Byrne-steele and J. D. Ng, Expression, purification and preliminary X-ray analysis of proliferating cell nuclear antigen from the archaeon Thermococcus thioreducens

W. Carrillo, A. García-ruiz, I. Recio, and M. V. Moreno-arribas, Antibacterial Activity of Hen Egg White Lysozyme Modified by Heat and Enzymatic Treatments against Oenological Lactic Acid Bacteria and Acetic Acid Bacteria, Journal of Food Protection, vol.77, issue.10, pp.1732-1739, 2014.
DOI : 10.4315/0362-028X.JFP-14-009

G. E. Matthyssens, G. Simons, and L. Kanarek, Study of the Thermal-Denaturation Mechanism of Hen Egg-White Lysozyme through Proteolytic Degradation, European Journal of Biochemistry, vol.32, issue.4, pp.449-454, 1972.
DOI : 10.1002/bip.1966.360040808

S. Hikima, J. Hikima, J. Rojtinnakorn, I. Hirono, and T. Aoki, Characterization and function of kuruma shrimp lysozyme possessing lytic activity against Vibrio species, Gene, vol.316
DOI : 10.1016/S0378-1119(03)00761-3

R. B. Garriott and . Hoover, Thermococcus thioreducens sp. nov., a novel hyperthermophilic , obligately sulfur-reducing archaeon from a deep-sea hydrothermal vent

S. Fujiwara, M. Plazanet, F. Matsumoto, and T. Oda, Internal motions of actin characterized by quasielastic neutron scattering, European Biophysics Journal, vol.1764, issue.5, pp.661-671, 2011.
DOI : 10.1007/s00249-011-0669-4

F. Volino and A. J. Dianoux, Neutron incoherent scattering law for diffusion in a potential of spherical symmetry: general formalism and application to diffusion inside a sphere, Molecular Physics, vol.2, issue.2, pp.271-279, 1980.
DOI : 10.1080/00268978000102761

R. T. Azuah, L. R. Kneller, and Y. Qiu, DAVE: A Comprehensive Software Suite for the Reduction, Visualization, and Analysis of Low Energy Neutron Spectroscopic Data, Journal of Research of the National Institute of Standards and Technology, vol.114, issue.6
DOI : 10.6028/jres.114.025

. Sokolov, Dynamic transition in tRNA is solvent induced, J. Am. Chem. Soc, vol.128, pp.32-33, 2006.

S. Dellerue, A. Petrescu, J. C. Smith, and M. Bellissent, Radially Softening Diffusive Motions in a Globular Protein, Biophysical Journal, vol.81, issue.3, pp.1666-1676, 2001.
DOI : 10.1016/S0006-3495(01)75820-1

G. R. Kneller, Quasielastic neutron scattering and relaxation processes in proteins: analytical and simulation-based models, Physical Chemistry Chemical Physics, vol.87, issue.8, pp.2641-2655, 2005.
DOI : 10.1039/b502040a
URL : https://hal.archives-ouvertes.fr/hal-00088607

C. A. Angell, Formation of Glasses from Liquids and Biopolymers, Science, vol.267, issue.5206, pp.1924-1935, 1995.
DOI : 10.1126/science.267.5206.1924

P. Etchegoin, Glassylike low-frequency dynamics of globular proteins, Physical Review E, vol.58, issue.1, pp.845-848, 1998.
DOI : 10.1103/PhysRevE.58.845

I. E. Iben, D. Braunstein, W. Doster, H. Frauenfelder, M. K. Hong et al., Glassy behavior of a protein, Physical Review Letters, vol.62, issue.16, pp.1916-1919, 1989.
DOI : 10.1103/PhysRevLett.62.1916

J. L. Green, J. Fan, and C. A. Angell, The protein-glass analogy: New insight from homopeptide comparisons, The Journal of Physical Chemistry, vol.98, issue.51, pp.13780-13790, 1994.
DOI : 10.1021/j100102a052

W. Götze and L. Sjögren, Relaxation processes in supercooled liquids, Reports on Progress in Physics, vol.55, issue.3, pp.241-376, 1992.
DOI : 10.1088/0034-4885/55/3/001

K. Chou, Low-frequency motions in protein molecules. Beta-sheet and beta-barrel, Biophysical Journal, vol.48, issue.2, pp.289-297, 1985.
DOI : 10.1016/S0006-3495(85)83782-6

B. F. Rasmussen, A. M. Stock, D. Ringe, and G. A. Petsko, Crystalline ribonuclease A loses function below the dynamical transition at 220 K, Nature, vol.357, issue.6377, pp.423-424, 1992.
DOI : 10.1038/357423a0

D. Ringe and G. A. Petsko, The ???glass transition??? in protein dynamics: what it is, why it occurs, and how to exploit it, Biophysical Chemistry, vol.105, issue.2-3, pp.667-680, 2003.
DOI : 10.1016/S0301-4622(03)00096-6

L. Meinhold, J. C. Smith, and A. H. Kitao, Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation, Proceedings of the National Academy of Sciences, vol.234, issue.4
DOI : 10.1006/jmbi.1993.1671
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2077243

P. A. Calligari, V. Calandrini, J. Ollivier, J. B. Artero, M. Hartlein et al., Adaptation of Extremophilic Proteins with Temperature and Pressure: Evidence from Initiation Factor 6, The Journal of Physical Chemistry B, vol.119, issue.25, pp.7860-7873, 2015.
DOI : 10.1021/acs.jpcb.5b02034
URL : https://hal.archives-ouvertes.fr/hal-01170680

Y. O. Kamatari, H. Yamada, K. Akasaka, J. A. Jones, C. M. Dobson et al., Response of native and denatured hen lysozyme to high pressure studied by 15N/1H NMR spectroscopy, European Journal of Biochemistry, vol.268, issue.6, pp.1782-1793, 2001.
DOI : 10.1046/j.1432-1033.2001.02050.x

B. W. Matthews, Proteins under pressure, Proceedings of the National Academy of Sciences, vol.19, issue.4, pp.6792-6793, 2012.
DOI : 10.1002/pro.344

M. Refaee, T. Tezuka, K. Akasaka, and M. P. Williamson, Pressure-dependent Changes in the Solution Structure of Hen Egg-white Lysozyme, Journal of Molecular Biology, vol.327, issue.4, pp.857-865, 2003.
DOI : 10.1016/S0022-2836(03)00209-2

E. Dahlhoff and G. N. Somero, Pressure and temperature adaptation of Cytosolic Malate-Dehydrogenases of shallow-living and deep-living marine-invertebrates -Evidence for high body temperatures in hydrothermal vent animals, J. Exp. Biol, vol.159, pp.473-487, 1991.

K. Palczewski, G Protein???Coupled Receptor Rhodopsin, Annual Review of Biochemistry, vol.75, issue.1, pp.743-767, 2006.
DOI : 10.1146/annurev.biochem.75.103004.142743

D. M. Rosenbaum, S. G. Rasmussen, and B. K. Kobilka, The structure and function of G-protein-coupled receptors, Nature, vol.14, issue.7245, pp.356-363, 2009.
DOI : 10.1038/nature08144

K. D. Ridge and K. Palczewski, Visual Rhodopsin Sees the Light: Structure and Mechanism of G Protein Signaling, Journal of Biological Chemistry, vol.282, issue.13, pp.9297-9301, 2007.
DOI : 10.1074/jbc.R600032200

I. S. Moreira, Structural features of the G-protein/GPCR interactions, Biochimica et Biophysica Acta (BBA) - General Subjects, vol.1840, issue.1, pp.16-33, 2014.
DOI : 10.1016/j.bbagen.2013.08.027

X. E. Zhou, K. Melcher, and H. E. Xu, Structure and activation of rhodopsin, Acta Pharmacologica Sinica, vol.53, issue.3, pp.291-299, 2012.
DOI : 10.1073/pnas.241410198

T. W. Schwartz and W. L. Hubbell, Structural biology: A moving story of receptors, Nature, vol.363, issue.7212, pp.473-474, 2008.
DOI : 10.1038/455473a

M. C. Lagerström and H. B. Schioth, Structural diversity of G protein-coupled receptors and significance for drug discovery, Nature Reviews Drug Discovery, vol.11, issue.4, pp.339-357, 2008.
DOI : 10.1038/nrd2518

E. Malmerberg, P. H. Bovee-geurts, G. Katona, X. Deupi, D. Arnlund et al., Conformational activation of visual rhodopsin in native disc membranes, Conformational activation of visual rhodopsin in native disc membranes, p.26, 2015.
DOI : 10.1002/anie.200900741

T. Kim, T. Schlieter, S. Haase, and U. Alexiev, Activation and molecular recognition of the GPCR rhodopsin ??? Insights from time-resolved fluorescence depolarisation and single molecule experiments, European Journal of Cell Biology, vol.91, issue.4, pp.300-310, 2012.
DOI : 10.1016/j.ejcb.2011.03.009

C. Altenbach, A. K. Kusnetzow, O. P. Ernst, K. P. Hofmann, and W. L. Hubbell, High-resolution distance mapping in rhodopsin reveals the pattern of helix movement due to activation, Proceedings of the National Academy of Sciences, vol.84, issue.24, pp.7439-7444, 2008.
DOI : 10.1073/pnas.84.24.8874

J. Li, P. C. Edwards, M. Burghammer, C. Villa, and G. F. Schertler, Structure of Bovine Rhodopsin in a Trigonal Crystal Form, Journal of Molecular Biology, vol.343, issue.5, pp.1409-1438, 2004.
DOI : 10.1016/j.jmb.2004.08.090

A. M. Preininger, J. Meiler, and H. E. Hamm, Conformational Flexibility and Structural Dynamics in GPCR-Mediated G Protein Activation: A Perspective, Journal of Molecular Biology, vol.425, issue.13, pp.2288-2298, 2013.
DOI : 10.1016/j.jmb.2013.04.011

H. Choe, Y. J. Kim, J. H. Park, T. Morizumi, E. F. Pai et al., Crystal structure of metarhodopsin II, Nature, vol.104, issue.7340, pp.651-655, 2011.
DOI : 10.1038/nature09789

T. Okada, O. P. Ernst, K. Palczewski, and K. P. Hofmann, Activation of rhodopsin: new insights from structural and biochemical studies, Trends in Biochemical Sciences, vol.26, issue.5, pp.318-324, 2001.
DOI : 10.1016/S0968-0004(01)01799-6

J. Standfuss, P. C. Edwards, A. D. Antona, M. Fransen, G. Xie et al., The structural basis of agonist-induced activation in constitutively active rhodopsin, Nature, vol.58, issue.7340, pp.656-660, 2011.
DOI : 10.1038/nature09795

. Schertler, Crystal structure of a thermally stable rhodopsin mutant, J. Mol. Biol, vol.372, pp.1179-1188, 2007.

D. Fotiadis, Y. Liang, S. Filipek, D. A. Saperstein, A. Engel et al., The G protein-coupled receptor rhodopsin in the native membrane, FEBS Letters, vol.98, issue.3, pp.281-288, 2004.
DOI : 10.1016/S0014-5793(04)00194-2

R. Medina, D. Perdomo, and J. Bubis, The Hydrodynamic Properties of Dark- and Light-activated States of n-Dodecyl ??-D-Maltoside-solubilized Bovine Rhodopsin Support the Dimeric Structure of Both Conformations, Journal of Biological Chemistry, vol.279, issue.38, pp.39565-39573, 2004.
DOI : 10.1074/jbc.M402446200

B. Jastrzebska, D. Fotiadis, G. F. Jang, R. E. Stenkamp, A. Engel et al., Functional and Structural Characterization of Rhodopsin Oligomers, Journal of Biological Chemistry, vol.281, issue.17, pp.11917-11922, 2006.
DOI : 10.1074/jbc.M600422200
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1618955

A. V. Botelho, T. Huber, T. P. Sakmar, and M. F. Brown, Curvature and Hydrophobic Forces Drive Oligomerization and Modulate Activity of Rhodopsin in Membranes, Biophysical Journal, vol.91, issue.12, pp.4464-4477, 2006.
DOI : 10.1529/biophysj.106.082776

M. V. Petoukhov and D. I. Svergun, Applications of small-angle X-ray scattering to biomacromolecular solutions, The International Journal of Biochemistry & Cell Biology, vol.45, issue.2, pp.429-437, 2013.
DOI : 10.1016/j.biocel.2012.10.017

L. He, A. Piper, F. Meilleur, R. Hernandez, W. T. Heller et al., Conformational Changes in Sindbis Virus Induced by Decreased pH Are Revealed by Small-Angle Neutron Scattering, Journal of Virology, vol.86, issue.4, pp.1982-1987, 2012.
DOI : 10.1128/JVI.06569-11
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3302394

H. Stuhrmann, Small-angle scattering and its interplay with crystallography, contrast variation in SAXS and SANS, Acta Crystallographica Section A Foundations of Crystallography, vol.132, issue.1, pp.181-191, 2008.
DOI : 10.1107/S0108767307046569

D. I. Svergun and M. H. Koch, Small-angle scattering studies of biological macromolecules in solution, Reports on Progress in Physics, vol.66, issue.10, p.1735, 2003.
DOI : 10.1088/0034-4885/66/10/R05

R. P. Rambo and J. A. Tainer, Bridging the solution divide: comprehensive structural analyses of dynamic RNA, DNA, and protein assemblies by small-angle X-ray scattering, Current Opinion in Structural Biology, vol.20, issue.1, pp.128-137, 2010.
DOI : 10.1016/j.sbi.2009.12.015

H. Takeno, A. Maehara, D. Yamaguchi, and S. Koizumi, A Structural Study of an Organogel Investigated by Small-Angle Neutron Scattering and Synchrotron Small-Angle X-ray Scattering, The Journal of Physical Chemistry B, vol.116, issue.26, pp.7739-7745, 2012.
DOI : 10.1021/jp3008514

P. Yin, B. Wu, E. Mamontov, L. L. Daemen, Y. Cheng et al., X-ray and Neutron Scattering Study of the Formation of Core???Shell-Type Polyoxometalates, Journal of the American Chemical Society, vol.138, issue.8, pp.2638-2643, 2016.
DOI : 10.1021/jacs.5b11465

R. K. Le, B. J. Harris, I. J. Iwuchukwu, B. D. Bruce, X. Cheng et al., Analysis of the solution structure of Thermosynechococcus elongatus photosystem I in n-dodecyl-??-d-maltoside using small-angle neutron scattering and molecular dynamics simulation, Archives of Biochemistry and Biophysics, vol.550, issue.551, pp.550-55150, 2014.
DOI : 10.1016/j.abb.2014.04.005

P. Chen and J. S. Hub, Structural Properties of Protein???Detergent Complexes from SAXS and MD Simulations, The Journal of Physical Chemistry Letters, vol.6, issue.24, pp.5116-5121, 2015.
DOI : 10.1021/acs.jpclett.5b02399

E. Di-cola, I. Grillo, and S. Ristori, Small Angle X-ray and Neutron Scattering: Powerful Tools for Studying the Structure of Drug-Loaded Liposomes, Pharmaceutics, vol.20, issue.2, 2016.
DOI : 10.1021/acs.langmuir.5b01365

D. Anunciado, D. K. Rai, S. Qian, V. Urban, and H. O. Neill, Small-angle neutron scattering reveals the assembly of alpha-synuclein in lipid membranes, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, vol.1854, issue.12
DOI : 10.1016/j.bbapap.2015.08.009

Y. N. Dahdal, V. Pipich, H. Rapaport, Y. Oren, R. Kasher et al., Smallangle neutron scattering studies of mineralization on BSA coated citrate capped gold 186

J. Lipfert and S. Doniach, Small-Angle X-Ray Scattering from RNA, Proteins, and Protein Complexes, Annual Review of Biophysics and Biomolecular Structure, vol.36, issue.1, pp.307-327, 2007.
DOI : 10.1146/annurev.biophys.36.040306.132655

U. S. Jeng, T. Lin, J. M. Lin, and D. L. Ho, Contrast variation SANS for the solution structure of the ??-amyloid peptide 1???40 influenced by SDS surfactants, Physica B: Condensed Matter, vol.385, issue.386, pp.385-386865, 2006.
DOI : 10.1016/j.physb.2006.05.128

. Heller, New insight into the structure of RNA in red clover necrotic mosaic virus and the role of divalent cations revealed by small-angle neutron scattering, Arch. Virol, vol.158, pp.1661-1669, 2013.

S. Mehan, V. K. Aswal, and J. Kohlbrecher, Cationic versus Anionic Surfactant in Tuning the Structure and Interaction of Nanoparticle, Protein, and Surfactant Complexes, Langmuir, vol.30, issue.33, pp.9941-9950, 2014.
DOI : 10.1021/la502410v

J. Lipfert, L. Columbus, V. B. Chu, S. A. Lesley, and S. Doniach, Size and Shape of Detergent Micelles Determined by Small-Angle X-ray Scattering, The Journal of Physical Chemistry B, vol.111, issue.43, pp.12427-12438, 2007.
DOI : 10.1021/jp073016l

A. M. Seddon, P. Curnow, and P. J. Booth, Membrane proteins, lipids and detergents: not just a soap opera, Biochimica et Biophysica Acta (BBA) - Biomembranes, vol.1666, issue.1-2, pp.105-117, 2004.
DOI : 10.1016/j.bbamem.2004.04.011
URL : http://doi.org/10.1016/j.bbamem.2004.04.011

A. V. Struts, U. Chawla, S. M. Perera, and M. F. Brown, Investigation of Rhodopsin Dynamics in Its Signaling State by Solid-State Deuterium NMR Spectroscopy, Methods Mol. Biol, vol.1271, pp.133-158, 2015.
DOI : 10.1007/978-1-4939-2330-4_10

E. Ritter, P. Piwowarski, P. Hegemann, and F. J. Bartl, Light-dark Adaptation of Channelrhodopsin C128T Mutant, Journal of Biological Chemistry, vol.288, issue.15, pp.10451-10458, 2013.
DOI : 10.1074/jbc.M112.446427

E. Ritter, K. Zimmermann, M. Heck, K. P. Hofmann, and F. J. Bartl, Transition of Rhodopsin into the Active Metarhodopsin II State Opens a New Light-induced Pathway Linked to Schiff Base Isomerization, Journal of Biological Chemistry, vol.279, issue.46, pp.48102-48111, 2004.
DOI : 10.1074/jbc.M406857200

M. Allaire and L. Yang, Biomolecular solution X-ray scattering at the National Synchrotron Light Source, Journal of Synchrotron Radiation, vol.18, issue.1, pp.41-44, 2011.
DOI : 10.1107/S0909049510036022
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3004252

W. T. Heller, G. W. Lynn, V. S. Urban, K. Weiss, and D. A. Myles, The Bio-SANS Small-Angle Neutron Scattering Instrument at Oak Ridge National Laboratory, Neutron News, vol.19, issue.2, pp.22-23, 2008.
DOI : 10.1080/10448630801975692

D. I. Svergun, S. Richard, M. H. Koch, Z. Sayers, S. Kuprin et al., Protein hydration in solution: Experimental observation by x-ray and neutron scattering, Proceedings of the National Academy of Sciences, vol.46, issue.3
DOI : 10.1016/S0022-2836(76)80071-X

R. C. Oliver, J. Lipfert, D. A. Fox, R. H. Lo, S. Doniach et al., Dependence of Micelle Size and Shape on Detergent Alkyl Chain Length and Head Group, PLoS ONE, vol.46, issue.468, p.62488, 2013.
DOI : 10.1371/journal.pone.0062488.s014

A. Caretta, P. J. Stein, and R. Tirindelli, Rhodopsin-detergent micelles aggregate upon activation of cyclic guanosine monophosphate phosphodiesterase, Biochemistry, vol.29, issue.11, pp.2652-2657, 1990.
DOI : 10.1021/bi00463a005

L. Columbus, J. Lipfert, H. Klock, I. Millett, S. Doniach et al., membrane proteins for structure determination, Protein Science, vol.15, issue.5, pp.961-975, 2006.
DOI : 10.1110/ps.051874706

V. R. Ramakrishnan, A. Darszon, and M. Montal, A small angle X-ray scattering study of a rhodopsin-lipid complex in hexane, J. Biol. Chem, vol.258, pp.4857-4860, 1983.

S. Abel, F. Dupradeau, E. P. Raman, A. D. Mackerell, and M. Marchi, Molecular Simulations of Dodecyl-??-maltoside Micelles in Water: Influence of the Headgroup Conformation and Force Field Parameters, The Journal of Physical Chemistry B, vol.115, issue.3, pp.487-499, 2011.
DOI : 10.1021/jp109545v
URL : https://hal.archives-ouvertes.fr/hal-00720021

K. Y. Chung, S. G. Rasmussen, T. Liu, S. Li, B. T. Devree et al., Conformational changes in the G protein Gs induced by the ??2 adrenergic receptor, Nature, vol.286, issue.7366, pp.611-615, 2011.
DOI : 10.1038/nature10488

. Babu, Molecular signatures of G-protein-coupled receptors, Nature, vol.494, pp.185-194, 2013.

A. V. Struts, G. F. Salgado, and M. F. Brown, Solid-state 2H NMR relaxation illuminates functional dynamics of retinal cofactor in membrane activation of rhodopsin, Proceedings of the National Academy of Sciences, vol.119, issue.2
DOI : 10.1016/0014-5793(80)80281-X

A. V. Struts, G. F. Salgado, K. Martnez-mayorga, and M. F. Brown, Retinal dynamics underlie its switch from inverse agonist to agonist during rhodopsin activation, Nature Structural & Molecular Biology, vol.18, issue.3
DOI : 10.1073/pnas.0701967104
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5283944

S. Kawamura, M. Gerstung, A. T. Colozo, J. Helenius, A. Maeda et al., Kinetic, Energetic, and Mechanical Differences between Dark-State Rhodopsin and Opsin, Structure, vol.21, issue.3, pp.426-437, 2013.
DOI : 10.1016/j.str.2013.01.011
URL : http://doi.org/10.1016/j.str.2013.01.011

M. Mahalingam, K. Martinez-mayorga, M. F. Brown, and R. Vogel, Two protonation switches control rhodopsin activation in membranes, Proceedings of the National Academy of Sciences, vol.81, issue.28, pp.17795-17800, 2008.
DOI : 10.1016/S0076-6879(82)81010-0
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2584695

S. O. Smith, Structure and Activation of the Visual Pigment Rhodopsin, Annual Review of Biophysics, vol.39, issue.1, pp.309-328, 2010.
DOI : 10.1146/annurev-biophys-101209-104901

T. Okada, K. Takeda, and T. Kouyama, Highly Selective Separation of Rhodopsin from Bovine Rod Outer Segment Membranes Using Combination of Divalent Cation and Alkyl(thio)glucoside, Photochemistry and Photobiology, vol.57, issue.5, pp.495-499, 1998.
DOI : 10.1002/jps.2600841014

E. Mamontov and X. Chu, Water???protein dynamic coupling and new opportunities for probing it at low to physiological temperatures in aqueous solutions, Physical Chemistry Chemical Physics, vol.88, issue.33
DOI : 10.1039/c2cp41443k

L. Hong, N. Smolin, B. Lindner, A. P. Sokolov, and J. C. Smith, Three Classes of Motion in the Dynamic Neutron-Scattering Susceptibility of a Globular Protein, Physical Review Letters, vol.107, issue.14
DOI : 10.1103/PhysRevLett.107.148102

X. Brown and . Chu, Quasi-elastic neutron scattering reveals ligand-induced protein dynamics of a G-protein-coupled receptor, J. Phys.Chem. Lett, vol.7, pp.4130-4136, 2016.

M. I. Aveldaño, Phospholipid Solubilization during Detergent Extraction of Rhodopsin from Photoreceptor Disk Membranes, Archives of Biochemistry and Biophysics, vol.324, issue.2, pp.331-343, 1995.
DOI : 10.1006/abbi.1995.0046

X. Chu, E. Mamontov, H. O. Neill, and Q. Zhang, Apparent Decoupling of the Dynamics of a Protein from the Dynamics of its Aqueous Solvent, The Journal of Physical Chemistry Letters, vol.3, pp.380-385, 2012.
DOI : 10.1021/jz201435q

S. M. Chathoth, E. Mamontov, Y. B. Melnichenko, and M. Zamponi, Diffusion and adsorption of methane confined in nano-porous carbon aerogel: A combined quasi-elastic and small-angle neutron scattering study, Microporous and Mesoporous Materials, vol.132, issue.1-2
DOI : 10.1016/j.micromeso.2010.02.012

R. Vogel and F. Siebert, Conformations of the Active and Inactive States of Opsin, Journal of Biological Chemistry, vol.276, issue.42, pp.38487-38493, 2001.
DOI : 10.1074/jbc.M105423200

D. Vitkup, D. Ringe, G. A. Petsko, and M. Karplus, Solvent mobility and the protein 'glass' transition, Nat. Struct. Mol. Biol, vol.7, issue.10, pp.34-38, 1038.

S. Chen, L. Liu, E. Fratini, P. Baglioni, A. Faraone et al., Observation of fragile-to-strong dynamic crossover in protein hydration water, Proc. Natl. Acad
DOI : 10.1103/PhysRevLett.85.4317

N. Leioatts, B. Mertz, K. Martinez-mayorga, T. D. Romo, M. C. Pitman et al., Retinal Ligand Mobility Explains Internal Hydration and Reconciles Active Rhodopsin Structures, Biochemistry, vol.53, issue.2, pp.376-385, 2014.
DOI : 10.1021/bi4013947
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4096112

J. A. Mccommon and M. Karplus, The dynamic picture of protein structure, Accounts of Chemical Research, vol.16, issue.6, pp.187-193, 1983.
DOI : 10.1021/ar00090a001

M. Karplus, J. A. Mccammon, and W. L. Peticolas, The Internal Dynamics of Globular Protein, Critical Reviews in Biochemistry, vol.280, issue.27, pp.293-349, 1981.
DOI : 10.1016/0022-2836(80)90286-7

W. Nadler, A. T. Brunger, K. Schulten, and M. Karplus, Molecular and stochastic dynamics of proteins., Proceedings of the National Academy of Sciences, vol.84, issue.22, pp.7933-7937, 1987.
DOI : 10.1073/pnas.84.22.7933

K. Chou, Low-frequency collective motion in biomacromolecules and its biological functions, Biophysical Chemistry, vol.30, issue.1, pp.3-48, 1988.
DOI : 10.1016/0301-4622(88)85002-6

K. G. Brown, S. C. Erfurth, E. W. Small, and W. L. Peticolas, Conformationally Dependent Low-Frequency Motions of Proteins by Laser Raman Spectroscopy, Proc. Natl
DOI : 10.1073/pnas.69.6.1467

W. Schirmacher, G. Diezemann, and C. Ganter, Harmonic Vibrational Excitations in Disordered Solids and the ???Boson Peak???, Physical Review Letters, vol.81, issue.1, pp.136-139, 1998.
DOI : 10.1103/PhysRevLett.81.136

H. Shintani and H. Tanaka, Universal link between the boson peak and transverse phonons in glass, Nature Materials, vol.99, issue.11, pp.870-877, 2008.
DOI : 10.1038/nmat2293

J. D. Nickels, S. Perticaroli, H. O. Neill, Q. Zhang, G. Ehlers et al., Coherent Neutron Scattering and Collective Dynamics in the Protein, GFP, Biophysical Journal, vol.105, issue.9
DOI : 10.1016/j.bpj.2013.09.029

S. Perticaroli, J. D. Nickels, G. Ehlers, E. Mamontov, and A. P. Sokolov, Dynamics and Rigidity in an Intrinsically Disordered Protein, ??-Casein, The Journal of Physical Chemistry B, vol.118, issue.26, pp.7317-7326, 2014.
DOI : 10.1021/jp503788r

J. A. Fornés, H-Bond vibrations of the ??-helix, Physical Chemistry Chemical Physics, vol.3, issue.6, pp.1086-1088, 2001.
DOI : 10.1039/b008450f

K. Chou, Low-frequency vibrations of helical structures in protein molecules, Biochemical Journal, vol.209, issue.3, pp.573-583, 1983.
DOI : 10.1042/bj2090573

J. P. Klinman and A. Kohen, Hydrogen Tunneling Links Protein Dynamics to Enzyme Catalysis, Annual Review of Biochemistry, vol.82, issue.1, pp.471-496, 2013.
DOI : 10.1146/annurev-biochem-051710-133623
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066974

C. M. Cheatum and A. Kohen, Relationship of Femtosecond???Picosecond Dynamics to Enzyme-Catalyzed H-Transfer, Top. Curr. Chem, vol.337, pp.1-39
DOI : 10.1007/128_2012_407

S. D. Schwartz and V. L. Schramm, Enzymatic transition states and dynamic motion in barrier crossing, Nature Chemical Biology, vol.38, issue.8, pp.551-558, 2009.
DOI : 10.1038/nchembio.202
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859820

G. Careri, P. Fasella, E. Gratton, and W. P. Jencks, Statistical Time Events in Enzymes: A Physical Assessmen, CRC Critical Reviews in Biochemistry, vol.11, issue.2, pp.141-164, 1975.
DOI : 10.1073/pnas.38.10.855

V. V. Brazhkin and K. Trachenko, Collective Excitations and Thermodynamics of Disordered State: New Insights into an Old Problem, The Journal of Physical Chemistry B, vol.118, issue.39, pp.11417-11427, 2014.
DOI : 10.1021/jp503647s

J. Suck, Inelastic neutron scattering applied to the investigation of collective excitations in topologically disordered matter, Condensed Matter Physics, vol.11, issue.1, pp.7-18, 2008.
DOI : 10.5488/CMP.11.1.7

E. Burkel, Phonon spectroscopy by inelastic x-ray scattering, Reports on Progress in Physics, vol.63, issue.2, pp.171-232, 2000.
DOI : 10.1088/0034-4885/63/2/203

A. Cunsolo, C. N. Kodituwakku, F. Bencivenga, M. Frontzek, B. M. Leu et al., Transverse dynamics of water across the melting point: A parallel neutron and x-ray inelastic scattering study, Physical Review B, vol.85, issue.17, pp.174305-174306, 2012.
DOI : 10.1103/PhysRevB.85.174305

M. C. Bellissent-funel, J. Teixeira, S. Chen, B. Dorner, H. D. Middendorf et al., Low-frequency collective modes in dry and hydrated proteins, Biophysical Journal, vol.56, issue.4
DOI : 10.1016/S0006-3495(89)82718-3
URL : http://doi.org/10.1016/s0006-3495(89)82718-3

G. N. Phillips-jr, Structure and dynamics of green fluorescent protein, Current Opinion in Structural Biology, vol.7, issue.6, pp.821-827, 1997.
DOI : 10.1016/S0959-440X(97)80153-4

F. Yang, L. G. Moss, and G. N. Phillips-jr, The molecular structure of green fluorescent protein, Nature Biotechnology, vol.249, issue.10, pp.1246-1251, 1996.
DOI : 10.1016/S0968-0004(00)89080-5

W. Sturhahn, Protein elasticity probed with two synchrotron-based techniques

B. M. Leu, J. T. Sage, N. J. Silvernail, W. R. Scheidt, A. Alatas et al., Bulk Modulus of a Protein Active-Site Mimic, The Journal of Physical Chemistry B, vol.115, issue.15, pp.4469-4473, 2011.
DOI : 10.1021/jp112007z

K. Yoshida, S. Hosokawa, A. Q. Baron, and T. Yamaguchi, Collective dynamics of hydrated ??-lactogloblin by inelastic x-ray scattering, The Journal of Chemical Physics, vol.133, issue.13, pp.134501-134502, 2010.
DOI : 10.1016/0031-8914(59)90006-0

Z. Wang, C. E. Bertrand, W. S. Chiang, E. Fratini, P. Baglioni et al., Inelastic X-ray Scattering Studies of the Short-Time Collective Vibrational Motions in Hydrated Lysozyme Powders and Their Possible Relation to Enzymatic Function, The Journal of Physical Chemistry B, vol.117, issue.4, pp.1186-1195, 2013.
DOI : 10.1021/jp312842m

W. T. Heller, H. M. O-'neill, Q. Zhang, and G. A. Baker, Characterization of the Influence of the Ionic Liquid 1-Butyl-3-methylimidazolium Chloride on the Structure and Thermal Stability of Green Fluorescent Protein, The Journal of Physical Chemistry B, vol.114, issue.43, pp.13866-13871, 2010.
DOI : 10.1021/jp105611b

G. E. Granroth, A. I. Kolesnikov, T. E. Sherline, J. P. Clancy, K. A. Ross et al., SEQUOIA: A Newly Operating Chopper Spectrometer at the SNS, Phys.: Conf. Ser, p.12058, 2010.
DOI : 10.1088/1742-6596/251/1/012058

A. I. Said and . Kolesnikov, Water dynamics in a lithium chloride aqueous solution probed by brillouin neutron and X-ray scattering, J. Phys. Condens. Matter, vol.24, pp.64102-64103, 2012.

A. Orecchini, A. Paciaroni, A. De-francesco, C. Petrillo, and F. Sacchetti, Collective Dynamics of Protein Hydration Water by Brillouin Neutron Spectroscopy, Journal of the American Chemical Society, vol.131, issue.13, pp.4664-4669, 2009.
DOI : 10.1021/ja807957p

E. Cornicchi, F. Sebastiani, A. De-francesco, A. Orecchini, A. Paciaroni et al., Collective density fluctuations of DNA hydration water in the time-window below 1 ps, The Journal of Chemical Physics, vol.135, issue.2, pp.25101-25102, 2011.
DOI : 10.1073/pnas.0400157101

D. Liu, X. Chu, M. Lagi, Y. Zhang, E. Fratini et al., Studies of Phononlike Low-Energy Excitations of Protein Molecules by Inelastic X-Ray Scattering, Physical Review Letters, vol.101, issue.13, pp.135501-135502, 2008.
DOI : 10.1103/PhysRevLett.101.135501

A. Paciaroni, A. Orecchini, M. Haertlein, M. Moulin, V. Conti-nibali et al., Vibrational Collective Dynamics of Dry Proteins in the Terahertz Region, The Journal of Physical Chemistry B, vol.116, issue.12, pp.3861-3865, 2012.
DOI : 10.1021/jp211190q

E. Mamontov, S. B. Vakhrushev, Y. A. Kumzerov, A. Alatas, and H. Sinn, Acoustic phonons in chrysotile asbestos probed by high-resolution inelastic x-ray scattering, Solid State Communications, vol.149, issue.15-16, pp.589-592, 2009.
DOI : 10.1016/j.ssc.2009.01.033

F. Sette, M. H. Krisch, C. Masciovecchio, G. Ruocco, and G. Monaco, Dynamics of Glasses and Glass-Forming Liquids Studied by Inelastic X-ray Scattering, Science, vol.280, issue.5369, pp.1550-1555, 1998.
DOI : 10.1126/science.280.5369.1550

J. Teixeira, M. C. Bellissent-funel, S. H. Chen, and B. Dorner, Observation of New Short-Wavelength Collective Excitations in Heavy Water by Coherent Inelastic Neutron Scattering, Physical Review Letters, vol.54, issue.25, pp.2681-2683, 1985.
DOI : 10.1103/PhysRevLett.54.2681

H. Pfeiffer and K. Heremans, Apparent sound velocity of lysozyme in aqueous solutions, Chemical Physics Letters, vol.361, issue.3-4, pp.226-230, 2002.
DOI : 10.1016/S0009-2614(02)00809-6

K. Achterhold and F. G. Parak, Protein dynamics: determination of anisotropic vibrations at the haem iron of myoglobin, Journal of Physics: Condensed Matter, vol.15, issue.18, pp.1683-1692, 2002.
DOI : 10.1088/0953-8984/15/18/302

Y. Levy and J. N. Onuchic, WATER MEDIATION IN PROTEIN FOLDING AND MOLECULAR RECOGNITION, Annual Review of Biophysics and Biomolecular Structure, vol.35, issue.1, pp.389-415, 2006.
DOI : 10.1146/annurev.biophys.35.040405.102134

V. Conti-nibali, G. D. Angelo, A. Paciaroni, D. J. Tobias, and M. Tarek, On the Coupling between the Collective Dynamics of Proteins and Their Hydration Water, The Journal of Physical Chemistry Letters, vol.5, issue.7
DOI : 10.1021/jz500023e

X. Chu, U. R. Shrestha, H. M. O-'neill, Q. Zhang, A. I. Kolesnikov et al., Investigation of Phonon-Like Excitations in Hydrated Protein Powders by Neutron Scattering, Biophysical Journal, vol.106, issue.2, p.236, 2014.
DOI : 10.1016/j.bpj.2013.11.1383

U. R. Shrestha, D. Bhowmik, K. W. Van-delinder, E. Mamontov, H. O. Neill et al., Collective Excitations in Protein as a Measure of Balance Between its Softness and Rigidity, The Journal of Physical Chemistry B, vol.121, issue.5, 2017.
DOI : 10.1021/acs.jpcb.6b10245

T. R. Guizado, Analysis of the structure and dynamics of human serum albumin, Journal of Molecular Modeling, vol.272, issue.10
DOI : 10.1007/s00894-014-2450-y

M. Fasano, S. Curry, E. Terreno, M. Galliano, G. Fanali et al., The extraordinary ligand binding properties of human serum albumin, IUBMB Life (International Union of Biochemistry and Molecular Biology: Life), vol.1747, issue.12, pp.787-796, 2005.
DOI : 10.1080/15216540500404093

F. Yang, Y. Zhang, and H. Liang, Interactive Association of Drugs Binding to Human Serum Albumin, International Journal of Molecular Sciences, vol.18, issue.5, pp.3580-3595, 2014.
DOI : 10.1111/cbdd.12270

L. Galantini, C. Leggio, P. V. Konarev, and N. V. , Human serum albumin binding ibuprofen: A 3D description of the unfolding pathway in urea, Biophysical Chemistry, vol.147, issue.3, pp.111-122, 2010.
DOI : 10.1016/j.bpc.2010.01.002
URL : https://hal.archives-ouvertes.fr/hal-00618976

S. Baroni, M. Mattu, A. Vannini, R. Cipollone, S. Aime et al., Effect of ibuprofen and warfarin on the allosteric properties of haem-human serum albumin, European Journal of Biochemistry, vol.47, issue.23, pp.6214-6220, 2001.
DOI : 10.1046/j.0014-2956.2001.02569.x

A. Alatas, B. M. Leu, J. Zhao, H. Yava¸syava¸s, T. S. Toellner et al., Improved focusing capability for inelastic X-ray spectrometer at 3-ID of the APS: A combination of toroidal and Kirkpatrick-Baez (KB) mirrors, Sec A: Accelerators, Spectrometers, Detectors and Associated Equipment, pp.166-168, 2011.
DOI : 10.1016/j.nima.2010.11.068

J. P. Sutter, T. S. Toellner, and J. Zhao, An inelastic X-ray spectrometer with 2.2 meV energy resolution, Nucl. Instr. Meth. Phys. Res. Sec A: Accelerators, Spectrometers, Detectors and Associated Equipment, issue.2, pp.467-4681545, 2001.

T. S. Toellner, A. Alatas, and A. H. Said, Six-reflection meV-monochromator for synchrotron radiation, Journal of Synchrotron Radiation, vol.73, issue.468, pp.605-611, 2011.
DOI : 10.1107/S0909049511017535
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3121233

A. M. Gaspar, S. Busch, M. S. Appavou, W. Haeussler, R. Georgii et al., Using polarization analysis to separate the coherent and incoherent scattering from protein samples, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, vol.1804, issue.1, pp.76-82, 2010.
DOI : 10.1016/j.bbapap.2009.06.024
URL : http://mediatum.ub.tum.de/doc/1213661/document.pdf

B. Farruggia and G. A. Picó, Thermodynamic features of the chemical and thermal denaturations of human serum albumin, International Journal of Biological Macromolecules, vol.26, issue.5, pp.317-323, 1999.
DOI : 10.1016/S0141-8130(99)00054-9

M. Ferrand, A. J. Dianoux, W. Petry, and G. Zacca¨?zacca¨?, Thermal motions and function of bacteriorhodopsin in purple membranes: effects of temperature and hydration studied by neutron scattering., Proceedings of the National Academy of Sciences, vol.90, issue.20, pp.9668-9672, 1993.
DOI : 10.1073/pnas.90.20.9668

A. Schlessinger and B. Rost, Protein flexibility and rigidity predicted from sequence, Proteins: Structure, Function, and Bioinformatics, vol.6, issue.Suppl 6, pp.115-126, 2005.
DOI : 10.1002/prot.20587
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.567.9405

M. Z. Kamal, T. A. Mohammad, G. Krishnamoorthy, and N. M. Rao, Role of Active Site Rigidity in Activity: MD Simulation and Fluorescence Study on a Lipase Mutant, PLoS ONE, vol.18, issue.4, p.35188, 2012.
DOI : 10.1371/journal.pone.0035188.s009

K. Opron, K. Xia, and G. W. Wei, Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis, The Journal of Chemical Physics, vol.2, issue.23, pp.234105-234106, 2014.
DOI : 10.1073/pnas.2235686100
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4098052

I. Petitpas, A. A. Bhattacharya, S. Twine, M. East, and S. Curry, Crystal Structure Analysis of Warfarin Binding to Human Serum Albumin: ANATOMY OF DRUG SITE I, Journal of Biological Chemistry, vol.276, issue.25
DOI : 10.1074/jbc.M100575200

G. F. Ames, Structure and mechanism of bacterial periplasmic transport systems
DOI : 10.1007/bf00762135

R. Tam and M. H. Saier, Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria, Microbiol. Rev, vol.57, pp.320-346, 1993.

A. J. Sharff, L. E. Rodseth, J. C. Spurlino, and F. A. Quiocho, Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of the maltodextrin binding protein involved in active transport and chemotaxis, Biochemistry, vol.31, issue.44, pp.10657-10663, 1992.
DOI : 10.1021/bi00159a003

J. T. Park, D. Raychaudhuri, H. Li, S. Normark, and D. Mengin-lecreulx, MppA, a periplasmic binding protein essential for import of the bacterial cell wall peptidelalanyl-?-d-glutamyl-meso-diaminopimelate, J. Bacteriol, vol.180, pp.1215-1223, 1998.

S. Létoffé, P. Delepelaire, and C. Wandersman, The housekeeping dipeptide permease is the Escherichia coli heme transporter and functions with two optional peptide binding proteins, Proceedings of the National Academy of Sciences, vol.240, issue.9, pp.12891-12896, 2006.
DOI : 10.1016/S0378-1119(02)00856-9

A. Maqbool, V. M. Levdikov, E. V. Blagova, M. Herve, R. S. Horler et al., Compensating Stereochemical Changes Allow Murein Tripeptide to Be Accommodated in a Conventional Peptide-binding Protein, Journal of Biological Chemistry, vol.286, issue.36, pp.31512-31521, 2011.
DOI : 10.1074/jbc.M111.267179

H. D. Mertens and D. I. Svergun, Structural characterization of proteins and complexes using small-angle X-ray solution scattering, Journal of Structural Biology, vol.172, issue.1, pp.128-141, 2010.
DOI : 10.1016/j.jsb.2010.06.012

J. G. Duman, Antifreeze and Ice Nucleator Proteins in Terrestrial Arthropods, Annual Review of Physiology, vol.63, issue.1, pp.327-357, 2001.
DOI : 10.1146/annurev.physiol.63.1.327

M. Leitner and . Havenith, Long-range protein-water dynamics in hyperactive insect antifreeze proteins, Proc. Natl. Acad. Sci. U. S. A, vol.110, pp.1617-1622, 2013.

A. D. Haymet, L. G. Ward, M. M. Harding, and C. A. Knight, Valine substituted winter flounder `antifreeze': preservation of ice growth hysteresis, FEBS Letters, vol.92, issue.3, pp.301-306, 1998.
DOI : 10.1016/S0014-5793(98)00652-8
URL : http://hdl.handle.net/1885/73481

S. Venketesh and C. Dayananda, Properties, Potentials, and Prospects of Antifreeze Proteins, Critical Reviews in Biotechnology, vol.273, issue.4, pp.57-82, 2008.
DOI : 10.1271/bbb.62.1205

V. N. Mochalin, O. Shenderova, D. L. Ho, and Y. Gogotsi, The properties and applications of nanodiamonds, Nature Nanotechnology, vol.3, issue.1, pp.11-23, 2012.
DOI : 10.1038/nnano.2011.209

X. Li, J. Shao, Y. Qin, C. Shao, T. Zheng et al., TAT-conjugated nanodiamond for the enhanced delivery of doxorubicin, Journal of Materials Chemistry, vol.2, issue.22, pp.7966-7973, 2011.
DOI : 10.1039/c1jm10653h

M. V. Kharlamova, V. N. Mochalin, M. R. Lukatskaya, J. Niu, V. Presser et al., Adsorption of proteins in channels of carbon nanotubes: Effect of surface chemistry, Materials Express, vol.3, issue.1, pp.1-10, 2013.
DOI : 10.1166/mex.2013.1102

V. C. Sanchez, A. Jachak, R. H. Hurt, and A. B. Kane, Biological Interactions of Graphene-Family Nanomaterials: An Interdisciplinary Review, Chemical Research in Toxicology, vol.25, issue.1, pp.15-34, 2012.
DOI : 10.1021/tx200339h

Z. Chen, W. Ren, L. Gao, B. Liu, S. Pei et al., Three-dimensional flexible and conductive interconnected graphene networks grown by chemical vapour deposi- 200
DOI : 10.1038/nmat3001

H. Hu, Z. Zhao, W. Wan, Y. Gogotsi, and J. Qiu, Ultralight and Highly Compressible Graphene Aerogels, Advanced Materials, vol.50, issue.15, pp.2219-2223, 2013.
DOI : 10.1002/adma.201204530

F. Yavari, Z. Chen, A. V. Thomas, W. Ren, H. Cheng et al., High Sensitivity Gas Detection Using a Macroscopic Three-Dimensional Graphene Foam Network, Scientific Reports, vol.4, issue.1
DOI : 10.1016/0925-4005(91)80151-9
URL : http://doi.org/10.1038/srep00166

N. Li, Q. Zhang, S. Gao, Q. Song, R. Huang et al., Three-dimensional graphene foam as a biocompatible and conductive scaffold for neural stem cells, Scientific Reports, vol.38, issue.1, p.1604, 2013.
DOI : 10.1002/(SICI)1097-4695(199901)38:1<65::AID-NEU5>3.0.CO;2-Q
URL : http://doi.org/10.1038/srep01604

X. Sun, Z. Liu, K. Welsher, J. T. Robinson, A. Goodwin et al., Nano-graphene oxide for cellular imaging and drug delivery, Nano Research, vol.1, issue.3, pp.203-212, 2008.
DOI : 10.1007/s12274-008-8021-8
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2834318

G. K. Dhindsa, D. Bhowmik, M. Goswami, H. O. Neill, E. Mamontov et al., Enhanced Dynamics of Hydrated tRNA on Nanodiamond Surfaces: A Combined Neutron Scattering and MD Simulation Study, The Journal of Physical Chemistry B
DOI : 10.1021/acs.jpcb.6b07511

@. Shrestha, U. Bhowmik, D. , V. Delinder, K. Mamontov et al., Collective Excitations in Protein as a Measure of Balance Between its Softness and Rigidity, The Journal of Physical Chemistry B, vol.121, issue.5, pp.923-930
DOI : 10.1021/acs.jpcb.6b10245

@. Shrestha, U. Bhowmik, D. Copley, J. Tyagi, M. Leão et al., Effects of pressure on the dynamics of an oligomeric protein from deep-sea hyperthermophile, Proc. Natl
DOI : 10.1038/337754a0

@. Bhowmik, D. Dhindsa, G. Shrestha, U. Mamontov, E. Chu et al., Effect of nanodiamond surfaces on drug delivery systems

@. Shrestha, U. Bhowmik, D. , O. Neill, H. Zhang et al., Investigation of glass-like low-frequency collective motions in green fluorescent protein

@. Shrestha, U. Bhowmik, D. Qian, S. Chu, and X. , Contrast match small-angle neutron scattering reveals the conformational change in photoactivation mechanism of rhodopsin

@. Shrestha, U. Bhowmik, D. Tyagi, M. Zhou, W. Mamontov et al., Diffusive motion of hydration shell on the surface of nanodiamonds shows an encouraging pathways for therapeutic drug delivery

@. Bhowmik, D. Shrestha, U. Dhindsa, G. Sharp, M. Stingaciu et al., Investigation of slow-domain motion of a large oligomeric protein using neutron spin-echo and small-anlgle neutron scattering

@. Shrestha, U. Bhowmik, D. Heller, W. Chu, and X. , Conformational stability of hyperthermophilic protein at high temperature studied by small-angle neutron scattering. (in prep.) AUTOBIOGRAPHICAL STATEMENT Utsab R. Shrestha Education 2012 - Ph.D. in Physics, Wayne State University 2012 -2015 M.S in Physics, Instructor, Gyankunj Higher Secondary School, 2004.