C. Haass and D. J. Selkoe, Soluble protein oligomers in neurodegeneration: lessons from the Alzheimer's amyloid ??-peptide, Nature Reviews Molecular Cell Biology, vol.26, issue.2, pp.101-112, 2007.
DOI : 10.1038/nrm2101

J. Hardy and D. J. Selkoe, The Amyloid Hypothesis of Alzheimer's Disease: Progress and Problems on the Road to Therapeutics, Science, vol.297, issue.5580, pp.353-356, 2002.
DOI : 10.1126/science.1072994

R. Roychaudhuri, M. Yang, M. M. Hoshi, and D. B. Teplow, Amyloid ??-Protein Assembly and Alzheimer Disease, Journal of Biological Chemistry, vol.284, issue.8, pp.4749-4753, 2009.
DOI : 10.1074/jbc.R800036200

A. K. Paravastu, I. Qahwash, R. D. Leapman, S. C. Meredith, and R. Tycko, Seeded growth of ??-amyloid fibrils from Alzheimer's brain-derived fibrils produces a distinct fibril structure, Proceedings of the National Academy of Sciences, vol.106, issue.18, pp.7443-7448, 2009.
DOI : 10.1073/pnas.0812033106

K. Ono, M. M. Condron, and D. B. Teplow, Structure-neurotoxicity relationships of amyloid ??-protein oligomers, Proceedings of the National Academy of Sciences, vol.106, issue.35, pp.14745-50, 2009.
DOI : 10.1073/pnas.0905127106

M. Ahmed, J. Davis, D. Aucoin, T. Sato, S. Ahuja et al., Structural conversion of neurotoxic amyloid-??1???42 oligomers to fibrils, Nature Structural & Molecular Biology, vol.155, issue.5, pp.561-567, 2010.
DOI : 10.1023/B:JNMR.0000019521.79321.3c

L. Yu, R. Edalji, J. E. Harlan, T. F. Holzman, A. P. Lopez et al., Structural Characterization of a Soluble Amyloid ??-Peptide Oligomer, Biochemistry, vol.48, issue.9, pp.1870-1877, 2009.
DOI : 10.1021/bi802046n

S. L. Bernstein, N. F. Dupuis, N. D. Lazo, T. Wyttenbach, M. M. Condron et al., Amyloid-?? protein oligomerization and the importance of tetramers and dodecamers in the aetiology of Alzheimer's disease, Nature Chemistry, vol.212, issue.4, pp.326-331, 2009.
DOI : 10.1038/nchem.247

T. Härd and C. Lendel, Inhibition of Amyloid Formation, Journal of Molecular Biology, vol.421, issue.4-5, pp.441-465, 2012.
DOI : 10.1016/j.jmb.2011.12.062

G. Von-helden, P. R. Kemper, N. G. Gotts, and M. T. Bowers, Isomers of Small Carbon Cluster Anions: Linear Chains with up to 20 Atoms, Science, vol.259, issue.5099, pp.1300-1302, 1993.
DOI : 10.1126/science.259.5099.1300

D. E. Clemmer and M. F. Jarrold, Ion Mobility Measurements and their Applications to Clusters and Biomolecules, Journal of Mass Spectrometry, vol.32, issue.6, pp.577-592, 1997.
DOI : 10.1002/(SICI)1096-9888(199706)32:6<577::AID-JMS530>3.0.CO;2-4

J. A. Silveira, K. L. Fort, D. Kim, K. A. Servage, N. A. Pierson et al., From Solution to the Gas Phase: Stepwise Dehydration and Kinetic Trapping of Substance P Reveals the Origin of Peptide Conformations, Journal of the American Chemical Society, vol.135, issue.51, pp.19147-53, 2013.
DOI : 10.1021/ja4114193

M. F. Bush, I. D. Campuzano, and C. Robinson, Ion Mobility Mass Spectrometry of Peptide Ions: Effects of Drift Gas and Calibration Strategies, Analytical Chemistry, vol.84, issue.16, pp.7124-7154, 2012.
DOI : 10.1021/ac3014498

D. E. Clemmer and M. F. Jarrold, Ion Mobility Measurements and their Applications to Clusters and Biomolecules, Journal of Mass Spectrometry, vol.32, issue.6, pp.577-592, 1997.
DOI : 10.1002/(SICI)1096-9888(199706)32:6<577::AID-JMS530>3.0.CO;2-4

A. A. Shvartsburg, R. R. Hudgins, P. Dugourd, and M. F. Jarrold, Structural information from ion mobility measurements: applications to semiconductor clusters, Chemical Society Reviews, vol.30, issue.1, pp.26-35, 2001.
DOI : 10.1039/a802099j

URL : https://hal.archives-ouvertes.fr/hal-00152781

P. Dugourd, R. R. Hudgins, D. E. Clemmer, and M. F. Jarrold, High-resolution ion mobility measurements, Review of Scientific Instruments, vol.68, issue.2, pp.1122-1129, 1997.
DOI : 10.1063/1.1147873

URL : https://hal.archives-ouvertes.fr/hal-00152770

T. Wyttenbach and M. T. Bowers, Gas-Phase Conformations: The Ion Mobility/Ion Chromatography Method, Mod. Mass Spectrom, vol.102, pp.207-232, 2003.
DOI : 10.1007/3-540-36113-8_6

C. Uetrecht, R. J. Rose, E. Van-duijn, K. Lorenzen, and A. J. Heck, Ion mobility mass spectrometry of proteins and proteinassemblies, Chem. Soc. Rev., vol.128, issue.5, pp.1633-55, 2010.
DOI : 10.1039/B914002F

C. Bleiholder, N. F. Dupuis, T. Wyttenbach, and M. T. Bowers, Ion mobility???mass spectrometry reveals a conformational conversion from random assembly to ??-sheet in amyloid fibril formation, Nature Chemistry, vol.1794, issue.2, pp.172-177, 2011.
DOI : 10.1002/bip.360400102

F. Canon, R. Ballivian, F. Chirot, R. Antoine, P. Sarni-manchado et al., Folding of a Salivary Intrinsically Disordered Protein upon Binding to Tannins, Journal of the American Chemical Society, vol.133, issue.20, pp.7847-7852, 2011.
DOI : 10.1021/ja200534f

URL : https://hal.archives-ouvertes.fr/hal-00875405

L. M. Young, P. Cao, D. P. Raleigh, A. E. Ashcroft, and S. E. Radford, Ion Mobility Spectrometry???Mass Spectrometry Defines the Oligomeric Intermediates in Amylin Amyloid Formation and the Mode of Action of Inhibitors, Journal of the American Chemical Society, vol.136, issue.2, pp.660-70, 2014.
DOI : 10.1021/ja406831n

S. Chen, D. H. Russell, and J. , How Closely Related Are Conformations of Protein Ions Sampled by IM-MS to Native Solution Structures?, Journal of The American Society for Mass Spectrometry, vol.16, issue.9, pp.1433-1476, 2015.
DOI : 10.1007/s13361-015-1191-1

D. Thirumalai, G. Reddy, and J. E. Straub, Role of Water in Protein Aggregation and Amyloid Polymorphism, Accounts of Chemical Research, vol.45, issue.1, pp.83-92, 2012.
DOI : 10.1021/ar2000869

T. Forster, Energiewanderung und Fluoreszenz, Die Naturwissenschaften, vol.37, issue.502, pp.166-175, 1946.
DOI : 10.1007/BF00585226

V. Frankevich, V. Chagovets, F. Widjaja, K. Barylyuk, Z. Y. Yang et al., Fluorescence resonance energy transfer of gas-phase ions under ultra high vacuum and ambient conditions, Phys. Chem. Chem. Phys., vol.339, issue.19, pp.8911-8920, 2014.
DOI : 10.1039/C3CP54521K

V. Frankevich, V. Chagovets, F. Widjaja, K. Barylyuk, Z. Yang et al., Fluorescence resonance energy transfer of gas-phase ions under ultra high vacuum and ambient conditions, Phys. Chem. Chem. Phys., vol.339, issue.19, pp.8911-8931, 2014.
DOI : 10.1039/C3CP54521K

F. O. Talbot, A. Rullo, H. Yao, and R. , Fluorescence Resonance Energy Transfer in Gaseous, Mass-Selected Polyproline Peptides, Journal of the American Chemical Society, vol.132, issue.45, pp.16156-16164, 2010.
DOI : 10.1021/ja1067405

R. Zenobi, Coming of Age: Gas-Phase Structural Information on Biomolecules by FRET, Analytical Chemistry, vol.87, issue.15, pp.7497-7498, 2015.
DOI : 10.1021/acs.analchem.5b02456

L. Stryer, Fluorescence Energy Transfer as a Spectroscopic Ruler, Annual Review of Biochemistry, vol.47, issue.1, pp.819-865, 1978.
DOI : 10.1146/annurev.bi.47.070178.004131

S. B. Nabuurs, C. A. Spronk, E. Krieger, H. Maassen, G. Vriend et al., Quantitative Evaluation of Experimental NMR Restraints, Journal of the American Chemical Society, vol.125, issue.39, pp.12026-12034, 2003.
DOI : 10.1021/ja035440f

P. Robustelli, K. Kohlhoff, A. Cavalli, and M. Vendruscolo, Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins, Structure, vol.18, issue.8, pp.923-933, 2010.
DOI : 10.1016/j.str.2010.04.016

S. Kalinin, T. Peulen, S. Sindbert, P. J. Rothwell, S. Berger et al., A toolkit and benchmark study for FRET-restrained high-precision structural modeling, Nature Methods, vol.475, issue.12, pp.1218-1227, 2012.
DOI : 10.1039/b614817d

J. Khandogin and C. L. Brooks, Linking folding with aggregation in Alzheimer's beta-amyloid peptides, Proceedings of the National Academy of Sciences, vol.104, issue.43, pp.16880-16885, 2007.
DOI : 10.1073/pnas.0703832104

X. Zhu, R. P. Bora, A. Barman, R. Singh, and R. Prabhakar, Dimerization of the Full-Length Alzheimer Amyloid ??-Peptide (A??42) in Explicit Aqueous Solution: A Molecular Dynamics Study, The Journal of Physical Chemistry B, vol.116, issue.15, pp.4405-4416, 2012.
DOI : 10.1021/jp210019h

F. Simona, G. Tiana, R. A. Broglia, and G. Colombo, Modeling the ??-helix to ??-hairpin transition mechanism and the formation of oligomeric aggregates of the fibrillogenic peptide A(12???28): insights from all-atom molecular dynamics simulations, Journal of Molecular Graphics and Modelling, vol.23, issue.3, pp.263-273, 2004.
DOI : 10.1016/j.jmgm.2004.07.004

G. M. Torrie and J. P. Valleau, Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling, Journal of Computational Physics, vol.23, issue.2, pp.187-199, 1977.
DOI : 10.1016/0021-9991(77)90121-8

P. Virnau and M. Müler, Calculation of free energy through successive umbrella sampling, The Journal of Chemical Physics, vol.120, issue.23, pp.10925-10930, 2004.
DOI : 10.1063/1.1739216

J. Kästner and W. Interdiscip, Umbrella sampling, Wiley Interdisciplinary Reviews: Computational Molecular Science, vol.8, issue.6, pp.932-942, 2011.
DOI : 10.1002/wcms.66

S. Park and K. Schulten, Calculating potentials of mean force from steered molecular dynamics simulations, The Journal of Chemical Physics, vol.120, issue.13, pp.5946-5961, 2004.
DOI : 10.1063/1.1651473

K. Minoukadeh, C. Chipot, and T. Lelièvre, Potential of Mean Force Calculations: A Multiple-Walker Adaptive Biasing Force Approach, Journal of Chemical Theory and Computation, vol.6, issue.4, pp.1008-1017, 2010.
DOI : 10.1021/ct900524t

URL : https://hal.archives-ouvertes.fr/hal-00674607

T. Lelievre, F. Otto, M. Rousset, and G. Stoltz, Long-time convergence of an adaptive biasing force method, Nonlinearity, vol.21, issue.6, pp.1155-1181, 2007.
DOI : 10.1088/0951-7715/21/6/001

URL : https://hal.archives-ouvertes.fr/hal-00153946

B. Ensing, M. D. Vivo, Z. Liu, P. Moore, and M. L. Klein, Metadynamics as a Tool for Exploring Free Energy Landscapes of Chemical Reactions, Accounts of Chemical Research, vol.39, issue.2, pp.73-81, 2006.
DOI : 10.1021/ar040198i

A. Laio and M. Parrinello, Escaping free-energy minima, Proceedings of the National Academy of Sciences, vol.99, issue.20, pp.12562-12566, 2002.
DOI : 10.1073/pnas.202427399

Y. Sugita, A. Kitao, and Y. Okamoto, Multidimensional replica-exchange method for free-energy calculations, The Journal of Chemical Physics, vol.113, issue.15, pp.6042-6051, 2000.
DOI : 10.1063/1.1308516

Y. Sugita and Y. Okamoto, Replica-exchange molecular dynamics method for protein folding, Chemical Physics Letters, vol.314, issue.1-2, pp.141-151, 1999.
DOI : 10.1016/S0009-2614(99)01123-9

F. Chirot, F. Calvo, F. Albrieux, J. Lemoine, Y. O. Tsybin et al., Statistical Analysis of Ion Mobility Spectrometry. I. Unbiased and Guided Replica-Exchange Molecular Dynamics, Journal of The American Society for Mass Spectrometry, vol.51, issue.2, pp.386-396, 2012.
DOI : 10.1007/s13361-011-0281-y

URL : https://hal.archives-ouvertes.fr/hal-00873906

B. Tarus, J. E. Straub, and D. Thirumalai, Probing the Initial Stage of Aggregation of the A??10-35-protein: Assessing the Propensity for Peptide Dimerization, Journal of Molecular Biology, vol.345, issue.5, pp.1141-1156, 2005.
DOI : 10.1016/j.jmb.2004.11.022

B. Tarus, T. T. Tran, J. Nasica-labouze, F. Sterpone, P. H. Nguyen et al., Structures of the Alzheimer???s Wild-Type A??1-40 Dimer from Atomistic Simulations, The Journal of Physical Chemistry B, vol.119, issue.33, pp.10478-87, 2015.
DOI : 10.1021/acs.jpcb.5b05593

F. Calvo, F. Chirot, F. Albrieux, J. Lemoine, Y. O. Tsybin et al., Statistical Analysis of Ion Mobility Spectrometry. II. Adaptively Biased Methods and Shape Correlations, Journal of The American Society for Mass Spectrometry, vol.22, issue.7, pp.1279-1288, 2012.
DOI : 10.1007/s13361-012-0391-1

URL : https://hal.archives-ouvertes.fr/hal-00873906

F. Albrieux, F. Calvo, F. Chirot, A. Vorobyev, Y. O. Tsybin et al., Conformation of Polyalanine and Polyglycine Dications in the Gas Phase: Insight from Ion Mobility Spectrometry and Replica-Exchange Molecular Dynamics, The Journal of Physical Chemistry A, vol.114, issue.25, pp.6888-6896, 2010.
DOI : 10.1021/jp102621m

F. Calvo and P. Dugourd, Theoretical Evidence for Temperature-induced Proton Mobility in Isolated Lysine-rich Polyalanines, The Journal of Physical Chemistry A, vol.112, issue.20, pp.4679-87, 2008.
DOI : 10.1021/jp711751f

F. Chirot, F. Calvo, F. Albrieux, J. Lemoine, Y. O. Tsybin et al., Statistical Analysis of Ion Mobility Spectrometry. I. Unbiased and Guided Replica-Exchange Molecular Dynamics, Journal of The American Society for Mass Spectrometry, vol.51, issue.2, pp.386-96, 2012.
DOI : 10.1007/s13361-011-0281-y

URL : https://hal.archives-ouvertes.fr/hal-00873906

P. E. Fraser, L. Lévesque, and D. R. Mclachlan, Alzheimer A?? Amyloid Forms an Inhibitory Neuronal Substrate, Journal of Neurochemistry, vol.250, issue.3, pp.1227-1230, 1994.
DOI : 10.1046/j.1471-4159.1994.62031227.x

M. Jin, N. Shepardson, T. Yang, G. Chen, D. Walsh et al., Soluble amyloid ??-protein dimers isolated from Alzheimer cortex directly induce Tau hyperphosphorylation and neuritic degeneration, Proceedings of the National Academy of Sciences, vol.108, issue.14, pp.5819-5824, 2011.
DOI : 10.1073/pnas.1017033108

J. J. Stewart, Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters, Journal of Molecular Modeling, vol.126, issue.1, pp.1-32, 2013.
DOI : 10.1007/s00894-012-1667-x

A. A. Shvartsburg and M. F. Jarrold, An exact hard-spheres scattering model for the mobilities of polyatomic ions, Chemical Physics Letters, vol.261, issue.1-2, pp.86-91, 1996.
DOI : 10.1016/0009-2614(96)00941-4

T. Lührs, C. Ritter, M. Adrian, D. Riek-loher, B. Bohrmann et al., 3D structure of Alzheimer's amyloid-??(1-42) fibrils, Proceedings of the National Academy of Sciences, vol.102, issue.48, pp.17342-17347, 2005.
DOI : 10.1073/pnas.0506723102

R. Tycko, Solid-State NMR Studies of Amyloid Fibril Structure, Annual Review of Physical Chemistry, vol.62, issue.1, pp.279-299, 2011.
DOI : 10.1146/annurev-physchem-032210-103539

D. A. Pearlman, D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham et al., AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules, Computer Physics Communications, vol.91, issue.1-3, pp.1-41, 1995.
DOI : 10.1016/0010-4655(95)00041-D

J. Wang, P. Cieplak, and P. Kollman, How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?, Journal of Computational Chemistry, vol.18, issue.12, pp.1049-1074, 2000.
DOI : 10.1002/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F