J. L. Abascal and C. Vega, A general purpose model for the condensed phases of water : TIP4P, Journal of Chemical Physics, vol.123, p.234505, 2005.

J. Abascal and C. Vega, A general purpose model for the condensed phases of water : TIP4P, J. Chem. Phys, vol.123, p.234505, 2005.

M. Abraham, T. Murtola, R. Schulz, S. Pall, J. Smith et al., High performance molecular simulations through multi-level parallelism from laptops to supercomputers, pp.19-25, 2015.

A. Aminé, , 2016.

J. Allison, R. Rivers, J. Christodoulou, M. Vendruscolo, and C. Dob-son, A Relationship between the Transient Structure in the Monomeric State and the Aggregation Propensities of ?-Synuclein and ?-Synuclein, Biochemistry, vol.53, pp.7170-7183, 2014.

S. Ambadipudi and M. Zweckstetter, Targeting intrinsically disordered proteins in rational drug discovery, Expert Opinion on Drug Discovery, vol.11, pp.65-77, 2016.

J. Andreani, G. Faure, and R. Guerois, InterEvScore : a novel coarsegrained interface scoring function using a multi-body statistical potential coupled to evolution, Bioinformatics, vol.29, pp.1742-1749, 2013.

C. B. Anfinsen, Principles that govern the folding of protein chains, Science, vol.181, pp.223-230, 1973.

M. E. Atyqy, Protéines, peptides et acides aminés, 2010.

A. Ball, A. Phillips, P. Nerenberg, N. Fawzi, D. Wemmer et al., Homogeneous and Heterogeneous Tertiary Structure Ensembles of Amyloid-? Peptides, Biochemistry, vol.50, pp.7612-7628, 2011.

K. Ball, A. Phillips, D. Wemmer, and T. Head-gordon, Differences in ?strand Populations of Monomeric A?40 and A?42, Biophys. J, vol.104, pp.2714-2724, 2013.

K. Ball, D. Wemmer, and T. Head-gordon, Comparison of Structure Determination Methods for Intrinsically Disordered Amyloid-? Peptides, J. Phys. Chem. B, vol.118, pp.6405-6416, 2014.

N. Basdevant, D. Borgis, and T. Ha-duong, A Coarse-Grained Protein-Protein Potential Derived from an All-Atom Force Field, Journal of Physical Chemistry B, vol.111, pp.9390-9399, 2007.

N. Basdevant, D. Borgis, and T. Ha-duong, Modeling Protein-Protein Recognition in Solution Using the Coarse-Grained Force Field SCORPION, Journal of Chemical Theory and Computation, vol.9, pp.803-813, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02112584

A. Battisti, G. Ciasca, A. Grottesi, and A. Tenenbaum, Thermal compaction of the intrinsically disordered protein tau : entropic, structural, and hydrophobic factors, Phys. Chem. Chem. Phys, vol.19, pp.8435-8446, 2017.

C. Becquart and M. Perez, Dynamique moléculaire appliquée aux matériaux 2010

H. Berendsen, J. Postma, W. Van-gunsteren, J. Hermans, and B. Pull-man, Interaction Models for Water in Relation to Protein Hydration, Nature, vol.11, pp.331-342, 1981.

H. Berendsen, J. Grigera, and T. Straatsma, The missing term in effective pair potentials, J. Phys. Chem, vol.91, pp.6269-6271, 1987.

K. Berlin, C. Castaneda, D. Schneidman-duhovny, A. Sali, A. Nava-tudela et al., Recovering a Representative Conformational Ensemble from Underdetermined Macromolecular Structural Data, J. Am. Chem. Soc, vol.135, pp.16595-16609, 2013.

P. Bernadó, E. Mylonas, M. Petoukhov, M. Blackledge, and D. Sver-gun, Structural Characterization of Flexible Proteins using Small-Angle X-ray Scattering, J. Am. Chem. Soc, vol.129, pp.5656-5664, 2007.

P. Bernadó and D. I. Svergun, Structural analysis of intrinsically disordered proteins by small-angle X-ray scattering, Mol. BioSyst, vol.8, pp.151-167, 2012.

C. Bertoncini, Y. Jung, C. Fernandez, W. Hoyer, C. Griesinger et al., Release of long-range tertiary interactions potentiates aggregation of natively unstructured ?-synuclein, Proceedings of the National Academy of Sciences, vol.102, pp.1430-1435, 2005.

R. Best and G. Hummer, Optimized Molecular Dynamics Force Fields Applied to the Helix-Coil Transition of Polypeptides, J. Phys. Chem. B, vol.113, pp.9004-9015, 2009.

R. Best and J. Mittal, Protein Simulations with an Optimized Water Model : Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse, J. Phys. Chem. B, vol.114, pp.14916-14923, 2010.

R. Best, W. Zheng, and J. Mittal, Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association, J. Chem. Theory Comput, vol.10, pp.5113-5124, 2014.

S. Bhattacharya and X. Lin, Recent Advances in Computational Protocols Addressing Intrinsically Disordered Proteins, Biomolecules, vol.9, 2019.

C. Boesch, A. Bundi, M. Oppliger, and K. Wüthrich, 1H Nuclear-Magnetic-Resonance Studies of the Molecular Conformation of Monomeric Glucagon in Aqueous Solution, European Journal of Biochemistry, vol.91, pp.209-214, 1978.

R. Bomblies, M. Luitz, S. Scanu, T. Madl, and M. Zacharias, Transient helicity in intrinsically disordered Axin-1 studied by NMR spectroscopy and molecular dynamics simulations, PLoS One, vol.12, p.174337, 2017.

M. Bonomi, C. Camilloni, A. Cavalli, and M. Vendruscolo, Metainference : a Bayesian inference method for heterogeneous systems, Sci. Adv, vol.2, p.1501177, 2016.

M. Bonomi, G. Heller, C. Camilloni, and M. Vendruscolo, Principles of protein structural ensemble determination, Curr. Opin. Struct. Biol, vol.42, pp.106-116, 2017.

M. Bonomi and C. Camilloni, Integrative structural and dynamical biology with PLUMED-ISDB, Bioinformatics, vol.33, pp.3999-4000, 2017.

W. Boomsma, J. Ferkinghoff-borg, and K. Lindorff-larsen, Combining Experiments and Simulations using the Maximum Entropy Principle, PLOS Comput. Biol, vol.10, p.1003406, 2014.

P. Boon, W. Saw, X. Lim, P. Raghuvamsi, R. Huber et al., Partial Intrinsic Disorder Governs the Dengue Capsid Protein Conformational Ensemble, ACS Chem. Biol, vol.13, pp.1621-1630, 2018.

C. Bracken, L. Iakoucheva, P. Romero, and A. Dunker, Combining Prediction, Computation and Experiment for the Characterization of Protein Disorder, Curr. Opin. Struct. Biol, vol.14, pp.570-576, 2004.

P. Brézellec, I. Vallet-gely, C. Possoz, S. Quevillon-cheruel, and J. Ferat, DciA is an ancestral replicative helicase operator essential for bacterial replication initiation, Nat Commun, vol.7, 2016.

P. Brézellec, M. Petit, S. Pasek, I. Vallet-gely, C. Possoz et al., Domestication of Lambda Phage Genes into a Putative Third Type of Replicative Helicase Matchmaker, Genome Biol Evol, vol.9, pp.1561-1566, 2017.

E. Brookes, P. Vachette, M. Rocco, and J. Pérez, US-SOMO HPLC-SAXS module : dealing with capillary fouling and extraction of pure component patterns from poorly resolved SEC-SAXS data, J Appl Cryst, vol.49, pp.1827-1841, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01451662

B. Brooks, C. Brooks, A. Mackerell, L. Nilsson, R. Petrella et al., CHARMM : the biomolecular simulation program, J. Comput. Chem, vol.30, pp.1545-1614, 2009.

S. Brown and T. Headgordon, Cool walking : A new Markov chain Monte Carlo sampling method, Journal of Computational Chemistry, vol.24, pp.68-76, 2003.

B. Brutscher, I. C. Felli, S. Gil-caballero, T. Ho?ek, R. Kümmerle et al., Intrinsically Disordered Proteins Studied by NMR Spectroscopy, pp.49-122, 2015.

C. Camilloni and M. Vendruscolo, Statistical Mechanics of the Denatured State of a Protein using Replica-Averaged Metadynamics, J. Am. Chem. Soc, vol.136, pp.8982-8991, 2014.

M. Carballo-pacheco and B. Strodel, Comparison of force fields for Alzheimer's A?42 : A case study for intrinsically disordered proteins, Protein Science, vol.26, pp.174-185, 2016.

M. Carlier, C. Husson, L. Renault, and D. Didry, International Review of Cell and Molecular Biology, pp.55-85, 2011.

D. Case, T. Darden, T. Cheatham, C. Simmerling, J. Wang et al., , 2012.

A. Cavalli, C. Camilloni, and M. Vendruscolo, Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle, J. Chem. Phys, vol.138, p.94112, 2013.

C. , M. Ha-duong, and T. , Caractérisation structurale des protéines intrinsèquement désordonnées liées aux pathologies humaines en vue de développer de nouvelles molécules thérapeutiques thèse de doct, 2016.

C. , M. Durand, D. Ha-duong, and T. , Molecular Dynamics Simulations Combined with Nuclear Magnetic Resonance and/or Small-Angle X-ray Scattering Data for Characterizing Intrinsically Disordered Protein Conformational Ensembles, J. Chem. Inf. Model, vol.59, pp.1743-1758, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02169939

C. , M. Deville, C. Pinet, L. Van-heijenoort, C. Du-rand et al., Structural Characterization of N-WASP Domain V Using MD Simulations with NMR and SAXS Data, Biophysical Journal, vol.116, pp.1216-1227, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02169943

, Chapitre 3 les protéines. A.Forme et structure des protéines 1.La forme des protéines est déterminée par leur séquence en acides aminés a.Acides aminés

, Chapitre 8 Structures tridimensionnelles des protéines 1.Structure secondaire A. Le groupement peptidique B. Structures en hélice C. Les structures D

Y. Chebaro, S. Pasquali, and P. Derreumaux, The Coarse-Grained OPEP Force Field for Non-Amyloid and Amyloid Proteins, J. Phys. Chem. B, vol.116, pp.8741-8752, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01498091

C. K. Chen, M. R. Sawaya, M. L. Phillips, E. Reisler, and M. E. Quinlan, Multiple Forms of Spire-Actin Complexes and their Functional Consequences, J. Biol. Chem, vol.287, pp.10684-10692, 2012.

J. Chen, W. Im, and C. Brooks, Balancing Solvation and Intramolecular Interactions, J. Am. Chem. Soc, vol.128, pp.3728-3736, 2006.

P. Chen and J. Hub, Interpretation of Solution X-Ray Scattering by Explicit-Solvent Molecular Dynamics, Biophys. J, vol.108, pp.2573-2584, 2015.

P. Chen and J. S. Hub, Validating Solution Ensembles from Molecular Dynamics Simulation by Wide-Angle X-ray Scattering Data, Biophysical Journal, vol.107, pp.435-447, 2014.

W. Chen, C. Shi, A. Mackerell, and J. Shen, Conformational Dynamics of Two Natively Unfolded Fragment Peptides : Comparison of the AMBER and CHARMM Force Fields, J. Phys. Chem. B, vol.119, pp.7902-7910, 2015.

X. Chen, F. Ni, X. Tian, E. Kondrashkina, Q. Wang et al., Structural Basis of Actin Filament Nucleation by Tandem W Domains, Cell Reports, vol.3, pp.1910-1920, 2013.

J. Cheng, A. Z. Randall, M. J. Sweredoski, and P. Baldi, SCRATCH : a protein structure and structural feature prediction server, Nucleic Acids Res, vol.33, pp.72-76, 2005.

Y. Cheng, C. J. Oldfield, J. Meng, P. Romero, V. N. Uversky et al., Mining alpha-helix-forming molecular recognition features with cross species sequence alignments, Biochemistry, vol.46, pp.13468-13477, 2007.

D. Chereau, F. Kerff, P. Graceffa, Z. Grabarek, K. Langsetmo et al., Actin-bound structures of Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 and the implications for filament assembly, Proceedings of the National Academy of Sciences, vol.102, pp.16644-16649, 2005.

C. Chipot, Les méthodes numériques de la dynamique moléculaire, 2002.

W. Choy and J. Forman-kay, Calculation of ensembles of structures representing the unfolded state of an SH3 domain, J. Mol. Biol, vol.308, pp.1011-1032, 2001.

A. Christensen, S. Sauer, and J. Jensen, Definitive Benchmark Study of Ring Current Effects on Amide Proton Chemical Shifts, J. Chem. Theory Comput, vol.7, pp.2078-2084, 2011.

A. Christensen, T. Linnet, M. Borg, W. Boomsma, K. Lindorff-larsen et al., Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics, PLOS One, vol.8, p.84123, 2013.

G. M. Clore, J. Iwahara, and . Theory, Practice, and Applications of Paramagnetic Relaxation Enhancement for the Characterization of Transient Low-Population States of Biological Macromolecules and Their Complexes, Chem. Rev, vol.109, pp.4108-4139, 2009.

T. Cordeiro, P. Chen, . De, A. Biasio, N. Sibille et al., Disentangling polydispersity in the PCNA-p15PAF complex, a disordered, transient and multivalent macromolecular assembly, Nucleic Acids Res, vol.45, p.1501, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02348011

S. Côté, P. Derreumaux, and N. Mousseau, Distinct Morphologies for Amyloid Beta Protein Monomer : A? 1-40 , A? 1-42 , and A? 1-40 (D23N), J. Chem. Theory Comput, vol.7, pp.2584-2592, 2011.

J. A. Cuff, M. E. Clamp, A. S. Siddiqui, M. Finlay, and G. J. Barton, JPred : a consensus secondary structure prediction server, Bioinformatics, vol.14, pp.892-893, 1998.

R. Cukier, Generating Intrinsically Disordered Protein Conformational Ensembles from a Database of Ramachandran Space Pair Residue Probabilities using a Markov Chain, J. Phys. Chem. B, vol.122, pp.9087-9101, 2018.

L. Cumberworth, M. M. Babu, and J. Gsponer, Promiscuity as a functional trait : intrinsically disordered regions as central players of interactomes, Biochemical Journal, 2013.

G. W. Daughdrill, G. J. Pielak, V. N. Uversky, M. S. Cortese, and A. K. Dunker, Protein Folding Handbook, pp.275-357, 2005.

X. Daura, K. Gademann, B. Jaun, D. Seebach, W. F. Van-gunsteren et al., Peptide Folding : When Simulation Meets Experiment

, Angewandte Chemie International Edition, vol.38, pp.236-240, 1999.

N. E. Davey, D. C. Shields, and R. J. Edwards, Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery, Bioinformatics, vol.25, pp.443-450, 2009.

D. C. and R. , Interactive molecular dynamics, Physica A, vol.240, pp.246-254, 1997.

M. Dedmon, K. Lindorff-larsen, J. Christodoulou, M. Vendruscolo, and C. Dobson, Mapping Long-Range Interactions in ?-Synuclein using Spin-Label NMR and Ensemble Molecular Dynamics Simulations, J. Am. Chem. Soc, vol.127, pp.476-477, 2005.

F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer et al., NMRPipe : a multidimensional spectral processing system based on UNIX pipes, J. Biomol. NMR, vol.6, pp.277-293, 1995.

J. M. Derry, H. D. Ochs, and U. Francke, Isolation of a novel gene mutated in Wiskott-Aldrich syndrome, Cell, vol.78, pp.635-644, 1994.

F. Diella, N. Haslam, C. Chica, A. Budd, S. Michael et al., Understanding eukaryotic linear motifs and their role in cell signaling and regulation, Front. Biosci, vol.13, pp.6580-6603, 2008.

F. M. Disfani, W. Hsu, M. J. Mizianty, C. J. Oldfield, B. Xue et al., MoRFpred, a computational tool for sequence-based prediction and characterization of short disorderto-order transitioning binding regions in proteins, Bioinformatics, vol.28, pp.75-83, 2012.

R. Dominguez, Actin filament nucleation and elongation factors -structure-function relationships, Critical Reviews in Biochemistry and Molecular Biology, vol.44, pp.351-366, 2009.

Z. Dosztányi, Prediction of protein disorder based on IUPred, Protein Science, vol.27, pp.331-340, 2018.

Z. Dosztányi, V. Csizmók, P. Tompa, and I. Simon, The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins, Journal of Molecular Biology, vol.347, pp.827-839, 2005.

Z. Dosztányi, B. Mészáros, and I. Simon, ANCHOR : web server for predicting protein binding regions in disordered proteins, Bioinformatics, vol.25, pp.2745-2746, 2009.

A. Drozdetskiy, C. Cole, J. Procter, and G. J. Barton, JPred4 : a protein secondary structure prediction server, Nucleic Acids Res, vol.43, pp.389-394, 2015.

Y. Duan, C. Wu, S. Chowdhury, M. Lee, G. Xiong et al., A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations, J. Comput. Chem, vol.24, pp.1999-2012, 2003.

A. M. Ducka, P. Joel, G. M. Popowicz, K. M. Trybus, M. Schleicher et al., Structures of actin-bound Wiskott-Aldrich syndrome protein homology 2 (WH2) domains of Spire and the implication for filament nucleation, Proc Natl Acad Sci, vol.107, pp.11757-11762, 2010.

A. K. Dunker, E. Garner, S. Guilliot, P. Romero, K. Albrecht et al., Protein disorder and the evolution of molecular recognition : theory, predictions and observations, Pac Symp Biocomput, pp.473-484, 1998.

A. K. Dunker, Z. Obradovic, P. Romero, E. C. Garner, and C. J. Brown, Intrinsic protein disorder in complete genomes, Genome Inform Ser Workshop Genome Inform, vol.11, pp.161-171, 2000.

A. K. Dunker, J. D. Lawson, C. J. Brown, R. M. Williams, P. Romero et al., Z. Intrinsically disordered protein. Journal of Molecular Graphics and Modelling, vol.19, pp.26-59, 2001.

A. K. Dunker, M. S. Cortese, P. Romero, L. M. Iakoucheva, and V. N. Uver-sky, Flexible nets : The roles of intrinsic disorder in protein interaction networks, FEBS Journal, vol.272, pp.5129-5148, 2005.

A. K. Dunker, I. Silman, V. N. Uversky, and J. L. Sussman, Function and structure of inherently disordered proteins, Current Opinion in Structural Biology, vol.18, pp.756-764, 2008.

A. Dunker, C. Brown, and . Obradovi?, Z. in Unfolded Proteins, pp.25-49, 2002.

K. Dunker, C. Brown, D. Lawson, L. Iakoucheva, and Z. Obradovi?, Intrinsic Disorder and Protein Function, Biochemistry, vol.41, pp.6573-6582, 2002.

V. Duong, Z. Chen, M. Thapa, and R. Luo, Computational Studies of Intrinsically Disordered Proteins, J. Phys. Chem. B, vol.122, pp.10455-10469, 2018.

H. J. Dyson and P. E. Wright, Unfolded Proteins and Protein Folding Studied by NMR, Chem. Rev, vol.104, pp.3607-3622, 2004.

H. J. Dyson and P. E. Wright, Intrinsically unstructured proteins and their functions, Nat Rev Mol Cell Biol, vol.6, pp.197-208, 2005.

R. J. Edwards, N. E. Davey, and D. C. Shields, SLiMFinder : A Probabilistic Method for Identifying Over-Represented, Convergently Evolved, Short Linear Motifs in Proteins, PLOS ONE, vol.2, p.967, 2007.

D. Eliezer, Biophysical characterization of intrinsically disordered proteins, Curr. Opin. Struct. Biol, vol.19, pp.23-30, 2009.

U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee et al., A smooth particle mesh Ewald method, Journal of chemical physics, vol.103, pp.8577-8593, 1995.

A. Estana, N. Sibille, E. Delaforge, M. Vaisset, J. Cortés et al., Realistic Ensemble Models of Intrinsically Disordered Proteins using a Structure-Encoding Coil Database, Structure, vol.27, pp.1-11, 2019.
URL : https://hal.archives-ouvertes.fr/hal-01954977

C. Etchebest, Cours modélisatoin moléculaire -Force Field, 2015.

J. Fawcett and T. Pawson, N-WASP Regulation-the Sting in the Tail, Science, vol.290, pp.725-726, 2000.

B. A. Fedorov, O. B. Ptitsyn, and L. A. Voronin, X-ray diffuse scattering by proteins in solution. Consideration of solvent influence, J Appl Crystallogr, vol.7, pp.181-186, 1974.

H. Feldman and C. Hogue, Probabilistic sampling of protein conformations : New hope for brute force ?, Proteins, vol.46, pp.8-23, 2002.

I. C. Felli and R. Pierattelli, Recent progress in NMR spectroscopy : Toward the study of intrinsically disordered proteins of increasing size and complexity, IUBMB Life, vol.64, pp.473-481, 2012.

, Intrinsically disordered proteins studied by NMR spectroscopy, 2015.

A. L. Fink, Natively unfolded proteins, Current Opinion in Structural Biology, vol.15, pp.35-41, 2005.

C. Fisher and C. Stultz, Constructing ensembles for intrinsically disordered proteins, Curr. Opin. Struct. Biol, vol.21, pp.426-431, 2011.

C. Fisher, A. Huang, and C. Stultz, Modeling Intrinsically Disordered Proteins with Bayesian Statistics, J. Am. Chem. Soc, vol.132, pp.14919-14927, 2010.

P. Flory, Principles of Polymer Chemistry, 1953.

A. V. Follis, C. A. Galea, and R. W. Kriwacki, Intrinsic protein flexibility in regulation of cell proliferation : advantages for signaling and opportunities for novel therapeutics, Adv. Exp. Med. Biol, vol.725, pp.27-49, 2012.

D. Franke, M. Petoukhov, P. Konarev, A. Panjkovich, A. Tuukkanen et al., ATSAS 2.8 : a comprehensive data analysis suite for small-Angle scattering from macromolecular solutions, J. Appl. Crystallogr, vol.50, pp.1212-1225, 2017.

D. Franke, C. M. Jeffries, and D. I. Svergun, Correlation Map, a goodnessof-fit test for one-dimensional X-ray scattering spectra, Nat. Methods, vol.12, pp.419-422, 2015.

J. Fred-dice, Peptide sequences that target cytosolic proteins for lysosomal proteolysis, Trends in Biochemical Sciences, vol.15, pp.305-309, 1990.

G. Fuentes, A. Nederveen, R. Kaptein, R. Boelens, and A. Bonvin, Describing Partially Unfolded States of Proteins from Sparse NMR Data, J. Biomol. NMR, vol.33, pp.175-186, 2005.

G. Fuertes, N. Banterle, K. Ruff, A. Chowdhury, D. Mercadante et al., Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements, Proceedings of the National Academy of Sciences, vol.114, pp.6342-6351, 2017.

H. Y. Fung, M. Birol, and E. Rhoades, IDPs in macromolecular complexes : the roles of multivalent interactions in diverse assemblies, Current Opinion in Structural Biology, vol.49, pp.36-43, 2018.

M. Fuxreiter, I. Simon, P. Friedrich, and P. Tompa, Preformed Structural Elements Feature in Partner Recognition by Intrinsically Unstructured Proteins, J. Mol. Biol, vol.338, pp.1015-1026, 2004.

M. Fuxreiter and P. Tompa, Fuzzy complexes : a more stochastic view of protein function, Adv. Exp. Med. Biol, vol.725, pp.1-14, 2012.

C. A. Galea, Y. Wang, S. G. Sivakolundu, and R. W. Kriwacki, Regulation of Cell Division by Intrinsically Unstructured Proteins ; Intrinsic Flexibility, Modularity and Signaling Conduits, Biochemistry, vol.47, pp.7598-7609, 2008.

E. Gallicchio and R. Levy, AGBNP : An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling, J. Comput. Chem, vol.25, pp.479-499, 2004.

D. Ganguly and J. Chen, Modulation of the Disordered Conformational Ensembles of the p53 Transactivation Domain by Cancer-Associated Mutations, PLoS Comput. Biol, vol.11, p.1004247, 2015.

N. Garner, . Cannon, N. Romero, . Obradovic, and N. Dunker, Predicting Disordered Regions from Amino Acid Sequence : Common Themes Despite Differing Structural Characterization, Genome Inform Ser Workshop Genome Inform, vol.9, pp.201-213, 1998.

A. S. Garza, N. Ahmad, and R. Kumar, Role of intrinsically disordered protein regions/domains in transcriptional regulation, Life Sciences, vol.84, pp.189-193, 2009.

J. Gaucher, C. Maugé, D. Didry, B. Guichard, L. Renault et al., Interactions of Isolated C-terminal Fragments of Neural Wiskott-Aldrich Syndrome Protein (N-WASP) with Actin and Arp2/3 Complex, Journal of Biological Chemistry, vol.287, pp.34646-34659, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02880625

S. Gerben, J. Lemkul, A. Brown, and D. Bevan, Comparing atomistic molecular mechanics force fields for a difficult target : a case study on the Alzheimer's amyloid ?-peptide, J. Biomol. Struct. Dyn, vol.32, pp.1817-1832, 2014.

T. Graen, R. Klement, A. Grupi, E. Haas, and H. Grubmüller, Transient Secondary and Tertiary Structure Formation Kinetics in the Intrinsically Disordered State of ?-Synuclein from Atomistic Simulations, Chem-PhysChem, vol.19, pp.2507-2511, 2018.

D. Granata, C. Camilloni, M. Vendruscolo, and A. Laio, Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics, Proc. Natl. Acad. Sci. U.S.A, vol.110, pp.6817-6822, 2013.

D. Granata, F. Baftizadeh, J. Habchi, C. Galvagnion, . De et al., The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments, Sci. Rep, vol.5, 2015.

S. Grudinin, M. Garkavenko, and A. Kazennov, Pepsi-SAXS : an adaptive method for rapid and accurate computation of small-Angle X-ray scattering profiles, Acta Crystallogr. D Struct. Biol, vol.73, pp.449-464, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01516719

J. Gsponer and M. Madan-babu, The rules of disorder or why disorder rules, Progress in Biophysics and Molecular Biology, vol.99, pp.94-103, 2009.

A. Guinier, La diffraction des rayons X aux très petits angles : application à l'étude de phénomènes ultramicroscopiques, Ann. Phys, vol.11, pp.161-237, 1939.

J. Habchi, P. Tompa, S. Longhi, and V. N. Uversky, Introducing Protein Intrinsic Disorder, Chem. Rev, vol.114, pp.6561-6588, 2014.

B. Han, Y. Liu, S. Ginzinger, and D. Wishart, SHIFTX2 : significantly improved protein chemical shift prediction, J. Biomol. NMR, vol.50, p.43, 2011.

K. Han, J. Syi, B. Brooks, and J. Ferretti, Solution conformations of the B-loop fragments of human transforming growth factor alpha and epidermal growth factor by 1H nuclear magnetic resonance and restrained molecular dynamics, Proc. Natl. Acad. Sci. U.S.A, vol.87, pp.2818-2822, 1990.

U. H. Hansmann, Parallel Tempering Algorithm for Conformational Studies of Biological Molecules, Chemical Physics Letters, vol.281, pp.140-150, 1997.

J. Hanson, Y. Yang, K. Paliwal, and Y. Zhou, Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks, Bioinformatics, vol.33, pp.685-692, 2017.

J. Hanson, K. Paliwal, and Y. Zhou, Accurate Single-Sequence Prediction of Protein Intrinsic Disorder by an Ensemble of Deep Recurrent and Convolutional Architectures, J. Chem. Inf. Model, vol.58, pp.2369-2376, 2018.

R. Heffernan, K. Paliwal, J. Lyons, A. Dehzangi, A. Sharma et al., Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning, Scientific Reports, vol.5, p.11476, 2015.

R. Heffernan, A. Dehzangi, J. Lyons, K. Paliwal, A. Sharma et al., Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins, Bioinformatics, vol.32, pp.843-849, 2016.

M. Heinig and D. Frishman, STRIDE : a web server for secondary structure assignment from known atomic coordinates of proteins, Nucleic Acids Res, vol.32, pp.500-502, 2004.

J. Henriques and M. Skepö, Molecular Dynamics Simulations of Intrinsically Disordered Proteins : On the Accuracy of the TIP4P-D Water Model and the Representativeness of Protein Disorder Models, J. Chem. Theory Comput, vol.12, pp.3407-3415, 2016.

J. Henriques, C. Cragnell, and M. Skepö, Molecular Dynamics Simulations of Intrinsically Disordered Proteins : Force Field Evaluation and Comparison with Experiment, J. Chem. Theory Comput, vol.11, pp.3420-3431, 2015.

J. Henriques, L. Arleth, K. Lindorff-larsen, and M. Skepö, On the Calculation of SAXS Profiles of Folded and Intrinsically Disordered Proteins from Computer Simulations, J. Mol. Biol, vol.430, pp.2521-2539, 2018.

M. Hertzog, C. Van-heijenoort, D. Didry, M. Gaudier, J. Coutant et al., The ?-Thymosin/WH2 Domain : Structural Basis for the Switch from Inhibition to Promotion of Actin Assembly, Cell, vol.117, pp.611-623, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00121857

B. Hess and . P-lincs, A Parallel Linear Constraint Solver for Molecular Simulation, Journal of Chemical Theory and Computation, vol.4, pp.116-122, 2008.

K. Hoffmann, M. Mcgovern, C. Chiu, and J. Pablo, Secondary Structure of Rat and Human Amylin across Force Fields, PLOS One, vol.10, p.134091, 2015.

W. G. Hoover, Canonical dynamics : Equilibrium phase-space distributions, Physical Review A, vol.31, pp.1695-1697, 1985.

H. Horn, W. Swope, J. Pitera, J. Madura, T. Dick et al., Development of an improved four-site water model for biomolecular simulations : TIP4P-Ew, J. Chem. Phys, vol.120, pp.9665-9678, 2004.

V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg et al., Comparison of multiple Amber force fields and development of improved protein backbone parameters, Proteins : Structure, Function, and Bioinformatics, vol.65, pp.712-725, 2006.

J. Huang and A. Mackerell, CHARMM36 all-atom additive protein force field : Validation based on comparison to NMR data, J. Comput. Chem, vol.34, pp.2135-2145, 2013.

J. Huang, S. Rauscher, G. Nawrocki, T. Ran, M. Feig et al., CHARMM36m : an improved force field for folded and intrinsically disordered proteins, Nat. Methods, vol.14, pp.71-73, 2017.

J. Hub, Interpreting solution X-ray scattering data using molecular simulations, Curr. Opin. Struct. Biol, vol.49, pp.18-26, 2018.

G. Hummer and J. Köfinger, Bayesian ensemble refinement by replica simulations and reweighting, J. Chem. Phys, vol.143, p.243150, 2015.

J. Hus, D. Marion, and M. Blackledge, Determination of Protein Backbone Structure Using Only Residual Dipolar Couplings, Journal of the American Chemical Society, vol.123, pp.1541-1542, 2001.

W. Im, M. Feig, and C. Brooks, An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins, Biophys. J, vol.85, pp.2900-2918, 2003.

W. Im, M. Lee, and C. Brooks, Generalized born model with a simple smoothing function, J. Comput. Chem, vol.24, pp.1691-1702, 2003.

C. Ioannou, P. M. Schaeffer, N. E. Dixon, and P. Soultanas, Helicase binding to DnaI exposes a cryptic DNA-binding site during helicase loading in Bacillus subtilis, Nucleic Acids Res, vol.34, pp.5247-5258, 2006.

G. J. Isralewitz-b and J. Baudry, Steered molecular dynamics investigations of protein function, J Mol Graph Model, vol.19, pp.13-25, 2001.

D. Jacques and J. Trewhella, Small-Angle scattering for structura biology-Expanding the frontier while avoiding the pitfalls, Protein Sci, vol.19, pp.642-657, 2010.

M. R. Jensen, R. W. Ruigrok, and M. Blackledge, Describing intrinsically disordered proteins at atomic resolution by NMR, Current Opinion in Structural Biology, vol.23, pp.426-435
URL : https://hal.archives-ouvertes.fr/hal-01321604

M. Jensen, G. Communie, E. Ribeiro, N. Martinez, A. Desfosses et al., Intrinsic disorder in measles virus nucleocapsids, Proc. Natl. Acad. Sci. U.S.A, vol.108, pp.9839-9844, 2011.

F. Jiang, W. Han, and Y. Wu, The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development, Phys. Chem. Chem. Phys, vol.15, pp.3413-3428, 2013.

F. Jiang, C. Zhou, and Y. Wu, Residue-Specific Force Field Based on the Protein Coil Library. RSFF1 : Modification of OPLS-AA/L, J. Phys. Chem. B, vol.118, pp.6983-6998, 2014.

W. Jorgensen, J. Chandrasekhar, J. Madura, R. Impey, and M. Klein, Comparison of simple potential functions for simulating liquid water, J. Chem. Phys, vol.79, pp.926-935, 1983.

W. Jorgensen, D. Maxwell, and J. Tirado-rives, Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids, J. Am. Chem. Soc, vol.118, pp.11225-11236, 1996.

G. Kaminski, R. Friesner, J. Tirado-rives, and W. Jorgensen, Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides, J. Phys. Chem. B, vol.105, pp.6474-6487, 2001.

J. Karp, E. Erylimaz, and D. Cowburn, Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins, J. Biomol. NMR, vol.61, pp.35-45, 2015.

J. Kemmink and R. Scheek, Dynamic modelling of a helical peptide in solution using NMR data : Multiple conformations and multi-spin effects, J. Biomol. NMR, vol.6, pp.33-40, 1995.

T. Kiefhaber, A. Bachmann, and K. S. Jensen, Dynamics and mechanisms of coupled protein folding and binding reactions, Current Opinion in Structural Biology, vol.22, pp.21-29, 2012.

A. Kikhney and D. Svergun, A practical guide to small angle X-ray scattering (SAXS) of flexible and intrinsically disordered proteins, FEBS Letters, vol.589, pp.2570-2577, 2015.

D. Kimanius, I. Pettersson, G. Schluckebier, E. Lindahl, M. An-dersson et al., J. Chem. Theory Comput, vol.11, pp.3491-3498, 2015.

M. Kjaergaard and F. M. Poulsen, Disordered proteins studied by chemical shifts, Progress in Nuclear Magnetic Resonance Spectroscopy, vol.60, pp.42-51, 2012.

M. S. Klausen, M. C. Jespersen, H. Nielsen, K. K. Jensen, V. I. Jurtz et al., NetSurfP-2.0 : Improved prediction of protein structural features by integrated deep learning, Proteins : Structure, Function, and Bioinformatics, vol.87, pp.520-527, 2019.

C. Knight and J. Hub, WAXSiS : a web server for the calculation of SAXS / WAXS curves based on explicit-solvent molecular dynamics, Nucl. Acids Res, vol.43, pp.225-230, 2015.

M. Knott and R. Best, A Preformed Binding Interface in the Unbound Ensemble of an Intrinsically Disordered Protein : Evidence from Molecular Simulations, PLoS Comput. Biol, vol.8, p.1002605, 2012.

K. Kohlhoff, P. Robustelli, A. Cavalli, X. Salvatella, and M. Vendrus-colo, Fast and Accurate Predictions of Protein NMR Chemical Shifts from Interatomic Distances, J. Am. Chem. Soc, vol.131, pp.13894-13895, 2009.

M. Kollmar, D. Lbik, and S. Enge, Evolution of the eukaryotic ARP2/3 activators of the WASP family : WASP, WAVE, WASH, and WHAMM, and the proposed new family members WAWH and WAML, BMC Research Notes, vol.5, p.88, 2012.

P. V. Konarev, V. V. Volkov, A. V. Sokolova, M. H. Koch, and D. I. Sver-gun, PRIMUS : a Windows PC-based system for small-angle scattering data analysis, J Appl Crystallogr, vol.36, pp.1277-1282, 2003.

D. E. Koshland, Application of a Theory of Enzyme Specificity to Protein Synthesis*, Proc Natl Acad Sci U S A, vol.44, pp.98-104, 1958.

S. Kosol, S. Contreras-martos, C. Cedeño, and P. Tompa, Structural Characterization of Intrinsically Disordered Proteins by NMR Spectroscopy, Molecules, vol.18, pp.10802-10828, 2013.

D. Kozakov, K. Li, D. R. Hall, D. Beglov, J. Zheng et al., Encounter complexes and dimensionality reduction in protein-protein association, vol.3, p.1370, 2014.

J. Kragelj, V. Ozenne, M. Blackledge, and M. R. Jensen, Conformational Propensities of Intrinsically Disordered Proteins from NMR Chemical Shifts, ChemPhysChem, vol.14, pp.3034-3045, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01321617

J. Krieger, G. Fusco, M. Lewitzky, P. Simister, J. Marchant et al., Conformational Recognition of an Intrinsically Disordered Protein, Biophys. J, vol.106, pp.1771-1779, 2014.

G. G. Krivov, M. V. Shapovalov, and R. L. Dunbrack, Improved prediction of protein side-chain conformations with SCWRL4, Proteins, vol.77, pp.778-795, 2009.

M. Krzeminski, J. A. Marsh, C. Neale, W. Choy, and J. D. Forman-kay, Characterization of disordered proteins with ENSEMBLE, Bioinformatics, vol.29, pp.398-399, 2013.

D. Kurzbach, G. Kontaxis, N. Coudevylle, and R. Konrat, Intrinsically Disordered Proteins Studied by NMR Spectroscopy, pp.149-185, 2015.

R. Laghaei, N. Mousseau, and G. Wei, Effect of the Disulfide Bond on the Monomeric Structure of Human Amylin Studied by Combined Hamiltonian and Temperature Replica Exchange Molecular Dynamics Simulations, J. Phys. Chem. B, vol.114, pp.7071-7077, 2010.

J. Lautz, H. Kessler, R. Boelens, R. Kaptein, and W. Van-gunsteren, Conformational analysis of a cyclic thymopoietin-analogue by 1H N.M.R. spectroscopy and restrained molecular dynamics simulations, Int. J. Pept. Protein Res, vol.30, pp.404-414, 1987.

T. Lazaridis and M. Karplus, Effective energy function for proteins in solution, Proteins : Struct., Funct., Bioinf, vol.35, pp.133-152, 1999.

T. Le-gall, P. R. Romero, M. S. Cortese, V. N. Uversky, and A. K. Dunker, Intrinsic disorder in the Protein Data Bank, J. Biomol. Struct. Dyn, vol.24, pp.325-342, 2007.

C. Lee, D. Kim, S. Lee, J. Su, and K. Han, Structural investigation on the intrinsically disordered N-terminal region of HPV16 E7 protein, BMB Rep, vol.49, pp.431-436, 2016.

C. Lee, L. Kalmar, B. Xue, P. Tompa, G. W. Daughdrill et al., Contribution of proline to the pre-structuring tendency of transient helical secondary structure elements in intrinsically disordered proteins, Biochimica et Biophysica Acta (BBA) -General Subjects, vol.1840, pp.993-1003, 2014.

S. H. Lee, F. Kerff, D. Chereau, F. Ferron, A. Klug et al., Structural basis for the actin-binding function of Missing-In-Metastasis, Structure, vol.15, pp.145-155, 2007.

H. Leung, O. Bignucolo, R. Aregger, S. Dames, A. Mazur et al., A Rigorous and Efficient Method to Reweight very Large Conformational Ensembles using Average Experimental Data and to Determine their Relative Information Content, J. Chem. Theory Comput, vol.12, pp.383-394, 2016.

M. Levitt, A simplified representation of protein conformations for rapid simulation of protein folding, Journal of Molecular Biology, vol.104, pp.59-107, 1976.

C. Leyrat, M. Renner, K. Harlos, and J. Grimes, Solution and Crystallographic Structures of the Central Region of the Phosphoprotein from Human Metapneumovirus, PLOS One, vol.8, p.80371, 2013.

N. Li, N. Romero, N. Rani, . Dunker, and N. Obradovic, Predicting Protein Disorder for N-, C-, and Internal Regions, Genome Informatics. Workshop on Genome Informatics, vol.10, pp.30-40, 1999.

J. Lincoff, S. Sasmal, and T. Head-gordon, Comparing generalized ensemble methods for sampling of systems with many degrees of freedom, J. Chem. Phys, vol.145, p.174107, 2016.

R. Linding, L. J. Jensen, F. Diella, P. Bork, T. J. Gibson et al., Protein Disorder Prediction : Implications for Structural Proteomics, Structure, vol.11, pp.1453-1459, 2003.

K. Lindorff-larsen, R. Best, M. Depristo, C. Dobson, and M. Vendrus-colo, Simultaneous determination of protein structure and dynamics, Nature, vol.433, p.5, 2005.

K. Lindorff-larsen, S. Piana, K. Palmo, P. Maragakis, J. L. Klepeis et al., Improved side-chain torsion potentials for the Amber ff99SB protein force field, Proteins : Structure, Function, and Bioinformatics, vol.78, pp.1950-1958, 2010.

G. Liu, A. Prabhakar, D. Aucoin, M. Simon, S. Sparks et al., Mechanistic Studies of Peptide Self-Assembly : Transient ?-Helices to Stable ?-Sheets, J. Am. Chem. Soc, vol.132, pp.18223-18232, 2010.

. Bibliographie,

H. Liu, D. Song, H. Lu, R. Luo, and H. Chen, Intrinsically disordered protein-specific force field CHARMM36IDPSFF, Chem. Biol. Drug Des, vol.92, pp.1722-1735, 2018.

X. Liu, J. Chen, and J. Chen, Residual Structure Accelerates Binding of Intrinsically Disordered ACTR by Promoting Efficient Folding upon Encounter, Journal of Molecular Biology, vol.431, pp.422-432, 2019.

C. D. Livingstone and G. J. Barton, Protein sequence alignments : a strategy for the hierarchical analysis of residue conservation, Comput Appl Biosci, vol.9, pp.745-756, 1993.

S. C. Lovell, I. W. Davis, W. B. Arendall, B. De, P. I. Word et al., Structure validation by C? geometry : ?, ? and C? deviation, Proteins : Structure, Function, and Bioinformatics, vol.50, pp.437-450, 2003.

Q. Luan, A. Zelter, M. J. Maccoss, T. N. Davis, and B. J. Nolen, Identification of Wiskott-Aldrich syndrome protein (WASP) binding sites on the branched actin filament nucleator Arp2/3 complex, Proceedings of the National Academy of Sciences, vol.115, pp.1409-1418, 2018.

Y. Luo, B. Ma, R. Nussinov, and G. Wei, Structural Insight into Tau Protein's Paradox of Intrinsically Disordered Behavior, Self-Acetylation Activity, and Aggregation, J. Phys. Chem. Lett, vol.5, pp.3026-3031, 2014.

A. Lyons, N. Gandhi, and R. Mancera, Molecular dynamics simulation of the phosphorylation-induced conformational changes of a tau peptide fragment : Tau Peptide Conformation Changes : An MD Study, Proteins, vol.82, pp.1907-1923, 2014.

A. Mackerell, D. Bashford, M. Bellott, R. Dunbrack, J. Evanseck et al., All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins, J. Phys. Chem. B, vol.102, pp.3586-3616, 1998.

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, J. Comput. Chem, vol.25, pp.1400-1415, 2004.

A. Mackerell, M. Feig, and C. Brooks, Improved Treatment of the Protein Backbone in Empirical Force Fields, J. Am. Chem. Soc, vol.126, pp.698-699, 2004.

J. Maier, C. Martinez, K. Kasavajhala, L. Wickstrom, K. Hauser et al., FF14SB : Improving the Accuracy of Protein Side Chain and Backbone Parameters from FF99SB, J. Chem. Theory Comput, vol.11, pp.3696-3713, 2015.

F. Malard, N. Assrir, M. Alami, S. Messaoudi, E. Lescop et al., Conformational Ensemble and Biological Role of the TCTP Intrinsically Disordered Region : Influence of Calcium and Phosphorylation, J. Mol. Biol, vol.430, pp.1621-1639, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02114798

J. Marley, M. Lu, and C. Bracken, A method for efficient isotopic labeling of recombinant proteins, J Biomol NMR, vol.20, pp.71-75, 2001.

J. A. Marsh, V. K. Singh, Z. Jia, and J. D. Forman-kay, Sensitivity of secondary structure propensities to sequence differences between ?-and ?-synuclein : Implications for fibrillation, Protein Sci, vol.15, pp.2795-2804, 2006.

S. Marsin, A. Yazid, J. Andreani, S. Baconnais, P. Legrand et al., DciA-chaperones helicases self-load on DNA, 2019.

J. Maupetit, P. Tuffery, and P. Derreumaux, A coarse-grained protein force field for folding and structure prediction, Proteins : Struct., Funct., Bioinf, vol.69, pp.394-408, 2007.

L. J. Mcguffin, K. Bryson, and D. T. Jones, The PSIPRED protein structure prediction server, Bioinformatics, vol.16, pp.404-405, 2000.

D. Mercadante, S. Milles, G. Fuertes, D. Svergun, E. Lemke et al., Kirkwood-Buff Approach Rescues Overcollapse of a Disordered Protein in Canonical Protein Force Fields, J. Phys. Chem. B, vol.119, pp.7975-7984, 2015.

K. Merchant, R. Best, J. Louis, I. Gopich, and W. Eaton, Characterizing the unfolded states of proteins using single-molecule FRET spectroscopy and molecular simulations, Proceedings of the National Academy of Sciences, vol.104, pp.1528-1533, 2007.

F. Merino, S. Pospich, J. Funk, T. Wagner, F. Küllmer et al., Structural transitions of F-actin upon ATP hydrolysis at near-atomic resolution revealed by cryo-EM, Nature Structural & Molecular Biology, vol.25, pp.528-537, 2018.

H. Miki and T. Takenawa, Regulation of Actin Dynamics by WASP Family Proteins, J Biochem, vol.134, pp.309-313, 2003.

H. Miki, K. Miura, and T. Takenawa, N-WASP, a novel actin-depolymerizing protein, regulates the cortical cytoskeletal rearrangement in a PIP2-dependent manner downstream of tyrosine kinases, The EMBO journal, vol.15, pp.5326-5335, 1996.

S. Milles, M. Jensen, C. Lazert, S. Guseva, S. Ivashchenko et al., An ultraweak interaction in the intrinsically disordered replication machinery is essential for measles virus function, Science Advances, vol.4, p.7778, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01911103

A. Mitsutake, Y. Sugita, and Y. Okamoto, Generalized-ensemble algorithms for molecular simulations of biopolymers, Biopolymers, vol.60, pp.96-123, 2001.

T. Mittag and J. Forman-kay, Atomic-level characterization of disordered protein ensembles, Curr. Opin. Struct. Biol, vol.17, pp.3-14, 2007.

J. Mittal, T. Yoo, G. Georgiou, and T. Truskett, Structural Ensemble of an Intrinsically Disordered Polypeptide, J. Phys. Chem. B, vol.117, pp.118-124, 2013.

S. Miyamoto and P. A. Kollman, SETTLE : an analytical version of the SHAKE and RATTLE algorithm for rigid water models, Journal of computational chemistry, vol.13, pp.952-962, 1992.

M. J. Mizianty, W. Stach, K. Chen, K. D. Kedarisetti, F. M. Disfani et al., Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources, Bioinformatics, vol.26, pp.489-496, 2010.

M. J. Mizianty, T. Zhang, B. Xue, Y. Zhou, A. K. Dunker et al., In-silico prediction of disorder content using hybrid sequence representation, BMC Bioinformatics, vol.12, p.245, 2011.

M. J. Mizianty, Z. Peng, L. Kurgan, and . Mfdp2, Intrinsically Disordered Proteins, vol.1, p.24428, 2013.

A. Mohan, C. Oldfield, P. Radivojac, V. Vacic, M. Cortese et al., Analysis of Molecular Recognition Features (MoRFs)

, J. Mol. Biol, vol.362, pp.1043-1059, 2006.

R. Mohana-borges, N. K. Goto, G. J. Kroon, H. J. Dyson, and P. E. Wright, Structural Characterization of Unfolded States of Apomyoglobin using Residual Dipolar Couplings, Journal of Molecular Biology, vol.340, pp.1131-1142, 2004.

L. Mollica, L. Bessa, X. Hanoulle, M. Jensen, M. Blackledge et al., Binding Mechanisms of Intrinsically Disordered Proteins : Theory, Simulation, and Experiment. Front. Mol. Biosci, vol.3, pp.1-18, 2016.

J. Mongan, C. Simmerling, J. Mccammon, D. Case, and A. Onufriev, Generalized Born Model with a Simple, Robust Molecular Volume Correction, J. Chem. Theory Comput, vol.3, pp.156-169, 2007.

M. Mukrasch, S. Bibow, J. Korukottu, S. Jeganathan, J. Biernat et al., Structural Polymorphism of 441-Residue Tau at Single Residue Resolution, PLOS Biol, vol.7, p.1000034, 2009.

B. Mészáros, G. Erd?s, and Z. Dosztányi, IUPred2A : context-dependent prediction of protein disorder as a function of redox state and protein binding, Nucleic Acids Res, vol.46, pp.329-337, 2018.

R. Nanga, J. Brender, S. Vivekanandan, and A. Ramamoorthy, Structure and membrane orientation of IAPP in its natively amidated form at physiological pH in a membrane environment, Biochim. Biophys. Acta -Biomembranes, vol.1808, pp.2337-2342, 2011.

C. Narayanan, D. Weinstock, K. Wu, J. Baum, and R. Levy, Investigation of the Polymeric Properties of ?-Synuclein and Comparison with NMR Experiments : A Replica Exchange Molecular Dynamics Study, J. Chem. Theory Comput, vol.8, pp.3929-3942, 2012.

S. Neal, A. Nip, H. Zhang, and D. Wishart, Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts, J. Biomol. NMR, vol.26, pp.215-240, 2003.

D. Nettels, S. Muller-spath, F. Kuster, H. Hofmann, D. Haenni et al., Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins, Proc. Natl. Acad. Sci. U.S.A, vol.106, pp.20740-20745, 2009.

K. Nishihara, M. Kanemori, M. Kitagawa, H. Yanagi, and T. Yura, Chaperone coexpression plasmids : differential and synergistic roles of DnaK-DnaJ-GrpE and GroEL-GroES in assisting folding of an allergen of Japanese cedar pollen, Cryj2, in Escherichia coli, Appl. Environ. Microbiol, vol.64, pp.1694-1699, 1998.

G. Nodet, L. Salmon, V. Ozenne, S. Meier, M. Jensen et al., Quantitative Description of Backbone Conformational Sampling of Unfolded Proteins at Amino Acid Resolution from NMR Residual Dipolar Couplings, J. Am. Chem. Soc, vol.131, pp.17908-17918, 2009.
URL : https://hal.archives-ouvertes.fr/hal-01696459

Y. Nominé and B. Kieffer, Déterminer la structure d'une protéine par RMN : un problème d'optimisation complexe -L'Actualité Chimique. l'actualité chimique 364-365, pp.48-55, 2012.

S. Nosé, A unified formulation of the constant temperature molecular dynamics methods, Journal of Chemical Physics, vol.81, pp.511-519, 1984.

M. Noval, M. Gallo, S. Perrone, A. Salvay, L. Chemes et al., Conformational Dissection of a Viral Intrinsically Disordered Domain Involved in Cellular Transformation, PLOS One, vol.8, p.72760, 2013.

Z. Obradovic, K. Peng, S. Vucetic, P. Radivojac, C. J. Brown et al., Predicting intrinsic disorder from amino acid sequence, Proteins, vol.53, issue.6, pp.566-572, 2003.

Z. Obradovic, K. Peng, S. Vucetic, P. Radivojac, and A. K. Dunker, Exploiting heterogeneous sequence properties improves prediction of protein disorder, Proteins, vol.61, pp.176-182, 2005.

C. J. Oldfield, Y. Cheng, M. S. Cortese, C. J. Brown, V. N. Uversky et al., Comparing and Combining Predictors of Mostly Disordered Proteins, Biochemistry, vol.44, 1989.

C. J. Oldfield, Y. Cheng, M. S. Cortese, P. Romero, V. N. Uversky et al., Coupled Folding and Binding with ?-Helix-Forming Molecular Recognition Elements, Biochemistry, vol.44, pp.12454-12470, 2005.

J. Olsen, K. Teilum, and B. Kragelund, Behaviour of intrinsically disordered proteins in protein-protein complexes with an emphasis on fuzziness, Cell. Mol. Life Sci, vol.74, pp.3175-3183, 2017.

O. Olubiyi and B. Strodel, Structures of the Amyloid ?-Peptides A?1-40 and A?1-42 as Influenced by pH and a d-Peptide, J. Phys. Chem. B, vol.116, pp.3280-3291, 2012.

Y. Ouyang, L. Zhao, and Z. Zhang, Characterization of the structural ensembles of p53 TAD2 by molecular dynamics simulations with different force fields, Phys. Chem. Chem. Phys, vol.20, pp.8676-8684, 2018.

V. Ozenne, F. Bauer, L. Salmon, J. Huang, M. Jensen et al., Flexible-meccano : a tool for the generation of explicit ensemble descriptions of intrinsically disordered proteins and their associated experimental observables, Bioinformatics, vol.28, pp.1463-1470, 2012.

F. Palazzesi, M. Prakash, M. Bonomi, and A. Barducci, Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States, J. Chem. Theory Comput, vol.11, pp.2-7, 2015.

A. Palma, C. Ortega, P. Romero, A. Garcia-v, C. Roman et al., Wiskott-Aldrich syndrome protein (WASp) and relatives : A many-sided family, Immunologia, vol.23, pp.217-230, 2004.

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

S. Patil, S. Xu, S. Sheftic, and A. Alexandrescu, Dynamic ?-Helix Structure of Micelle-bound Human Amylin, J. Biol. Chem, vol.284, pp.11982-11991, 2009.

M. Y. Pavlov and B. A. Fedorov, Improved technique for calculating Xray scattering intensity of biopolymers in solution : Evaluation of the form, volume, and surface of a particle, Biopolymers, vol.22, pp.1507-1522, 1983.

K. Peng, S. Vucetic, P. Radivojac, C. J. Brown, A. K. Dunker et al., Optimizing long intrinsic disorder predictors with protein evolutionary information, J Bioinform Comput Biol, vol.3, pp.35-60, 2005.

K. Peng, P. Radivojac, S. Vucetic, A. K. Dunker, and Z. Obradovic, Length-dependent prediction of protein intrinsic disorder, BMC Bioinformatics, vol.7, p.208, 2006.

Z. Peng, J. Yan, X. Fan, M. J. Mizianty, B. Xue et al., Exceptionally abundant exceptions : comprehensive characterization of intrinsic disorder in all domains of life, Cell. Mol. Life Sci, vol.72, pp.137-151, 2014.

J. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid et al., Scalable molecular dynamics with NAMD, J. Comput. Chem, vol.26, pp.1781-1802, 2005.

S. Piana, K. Lindorff-larsen, and D. Shaw, How Robust are Protein Folding Simulations with Respect to Force Field Parameterization ?, Biophys. J, vol.100, pp.47-49, 2011.

S. Piana, J. Klepeis, and D. Shaw, Assessing the accuracy of physical models used in protein-folding simulations : quantitative evidence from long molecular dynamics simulations, Curr. Opin. Struct. Biol, vol.24, pp.98-105, 2014.

S. Piana, A. Donchev, P. Robustelli, and D. Shaw, Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States, J. Phys. Chem. B, vol.119, pp.5113-5123, 2015.

S. Piana and A. Laio, A Bias-Exchange Approach to Protein Folding, J. Phys. Chem. B, vol.111, pp.4553-4559, 2007.

D. Piovesan, I. Walsh, G. Minervini, and S. C. Tosatto, FELLS : fast estimator of latent local structure, Bioinformatics, vol.33, pp.1889-1891, 2017.

D. Piovesan, F. Tabaro, L. Paladin, M. Necci, I. Mi?eti? et al., MobiDB 3.0 : more annotations for intrinsic disorder, conformational diversity and interactions in proteins, Nucleic Acids Res, vol.46, pp.471-476, 2018.

J. Pitera and J. Chodera, On the Use of Experimental Observations to Bias Simulated Ensembles, J. Chem. Theory Comput, vol.8, pp.3445-3451, 2012.

T. D. Pollard and G. G. Borisy, Cellular Motility Driven by Assembly and Disassembly of Actin Filaments, Cell, vol.112, pp.453-465, 2003.

K. E. Prehoda, J. A. Scott, R. D. Mullins, and W. A. Lim, Integration of Multiple Signals Through Cooperative Regulation of the

, Complex. Science, vol.290, pp.801-806, 2000.

P. Puntervoll, R. Linding, C. Gemünd, S. Chabanis-davidson, M. Mat-tingsdal et al., ELM server : a new resource for investigating short functional sites in modular eukaryotic proteins, Nucleic Acids Research, vol.31, pp.3625-3630, 2003.

R. Qi, Y. Luo, B. Ma, R. Nussinov, and G. Wei, Conformational Distribution and ?-Helix to ?-Sheet Transition of Human Amylin Fragment Dimer, Biomacromolecules, vol.15, pp.122-131, 2014.

P. Radivojac, L. M. Iakoucheva, C. J. Oldfield, Z. Obradovic, V. N. Uver-sky et al., Intrinsic Disorder and Functional Proteomics, Biophysical Journal, vol.92, pp.1439-1456, 2007.

C. Ramachandran, R. &. , and S. , Stereochemistry of polypeptide chain configurations, J. Mol. Biol, pp.95-99, 1963.

R. M. Rasia, E. Lescop, J. F. Palatnik, J. Boisbouvier, and B. Brutscher, Rapid measurement of residual dipolar couplings for fast fold elucidation of proteins, J. Biomol. NMR, vol.51, pp.369-378, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00689143

S. Rauscher and R. Pomès, Molecular simulations of protein disorder, Biochem. Cell Biol, vol.88, pp.269-290, 2010.

S. Rauscher, V. Gapsys, M. Gajda, M. Zweckstetter, G. De et al., Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field : A Comparison to Experiment, J. Chem. Theory Comput, vol.11, pp.5513-5524, 2015.

E. Ravera, L. Sgheri, G. Parigi, and C. Luchinat, A critical assessment of methods to recover information from averaged data, Phys. Chem. Chem. Phys, vol.18, pp.5686-5701, 2016.

G. Rebowski, S. Namgoong, M. Boczkowska, P. C. Leavis, J. Navaza et al., Structure of a Longitudinal Actin Dimer Assembled by Tandem W Domains : Implications for Actin Filament Nucleation, Journal of Molecular Biology, vol.403, pp.11-23, 2010.

V. Receveur-bréchot and D. Durand, How Random are Intrinsically Disordered Proteins ? A Small Angle Scattering Perspective, Current Protein & Peptide Science, vol.13, pp.55-75, 2012.

V. Receveur-bréchot, J. Bourhis, V. Uversky, B. Canard, and S. Lon-ghi, Assessing protein disorder and induced folding, Proteins, vol.62, pp.24-45, 2005.

L. Renault, C. Deville, and C. Van-heijenoort, Structural features and interfacial properties of WH2, ?-thymosin domains and other intrinsically disordered domains in the regulation of actin cytoskeleton dynamics, Cytoskeleton, vol.70, pp.686-705, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00912809

W. Rieping, M. Habeck, and M. Nilges, Inferential Structure Determination, Science, vol.309, pp.303-306, 2005.

P. Robustelli, N. Trbovic, R. Friesner, and A. Palmer, Conformational Dynamics of the Partially Disordered Yeast Transcription Factor GCN4, J. Chem. Theory Comput, vol.9, pp.5190-5200, 2013.

P. Robustelli, S. Piana, and D. Shaw, Developing a molecular dynamics force field for both folded and disordered protein states, Proc. Natl. Acad. Sci. U.S.A, vol.115, pp.4758-4766, 2018.

N. Romero, . Obradovic, and N. Dunker, Sequence Data Analysis for Long Disordered Regions Prediction in the Calcineurin Family, Genome Informatics. Workshop on Genome Informatics, vol.8, pp.110-124, 1997.

P. Romero, Z. Obradovic, C. Kissinger, J. E. Villafranca, and A. K. Dun-ker, Identifying disordered regions in proteins from amino acid se, Proceedings of International Conference on Neural Networks (ICNN'97), vol.1, pp.90-95, 1997.

P. Romero, Z. Obradovic, X. Li, E. C. Garner, C. J. Brown et al., Sequence complexity of disordered protein, Proteins, vol.42, pp.38-48, 2001.

D. Rosenman, C. Connors, W. Chen, C. Wang, and A. García, A? Monomers Transiently Sample Oligomer and Fibril-like Configurations : Ensemble Characterization using a Combined MD/NMR Approach, J. Mol. Biol, vol.425, pp.3338-3359, 2013.

B. Roux and J. Weare, On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method, J. Chem. Phys, vol.138, p.84107, 2013.

B. Rozycki, Y. Kim, and G. Hummer, SAXS Ensemble Refinement of ESCRT-III CHMP3 Conformational Transitions, Structure, vol.19, pp.109-116, 2011.

R. B. Russell and T. J. Gibson, A careful disorderliness in the proteome : Sites for interaction and targets for future therapies, FEBS Letters, vol.582, pp.1271-1275, 2008.

A. A. Russo, P. D. Jeffrey, A. K. Patten, J. Massagué, and N. P. Pavle-tich, Crystal structure of the p27 Kip1 cyclin-dependent-kinase inibitor bound to the cyclin A-Cdk2 complex, Nature, vol.382, p.325, 1996.

A. Saladin, S. Fiorucci, P. Poulain, C. Prévost, and M. Zacharias, PTools : an opensource molecular docking library, BMC Structural Biology, vol.9, p.27, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02545587

L. Salmon, G. Nodet, V. Ozenne, G. Yin, M. R. Jensen et al., Characterization of Long-Range Order in Intrinsically Disordered Proteins, J. Am. Chem. Soc, vol.132, pp.8407-8418, 2010.

R. Salomon-ferrer, D. Case, and R. Walker, An overview of the Amber biomolecular simulation package : Amber biomolecular simulation package, WIREs Comput. Mol. Sci, vol.3, pp.198-210, 2013.

N. Salvi, Intrinsically Disordered Proteins (éd. SALVI, N.), pp.37-64, 2019.

N. Salvi, Intrinsically Disordered Proteins : Dynamics, Binding, and Function, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02306829

M. Samsa, J. Mondotte, N. Iglesias, I. Assuncao-miranda, G. Barbosa-lima et al., Dengue Virus Capsid Protein Usurps Lipid Droplets for Viral Particle Formation, PLOS Pathogens, vol.5, pp.1-14, 2009.

K. Sasaki, S. Dockerill, D. A. Adamiak, I. J. Tickle, and T. Blundell, X-ray analysis of glucagon and its relationship to receptor binding, Nature, vol.257, pp.751-757, 1975.

S. Sasmal, J. Lincoff, and T. Head-gordon, Effect of a Paramagnetic Spin Label on the Intrinsically Disordered Peptide Ensemble of Amyloid-?, Biophys. J, vol.113, pp.1002-1011, 2017.

K. P. Schlitter-j and M. Engels, Targeted molecular dynamics : a new approach for searching pathways of conformational transitions, J Mol Graph, vol.12, pp.84-93, 1994.

R. Schneider, J. Huang, M. Yao, G. Communie, V. Ozenne et al., Towards a robust description of intrinsic protein disorder using nuclear magnetic resonance spectroscopy, vol.8, pp.58-68, 2011.

D. Schneidman-duhovny, M. Hammel, J. Tainer, and A. Sali, Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments, Biophys. J, vol.105, pp.962-974, 2013.

D. Schneidman-duhovny, M. Hammel, J. Tainer, A. Sali, and . Foxs, FoXSDock and MultiFoXS : Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles, Nucl. Acids Res, vol.44, pp.424-429, 2016.

M. Schor, A. Mey, and C. Macphee, Analytical methods for structural ensembles and dynamics of intrinsically disordered proteins, Biophys. Rev, vol.8, pp.429-439, 2016.

A. Schramm, C. Bignon, S. Brocca, R. Grandori, C. Santambrogio et al., An arsenal of methods for the experimental characterization of intrinsically disordered proteins -How to choose and combine them ?, Archives of Biochemistry and Biophysics, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02341641

M. Schwalbe, V. Ozenne, S. Bibow, M. Jaremko, L. Jaremko et al., Predictive Atomic Resolution Descriptions of Intrinsically Disordered hTau40 and ?-Synuclein in Solution from NMR and Small Angle Scattering, Structure, vol.22, pp.238-249, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01131132

C. P. Scipion, U. Ghoshdastider, F. J. Ferrer, T. Yuen, J. Wong-santichon et al., Structural evidence for the roles of divalent cations in actin polymerization and activation of ATP hydrolysis, PNAS, vol.115, pp.10345-10350, 2018.

K. Seidel, M. Etzkorn, R. Schneider, C. Ader, and M. Baldus, Comparative analysis of NMR chemical shift predictions for proteins in the solid phase, Solid State Nucl. Magn. Reson, vol.35, pp.235-242, 2009.

H. Seitz, C. Weigel, and W. Messer, The interaction domains of the DnaA and DnaB replication proteins of Escherichia coli, Molecular Microbiology, vol.37, pp.1270-1279, 2000.

N. Sgourakis, Y. Yan, S. Mccallum, C. Wang, and A. Garcia, The Alzheimer's Peptides A?40 and 42 Adopt Distinct Conformations in Water : A Combined MD / NMR Study, J. Mol. Biol, vol.368, pp.1448-1457, 2007.

N. Sgourakis, M. Merced-serrano, C. Boutsidis, P. Drineas, Z. Du et al., Atomic-level characterization of the ensemble of the A?(1-42) monomer in water using unbiased Molecular Dynamics simulations and spectral algorithms, J. Mol. Biol, vol.405, pp.570-583, 2011.

R. Sharma, Z. Raduly, M. Miskei, and M. Fuxreiter, Fuzzy complexes : Specific binding without complete folding, FEBS Lett, vol.589, pp.2533-2542, 2015.

D. E. Shaw, J. C. Chao, M. P. Eastwood, J. Gagliardo, J. P. Grossman et al., Anton, a special-purpose machine for molecular dynamics simulation, Communications of the ACM, vol.51, p.91, 2008.

D. E. Shaw, P. Maragakis, K. Lindorff-larsen, S. Piana, R. O. Dror et al., Atomic-Level Characterization of the Structural Dynamics of Proteins, Science, vol.330, pp.341-346, 2010.

Y. Shen and A. Bax, Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology, J. Biomol. NMR, vol.38, pp.289-302, 2007.

Y. Shen and A. Bax, SPARTA+ : a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network, J. Biomol. NMR, vol.48, pp.13-22, 2010.

N. Sibille and P. Bernadó, Structural characterization of intrinsically disordered proteins by the combined use of NMR and SAXS, Biochemical Society Transactions, vol.40, pp.955-962, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02347934

A. Sigalov, A. Zhuravleva, . Vladislav-yu, and V. Orekhov, Binding of intrinsically disordered proteins is not necessarily accompanied by a structural transition to a folded form, Biochimie, vol.89, pp.419-421, 2007.

J. Sipe, M. Benson, J. Buxbaum, S. Ikeda, G. Merlini et al., Amyloid fibril protein nomenclature : 2010 recommendations from the nomenclature committee of the International Society of Amyloidosis, Amyloid, vol.17, pp.101-104, 2010.

A. Somavarapu and K. Kepp, The Dependence of Amyloid-? Dynamics on Protein Force Fields and Water Models, ChemPhysChem, vol.16, pp.3278-3289, 2015.

D. Song, R. Luo, and H. Chen, The IDP-Specific Force Field FF14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins, J. Chem. Inf. Model, vol.57, pp.1166-1178, 2017.

P. Sormanni, C. Camilloni, P. Fariselli, and M. Vendruscolo, The s2D Method : Simultaneous Sequence-Based Prediction of the Statistical Populations of Ordered and Disordered Regions in Proteins, Journal of Molecular Biology, vol.427, pp.982-996, 2015.

Y. Sugita and Y. Okamoto, Replica-exchange molecular dynamics method for protein folding, Chemical Physics Letters, vol.314, pp.141-151, 1999.

D. Svergun, C. Barberato, and M. Koch, CRYSOL -a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates, J. Appl. Crystallogr, vol.28, pp.768-773, 1995.

D. Szöllösi, T. Horváth, K. Han, N. Dokholyan, P. Tompa et al., Discrete Molecular Dynamics can Predict Helical Prestructured Motifs in Disordered Proteins, PLoS One, vol.9, p.95795, 2014.

T. Takenawa and S. Suetsugu, The WASP-WAVE protein network : connecting the membrane to the cytoskeleton, Nature Reviews Molecular Cell Biology, vol.8, pp.37-48, 2007.

T. Terakawa and S. Takada, Multiscale Ensemble Modeling of Intrinsically Disordered Proteins : p53 N-Terminal Domain, Biophys. J, vol.101, pp.1450-1458, 2011.

T. Terakawa, J. Higo, and S. Takada, Multi-scale Ensemble Modeling of Modular Proteins with Intrinsically Disordered Linker Regions : Application to p53, Biophys. J, vol.107, pp.721-729, 2014.

P. Tompa and M. Fuxreiter, Fuzzy complexes : polymorphism and structural disorder in protein-protein interactions, Trends Biochem. Sci, vol.33, pp.2-8, 2008.

P. Tompa, Intrinsically unstructured proteins, Trends in Biochemical Sciences, vol.27, pp.527-533, 2002.

P. Tompa, The interplay between structure and function in intrinsically unstructured proteins, FEBS Letters, vol.579, pp.3346-3354, 2005.

P. Tompa, Intrinsically disordered proteins : a 10-year recap, Trends in Biochemical Sciences, vol.37, pp.509-516, 2012.

P. Tompa and P. Csermely, The role of structural disorder in the function of RNA and protein chaperones, The FASEB Journal, vol.18, pp.1169-1175, 2004.

L. Tran and T. Ha-duong, Insights into the Conformational Ensemble of Human Islet Amyloid Polypeptide from Molecular Simulations, Current Pharmaceutical Design, vol.22, pp.3601-3607, 2016.

L. Tran, N. Basdevant, C. Prévost, and T. Ha-duong, Structure of ringshaped A?42 oligomers determined by conformational selection, Sci. Rep, vol.6, 2016.

J. Trewhella, A. Duff, D. Durand, F. Gabel, J. Guss et al., publication guidelines for structural modelling of small-Angle scattering data from biomolecules in solution : an update, Acta Crystallogr. D Struct. Biol, vol.73, pp.710-728, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01593495

G. Tria, H. Mertens, M. Kachala, and D. Svergun, Advanced ensemble modelling of flexible macromolecules using X-ray solution scattering, IUCrJ, vol.2, pp.207-217, 2015.

F. Troilo, C. Bignon, S. Gianni, M. Fuxreiter, and S. Longhi, Intrinsically Disordered Proteins, pp.137-192, 2018.

V. N. Uversky, J. R. Gillespie, and A. L. Fink, Why are "natively unfolded" proteins unstructured under physiologic conditions ?, Proteins, vol.41, pp.415-427, 2000.

V. N. Uversky, C. J. Oldfield, and A. K. Dunker, IEEE 7th BIBE Invited Tutorial Lecture : Intrinsically Disordered Proteins in Human Diseases in 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering, pp.12-12, 2007.

V. N. Uversky, Intrinsically Disordered Proteins, 2014.

V. Uversky, Natively unfolded proteins : a point where biology waits for physics, Protein Sci, vol.11, pp.739-756, 2002.

V. Uversky, Intrinsically Disordered Proteins Studied by NMR Spectroscopy, pp.215-260, 2015.

V. Uversky, C. Oldfield, and A. Dunker, Showing your ID : intrinsic disorder as an ID for recognition, regulation and cell signaling, J. Mol. Recognit, vol.18, pp.343-384, 2005.

V. Uversky, C. Oldfield, and K. Dunker, Intrinsically Disordered Proteins in Human Diseases : Introducing the D2 Concept, Annu. Rev. Biophys, vol.37, pp.215-246, 2008.

V. Vacic, C. J. Oldfield, A. Mohan, P. Radivojac, M. S. Cortese et al., Characterization of Molecular Recognition Features, MoRFs, and Their Binding Partners, J. Proteome Res, vol.6, pp.2351-2366, 2007.

N. Vaidehi, A. Jain, and W. A. Goddard, Constant Temperature Constrained Molecular Dynamics : The NewtonEuler Inverse Mass Operator Method, J. Phys. Chem, vol.100, pp.10508-10517, 1996.

G. Van, W. Billeter, S. Eising, A. Hünenberger, P. Krü-ger et al., Force Fields and Topology Data Set, vol.3, 1996.

L. Van-der, R. Buljan, M. Lang, B. Weatheritt, R. J. Daughdrill et al., Classification of Intrinsically Disordered Regions and Proteins, Chem. Rev, vol.114, pp.6589-6631, 2014.

M. Varadi, S. Kosol, P. Lebrun, E. Valentini, M. Blackledge et al., pE-DB : a database of structural ensembles of intrinsically disordered and of unfolded proteins, Nucleic Acids Res, vol.42, pp.326-335, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01131133

M. Viet and M. Li, Amyloid peptide A?40 inhibits aggregation of A?42 : Evidence from molecular dynamics simulations, J. Chem. Phys, vol.136, p.245105, 2012.

J. A. Vila, Y. A. Arnautova, O. A. Martin, and H. A. Scheraga, Quantummechanics-derived 13C? chemical shift server (CheShift) for protein structure validation, Proc Natl Acad Sci U S A, vol.106, pp.16972-16977, 2009.

W. F. Vranken, W. Boucher, T. J. Stevens, R. H. Fogh, A. Pajon et al., The CCPN data model for NMR spectroscopy : Development of a software pipeline, Proteins : Structure, Function, and Bioinformatics, vol.59, pp.687-696, 2005.

S. Vucetic, C. J. Brown, A. K. Dunker, and Z. Obradovic, Flavors of protein disorder, Proteins, vol.52, 2003.

I. Walsh, A. J. Martin, T. Di-domenico, and S. C. Tosatto, ESpritz : accurate and fast prediction of protein disorder, Bioinformatics, vol.28, pp.503-509, 2012.

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 ?, J. Comput. Chem, vol.21, pp.1049-1074, 2000.

W. Wang, W. Ye, C. Jiang, R. Luo, and H. Chen, New Force Field on Modeling Intrinsically Disordered Proteins, vol.84, pp.253-269, 2014.

Y. Wang, X. Chu, S. Longhi, P. Roche, W. Han et al., Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein, Proc. Natl. Acad. Sci. U.S.A, vol.110, pp.3743-3752, 2013.

J. J. Ward, J. S. Sodhi, L. J. Mcguffin, B. F. Buxton, and D. T. Jones, Prediction and Functional Analysis of Native Disorder in Proteins from the Three Kingdoms of Life, Journal of Molecular Biology, vol.337, pp.635-645, 2004.

G. Wei, W. Xi, R. Nussinov, and B. Ma, Protein Ensembles : How Does Nature Harness Thermodynamic Fluctuations for Life ? The Diverse Functional Roles of Conformational Ensembles in the Cell, Chem. Rev, vol.116, pp.6516-6551, 2016.

J. A. Wells and C. L. Mcclendon, Reaching for high-hanging fruit in drug discovery at protein-protein interfaces, Nature, vol.450, pp.1001-1009, 2007.

B. Wen, J. Peng, X. Zuo, Q. Gong, and Z. Zhang, Characterization of Protein Flexibility using Small-Angle X-Ray Scattering and Amplified Collective Motion Simulations, Biophys. J, vol.107, pp.956-964, 2014.

J. Williamson, J. Loria, and A. Miranker, Helix Stabilization Precedes Aqueous and Bilayer-Catalyzed Fiber Formation in Islet Amyloid Polypeptide, J. Mol. Biol, vol.393, pp.383-396, 2009.

D. S. Wishart, C. G. Bigam, A. Holm, R. S. Hodges, B. D. Sykes et al., 13C and 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects, Journal of Biomolecular NMR, vol.5, pp.67-81, 1995.

G. Wood and U. Rothlisberger, Secondary Structure Assignment of Amyloid? Peptide using Chemical Shifts, J. Chem. Theory Comput, vol.7, pp.1552-1563, 2011.

P. E. Wright and H. J. Dyson, Intrinsically unstructured proteins : re-assessing the protein structure-function paradigm, Journal of Molecular Biology, vol.293, pp.321-331, 1999.

P. E. Wright and H. J. Dyson, Linking folding and binding, Current Opinion in Structural Biology, vol.19, pp.31-38, 2009.

P. E. Wright and H. J. Dyson, Intrinsically disordered proteins in cellular signalling and regulation, Nature Reviews Molecular Cell Biology, vol.16, pp.18-29, 2015.

S. Wu, D. Wang, J. Liu, Y. Feng, J. Weng et al., The Dynamic Multisite Interactions between Two Intrinsically Disordered Proteins, Angew. Chem. Int. Ed, vol.56, pp.7515-7519, 2017.

H. Xie, S. Vucetic, L. M. Iakoucheva, C. J. Oldfield, A. K. Dunker et al., Functional Anthology of Intrinsic Disorder. III. Ligands, Postranslational Modifications and Diseases Associated with Intrinsically Disordered Proteins, J Proteome Res, vol.6, pp.1917-1932, 2007.

X. Xu and D. Case, Automated prediction of 15N, 13C?, 13C? and 13C?he-mical shifts in proteins using a density functional database, J. Biomol. NMR, vol.21, pp.321-333, 2001.

Y. Xu, J. Shi, N. Yamamoto, J. A. Moss, P. K. Vogt et al., A credit-card library approach for disrupting protein-protein interactions, Bioorganic & Medicinal Chemistry, vol.14, pp.2660-2673, 2006.

Z. Xu and N. E. Dixon, Bacterial replisomes. Current Opinion in Structural Biology. Protein-nucleic acid interactions ? Catalysis and regulation, vol.53, pp.159-168, 2018.

. P. Xu-x and . A. Case-d, Probing multiple effects on 15N, 13C?, 13C?, and 13C' chemical shifts in peptides using density functional theory, Biopolymers, vol.65, pp.408-423, 2002.

B. Xue, D. Blocquel, J. Habchi, A. Uversky, L. Kurgan et al., Structural Disorder in Viral Proteins, Chem. Rev, vol.114, pp.6880-6911, 2014.

B. Xue, R. L. Dunbrack, R. W. Williams, A. K. Dunker, and V. N. Uversky, PONDR-FIT : A Meta-Predictor of Intrinsically Disordered Amino Acids, Biochimica et biophysica acta, vol.1804, pp.996-1010, 2010.

B. Xue, A. K. Dunker, and V. N. Uversky, Orderly order in protein intrinsic disorder distribution : disorder in 3500 proteomes from viruses and the three domains of life, Journal of Biomolecular Structure and Dynamics, vol.30, pp.137-149, 2012.

B. Xue, P. R. Romero, M. Noutsou, M. M. Maurice, S. G. Rüdiger et al., Stochastic machines as a colocalization mechanism for scaffold protein function, FEBS Lett, vol.587, pp.1587-1591, 2013.

S. Xun, F. Jiang, and Y. Wu, Intrinsically disordered regions stabilize the helical form of the C-terminal domain of RfaH : A molecular dynamics study, Bioorg. Med. Chem. Advances in Computational and Medicinal Chemistry, vol.24, pp.4970-4977, 2016.

H. Yamaguchi, H. Miki, S. Suetsugu, L. Ma, M. W. Kirschner et al., Two tandem verprolin homology domains are necessary for a strong activation of Arp2/3 complex-induced actin polymerization and induction of microspike formation by N-WASP, Proceedings of the National Academy of Sciences, vol.97, pp.12631-12636, 2000.

M. Yang and D. Teplow, Amyloid ?-Protein Monomer Folding : Free-Energy Surfaces Reveal Alloform-Specific Differences, J. Mol. Biol, vol.384, pp.450-464, 2008.

W. Ye, D. Ji, W. Wang, R. Luo, and H. Chen, Test and Evaluation of FF99IDPs Force Field for Intrinsically Disordered Proteins, J. Chem. Inf. Model, vol.55, pp.1021-1029, 2015.

I. Yonemoto, G. Kroon, H. Dyson, W. Balch, and J. Kelly, Amylin Proprotein Processing Generates Progressively More Amyloidogenic Peptides that Initially Sample the Helical State, Biochemistry, vol.47, pp.9900-9910, 2008.

M. Yoon, V. Venkatachalam, A. Huang, B. Choi, C. Stultz et al., Residual structure within the disordered C-terminal segment of p21Waf1 / Cip1 / Sdi1 and its implications for molecular recognition, Protein Sci, vol.18, pp.337-347, 2009.

D. J. Zea, A. M. Monzon, C. Gonzalez, M. S. Fornasari, S. C. Tosatto et al., Disorder transitions and conformational diversity cooperatively modulate biological function in proteins, Protein Science, vol.25, pp.1138-1146, 2016.

J. Zeng, F. Jiang, and Y. Wu, Mechanism of Phosphorylation-Induced Folding of 4E-BP2 Revealed by Molecular Dynamics Simulations, J. Chem. Theory Comput, vol.13, pp.320-328, 2017.

H. Zhang, S. Neal, D. S. Wishart, and . Refdb, A database of uniformly referenced protein chemical shifts, Journal of Biomolecular NMR, vol.25, pp.173-195, 2003.

W. Zhang and J. Chen, Replica exchange with guided annealing for accelerated sampling of disordered protein conformations, J. Comput. Chem, vol.35, pp.1682-1689, 2014.

Y. Zhang, B. Wen, J. Peng, X. Zuo, Q. Gong et al., Determining structural ensembles of flexible multi-domain proteins using small-Angle X-ray scattering and molecular dynamics simulations, Protein Cell, vol.6, pp.619-623, 2015.

C. Zhou, F. Jiang, and Y. Wu, Residue-Specific Force Field Based on Protein Coil Library. RSFF2 : Modification of AMBER FF99SB, J. Phys. Chem. B, vol.119, pp.1035-1047, 2015.

S. H. Zigmond, How Wasp Regulates Actin Polymerization, The Journal of Cell Biology, vol.150, pp.117-120, 2000.

M. Zweckstetter and A. Bax, Prediction of Sterically Induced Alignment in a Dilute Liquid Crystalline Phase : Aid to Protein Structure Determination by NMR, J. Am. Chem. Soc, vol.122, pp.3791-3792, 2000.

M. Zweckstetter, NMR : prediction of molecular alignment from structure using the PALES software, Nat. Protocols, vol.3, pp.679-690, 2008.