S. Cho, J. J. Beintema, and J. Zhang, The ribonuclease A superfamily of mammals and birds: identifying new members and tracing evolutionary histories, Genomics, vol.85, issue.2, p.15676279, 2005.

B. R. Kelemen, L. W. Schultz, R. Y. Sweeney, and R. T. Raines, Excavating an active site: the nucleobase specificity of ribonuclease A, Biochemistry, vol.39, issue.47, pp.14487-94, 2000.

K. R. Acharya, D. D. Leonidas, A. C. Papageorgiou, N. Russo, and R. Shapiro, Structural studies on angiogenin, a protein implicated in neovascularization during tumour growth, Angiogenesis, vol.298, pp.165-78, 1998.

R. Shapiro, Structural features that determine the enzymatic potency and specificity of human angiogenin: Threonine-80 and residues 58-70 and 116-123, Biochemistry, vol.37, issue.19, p.9578571, 1998.

D. Gagne and N. Doucet, Structural and functional importance of local and global conformational fluctuations in the RNase A superfamily, FEBS Journal, p.23763751, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01130977

S. Sorrentino, The eight human "canonical" ribonucleases: Molecular diversity, catalytic properties, and special biological actions of the enzyme proteins, FEBS Letters, vol.584, issue.11, p.20388512, 2010.

R. T. Raines and A. Ribonuclease, Chem Rev, vol.98, issue.3, p.11848924, 1998.

S. Sorrentino, M. Naddeo, A. Russo, D. 'alessio, and G. , Degradation of double-stranded RNA by human pancreatic ribonuclease: crucial role of noncatalytic basic amino acid residues, Biochemistry, vol.42, issue.34, pp.10182-90, 2003.

G. Prats-ejarque, J. Arranz-trullen, J. A. Blanco, D. Pulido, M. V. Nogues et al., The first crystal structure of human RNase 6 reveals a novel substrate-binding and cleavage site arrangement, Biochemical Journal, vol.473, issue.11, pp.1523-1559, 2016.

B. M. Fisher, L. W. Schultz, and R. T. Raines, Coulombic effects of remote subsites on the active site of ribonuclease A, Biochemistry, vol.37, issue.50, pp.17386-401, 1998.

K. I. Panov, E. Y. Kolbanovskaya, A. L. Okorokov, T. B. Panova, T. Van-scheltinga et al., Ribonuclease A mutant His119 Asn: the role of histidine in catalysis, FEBS Letters, vol.398, issue.1, p.8946953, 1996.

S. B. Delcardayre and R. T. Raines, Structural determinants of enzymatic processivity, Biochemistry, vol.33, pp.6031-6038, 1920.

A. M. Jardine, D. D. Leonidas, J. L. Jenkins, C. Park, R. T. Raines et al., Cleavage of 3',5'-pyrophosphate-linked dinucleotides by ribonuclease A and angiogenin, Biochemistry, vol.40, issue.34, pp.10262-72, 2001.

T. A. Klink, K. J. Woycechowsky, K. M. Taylor, and R. T. Raines, Contribution of disulfide bonds to the conformational stability and catalytic activity of ribonuclease A, European Journal of Biochemistry, vol.267, issue.2, p.10632727, 2000.

T. J. Rutkoski, Engineering Ribonuclease-based Cancer Therapeutics: University of Wisconsin, 2008.

P. Dey, A. Islam, F. Ahmad, and J. K. Batra, Role of unique basic residues of human pancreatic ribonuclease in its catalysis and structural stability, Biochemical and Biophysical Research Communications, vol.360, issue.4, p.17631275, 2007.

D. Gaur and J. K. Batra, Role of aspartic acid 121 in human pancreatic ribonuclease catalysis. Molelcular and Cellular Biochemistry, vol.275, p.16335788, 2005.

H. F. Rosenberg and K. D. Dyer, Eosinophil cationic protein and eosinophil-derived neurotoxin. Evolution of novel function in a primate ribonuclease gene family, Journal of Biological Chemistry, vol.270, issue.37, p.7665566, 1995.

D. Sikriwal, D. Seth, S. Parveen, A. Malik, S. Broor et al., An insertion in loop L7 of human eosinophilderived neurotoxin is crucial for its antiviral activity, Journal of Cellular Biochemistry, vol.113, issue.10, p.22581709, 2012.

C. Chang, D. L. Newton, S. M. Rybak, and A. Wlodawer, Crystallographic and functional studies of a modified form of eosinophil-derived neurotoxin (EDN) with novel biological activities, Journal of Molecular Biology, vol.317, issue.1, p.11916383, 2002.

D. Sikriwal, D. Seth, and J. K. Batra, Role of catalytic and non-catalytic subsite residues in ribonuclease activity of human eosinophil-derived neurotoxin, Biological Chemistry, vol.390, issue.3, pp.225-259, 2009.

E. Boix, Eosinophil cationic protein, Methods in Enzymology, vol.341, issue.01, p.11582785, 2001.
URL : https://hal.archives-ouvertes.fr/hal-00479136

A. Singh and J. K. Batra, Role of unique basic residues in cytotoxic, antibacterial and antiparasitic activities of human eosinophil cationic protein, Biological Chemistry, vol.392, issue.4, p.21303303, 2011.

J. Hofsteenge, C. Moldow, A. M. Vicentini, O. Zelenko, Z. Jarai-kote et al., A single amino acid substitution changes ribonuclease 4 from a uridine-specific to a cytidine-specific enzyme, Biochemistry, vol.37, issue.26, p.9649305, 1998.

N. Russo, K. R. Acharya, B. L. Vallee, and R. Shapiro, A combined kinetic and modeling study of the catalytic center subsites of human angiogenin, Proceedings of the National Academy of Sciences USA, vol.93, issue.2, p.8570639, 1996.

N. Russo, V. Nobile, D. Donato, A. Riordan, J. F. Vallee et al., The C-terminal region of human angiogenin has a dual role in enzymatic activity, Proceedings of the National Academy of Sciences USA, vol.93, issue.8, p.8622921, 1996.

J. Harder and J. M. Schroder, RNase 7, a novel innate immune defense antimicrobial protein of healthy human skin, Journal of Biological Chemistry, vol.277, issue.48, p.12244054, 2002.

E. Boix, J. A. Blanco, M. V. Nogues, and M. Moussaoui, Nucleotide binding architecture for secreted cytotoxic endoribonucleases, Biochimie, vol.95, issue.6, p.23274129, 2013.

S. Sorrentino and D. G. Glitz, Ribonuclease activity and substrate preference of human eosinophil cationic protein (ECP), FEBS Lett, vol.288, p.1715291, 1991.

C. Narayanan, D. N. Bernard, K. Bafna, D. Gagne, C. S. Chennubhotla et al., Conservation of Dynamics Associated with Biological Function in an Enzyme Superfamily, Structure, vol.26, issue.3, p.29478822, 2018.
URL : https://hal.archives-ouvertes.fr/pasteur-01856081

K. E. Kover, M. Bruix, J. Santoro, G. Batta, D. V. Laurents et al., The solution structure and dynamics of human pancreatic ribonuclease determined by NMR spectroscopy provide insight into its remarkable biological activities and inhibition, Journal of Molecular Biology, vol.379, issue.5, p.18495155, 2008.

G. J. Swaminathan, D. E. Holloway, K. Veluraja, and K. R. Acharya, Atomic resolution (0.98 A) structure of eosinophil-derived neurotoxin, Biochemistry, vol.41, issue.10, pp.3341-52, 2002.

E. Boix, D. D. Leonidas, Z. Nikolovski, M. V. Nogues, C. M. Cuchillo et al., Crystal structure of eosinophil cationic protein at 2.4 A resolution, Biochemistry, vol.38, issue.51, pp.16794-801, 1999.

S. S. Terzyan, R. Peracaula, R. De-llorens, Y. Tsushima, H. Yamada et al., The three-dimensional structure of human RNase 4, unliganded and complexed with d(Up), reveals the basis for its uridine selectivity, Journal of Molecular Biology, vol.285, issue.1, p.9878400, 1999.

K. R. Acharya, R. Shapiro, S. C. Allen, J. F. Riordan, and B. L. Vallee, Crystal structure of human angiogenin reveals the structural basis for its functional divergence from ribonuclease, Proceedings of the National Academy of Sciences, vol.91, p.8159679, 1994.

Y. C. Huang, Y. M. Lin, T. W. Chang, S. J. Wu, Y. S. Lee et al., The flexible and clustered lysine residues of human ribonuclease 7 are critical for membrane permeability and antimicrobial activity, Journal of Biological Chemistry, vol.282, issue.7, p.17150966, 2007.

A. Wlodawer, L. A. Svensson, L. Sjolin, and G. L. Gilliland, Structure of phosphate-free ribonuclease A refined at 1.26 A, Biochemistry, vol.27, issue.8, p.3401445, 1988.

N. Doucet, Human RNase 6. In Preparation, 2018.

D. Case, V. Babin, J. Berryman, R. Betz, Q. Cai et al., Amber 14, 2014.

J. C. Fontecilla-camps, R. De-llorens, M. H. Le-du, and C. M. Cuchillo, Crystal structure of ribonuclease A.d(ApTpApApG) complex. Direct evidence for extended substrate recognition, J Biol Chem, vol.269, issue.34, p.8063789, 1994.

H. Berendsen, J. R. Grigera, and T. P. Straatsma, The Missing Term in Effective Pair Potentials. The journal of physical chemistry B, vol.91, pp.6269-71, 1987.

P. K. Agarwal, Cis/trans isomerization in HIV-1 capsid protein catalyzed by cyclophilin A: insights from computational and theoretical studies, Proteins: Structure, Function, and Bioinformatics, vol.56, issue.3, p.15229879, 2004.

A. Ramanathan, P. K. Agarwal, M. Kurnikova, and C. J. Langmead, An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations, Journal of Computational Biology, vol.17, issue.3, p.20377447, 2010.

T. Darden, D. York, and L. Pedersen, Particle mesh Ewald-an Nlog(N) method for Ewald sums in large systems, J Chem Phys, vol.98, pp.10089-92, 1993.

J. Ryckaert, G. Ciccotti, and H. Berendsen, Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes, J Comput Phys, vol.23, pp.327-368, 1977.

D. G. Herries, A. P. Mathias, and B. R. Rabin, The active site and mechanism of action of bovine pancreatic ribonuclease. 3. The pH-dependence of the kinetic parameters for the hydrolysis of cytidine 2',3'-phosphate, Biochem J, vol.85, pp.127-161, 1962.

B. Elsasser, G. Fels, and J. H. Weare, QM/MM simulation (B3LYP) of the RNase A cleavage-transesterification reaction supports a triester A(N) + D(N) associative mechanism with an O2' H internal proton transfer, J Am Chem Soc, vol.136, issue.3, pp.927-963, 2014.

D. A. Beck and V. Daggett, Methods for molecular dynamics simulations of protein folding/unfolding in solution, Methods, vol.34, issue.1, p.15283920, 2004.

D. Gagne, C. Narayanan, N. Nguyen-thi, L. D. Roux, D. N. Bernard et al., Ligand Binding Enhances Millisecond Conformational Exchange in Xylanase B2 from Streptomyces lividans, Biochemistry, vol.55, issue.30, p.27387012, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01351169

S. Shukla, K. Bafna, C. Gullett, D. Myles, P. K. Agarwal et al., Differential Substrate Recognition by Maltose Binding Proteins Influenced by Structure and Dynamics, Biochemistry, vol.57, issue.40, p.30204415, 2018.

N. A. Baker, D. Sept, S. Joseph, M. J. Holst, and J. A. Mccammon, Electrostatics of nanosystems: application to microtubules and the ribosome, Proceedings of the National Academy of Sciences USA, vol.98, issue.18, p.11517324, 2001.

A. Ramanathan and P. K. Agarwal, Computational Identification of Slow Conformational Fluctuations in Proteins. The journal of physical chemistry B, vol.113, pp.16669-80, 2009.

P. K. Agarwal, C. Schultz, A. Kalivretenos, B. Ghosh, and S. E. Broedel, Engineering a Hyper-catalytic Enzyme by Photoactivated Conformation Modulation, The Journal of Physical Chemistry Letters, vol.3, issue.9, pp.1142-1148, 2012.

H. F. Rosenberg and K. D. Dyer, Molecular cloning and characterization of a novel human ribonuclease (RNase k6): increasing diversity in the enlarging ribonuclease gene family, Nucleic Acids Research, vol.24, issue.18, p.8836175, 1996.

E. Chatani and R. Hayashi, Functional and structural roles of constituent amino acid residues of bovine pancreatic ribonuclease A, Journal of Bioscience and Bioengineering, vol.92, issue.2, p.16233067, 2001.

N. Doucet, G. Khirich, E. L. Kovrigin, and J. P. Loria, Alteration of hydrogen bonding in the vicinity of histidine 48 disrupts millisecond motions in RNase A, Biochemistry, vol.50, issue.10, 2011.

N. Doucet, E. D. Watt, and J. P. Loria, The flexibility of a distant loop modulates active site motion and product release in ribonuclease A, Biochemistry, vol.48, issue.30, pp.7160-7168, 2009.

A. Ramanathan and P. K. Agarwal, Evolutionarily Conserved Linkage between Enzyme Fold, Flexibility, and Catalysis, ARTN e1001193, vol.9, p.22087074, 2011.

D. G. Anderson, G. G. Hammes, and F. G. Walz, Binding of phosphate ligands to ribonuclease A. Biochemistry, vol.7, pp.1637-1682, 1968.

M. Flogel, A. Albert, and R. Biltonen, The magnitude of electrostatic interactions in inhibitor binding and during catalysis by ribonuclease A, Biochemistry, vol.14, issue.12, pp.2616-2637, 1975.

G. Li and Q. Cui, What is so special about Arg 55 in the catalysis of cyclophilin A? insights from hybrid QM/ MM simulations, Journal of the American Chemical Society, vol.125, issue.49, pp.15028-15066, 2003.

Z. D. Nagel and J. P. Klinman, A 21st century revisionist's view at a turning point in enzymology, Nature Chemical Biology, vol.5, issue.8, pp.543-50, 2009.

M. R. Duff, J. M. Borreguero, M. J. Cuneo, A. Ramanathan, J. He et al., Modulating Enzyme Activity by Altering Protein Dynamics with Solvent, Biochemistry, vol.57, issue.29, p.29901984, 2018.

L. Li, S. Ghimire-rijal, S. L. Lucas, C. B. Stanley, E. Wright et al., Periplasmic Binding Protein Dimer Has a Second Allosteric Event Tied to Ligand Binding, Biochemistry, vol.56, issue.40, p.28876049, 2017.

C. Narayanan, D. N. Bernard, K. Bafna, D. Gagne, P. K. Agarwal et al., Ligand-Induced Variations in Structural and Dynamical Properties Within an Enzyme Superfamily, Frontiers in Molecular Biosciences, vol.5, p.29946547, 2018.

P. Koczera, L. Martin, G. Marx, and T. Schuerholz, The Ribonuclease A Superfamily in Humans: Canonical RNases as the Buttress of Innate Immunity, International Journal of Molecular Sciences, vol.17, issue.8, 2016.

D. Gagne, C. Narayanan, and N. Doucet, Network of long-range concerted chemical shift displacements upon ligand binding to human angiogenin, Protein Science, vol.24, issue.4, p.25450558, 2015.