Domain combinations in archaeal, eubacterial and eukaryotic proteomes, J Mol Biol, vol.310, issue.2, p.11428892, 2001. ,
Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions, J Mol Biol, vol.348, issue.1, p.15808866, 2005. ,
The relationship between domain duplication and recombination, J Mol Biol, vol.346, issue.1, p.15663950, 2005. ,
Selective forces acting during multi-domain protein evolution: the case of multi-domain globins, Springerplus, vol.4, p.4503718, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01177910
How do new proteins arise?, Curr Opin Struct Biol, vol.20, issue.3, p.20347587, 2010. ,
Stability of domain structures in multi-domain proteins, Sci Rep, p.3216527, 2011. ,
The folding and evolution of multidomain proteins, Nat Rev Mol Cell Biol, vol.8, issue.4, 2007. ,
A database of domain definitions for proteins with complex interdomain geometry, PLoS One, vol.4, issue.4, p.2662426, 2009. ,
An ambiguity principle for assigning protein structural domains, Sci Adv, vol.3, issue.1, p.5235333, 2017. ,
Modulation of global low-frequency motions underlies allosteric regulation: demonstration in CRP/FNR family transcription factors, PLoS Biol, vol.11, issue.9, p.3769225, 2013. ,
Dynamic allostery: linkers are not merely flexible. Structure, vol.19, p.21742258, 2011. ,
Investigating Dynamic Interdomain Allostery in Pin1, Epub 2015/10/27, vol.7, p.4610412, 2015. ,
The geometry of domain combination in proteins, J Mol Biol, vol.315, issue.4, p.11812158, 2002. ,
A functional role for protein cavities in domain: domain motions, J Mol Biol, vol.261, issue.2, p.8757295, 1996. ,
Protein domain interfaces: characterization and comparison with oligomeric protein interfaces, Protein Eng, vol.13, issue.2, pp.77-82, 2000. ,
Folding of multidomain proteins: biophysical consequences of tethering even in apparently independent folding, Proteins, vol.80, issue.12, p.22890725, 2012. ,
Asymmetric effect of domain interactions on the kinetics of folding in yeast phosphoglycerate kinase, Epub 2005/05/11, vol.14, p.2253372, 2005. ,
Protein Assembly and Building Blocks: Beyond the Limits of the LEGO Brick Metaphor. Biochemistry, vol.56, p.28809494, 2017. ,
Kinetic stabilisation of a modular protein by domain interactions, FEBS Lett, vol.438, issue.1-2, 1998. ,
Titin; a multidomain protein that behaves as the sum of its parts, J Mol Biol, vol.315, issue.4, p.11812150, 2002. ,
Residues crucial for maintaining short paths in network communication mediate signaling in proteins, Mol Syst Biol, vol.2, p.1681495, 2006. ,
Protein frustratometer: a tool to localize energetic frustration in protein molecules, Nucleic Acids Res, vol.40, p.3394345, 2012. ,
Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes, Structure, vol.13, issue.6, p.1489920, 2005. ,
Two structures of cyclophilin 40: folding and fidelity in the TPR domains, Structure, vol.9, issue.5, pp.431-439, 2001. ,
Kinetic and proteomic analyses of S-nitrosoglutathione-treated hexokinase A: consequences for cancer energy metabolism, Amino Acids, vol.32, issue.4, p.17051422, 2007. ,
Expression of human brain hexokinase in Escherichia coli: purification and characterization of the expressed enzyme, Biochem Biophys Res Commun, vol.177, issue.1, pp.305-316, 1991. ,
Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins, BMC Struct Biol, vol.12, p.3427047, 2012. ,
URL : https://hal.archives-ouvertes.fr/inserm-00725334
Comparing interfacial dynamics in protein-protein complexes: an elastic network approach, BMC Struct Biol, vol.10, p.2927602, 2010. ,
Two pathways mediate interdomain allosteric regulation in pin1, Structure, vol.23, issue.1, p.25543254, 2015. ,
, , p.4286514
Dynamic Allostery Modulates Catalytic Activity by Modifying the Hydrogen Bonding Network in the Catalytic Site of Human Pin1, Molecules, vol.22, issue.6, 2017. ,
Long-range intra-protein communication can be transmitted by correlated side-chain fluctuations alone, PLoS Comput Biol, vol.7, issue.9, p.3182858, 2011. ,
Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites, Proc Natl Acad Sci U S A, vol.109, issue.29, p.3406870, 2012. ,
Artificial proteins as allosteric modulators of PDZ3 and SH3 in two-domain constructs: A computational characterization of novel chimeric proteins, Proteins, vol.84, issue.10, p.27273513, 2016. ,
Is allostery an intrinsic property of all dynamic proteins?, Proteins, vol.57, issue.3, p.15382234, 2004. ,
The underappreciated role of allostery in the cellular network, Annu Rev Biophys, vol.42, p.23451894, 2013. ,
The origin of allosteric functional modulation: multiple pre-existing pathways, Structure, vol.17, issue.8, p.2749652, 2009. ,
Modulations of DNA Contacts by Linker Histones and Post-translational Modifications Determine the Mobility and Modifiability of Nucleosomal H3 Tails, Mol Cell, vol.61, issue.2, p.26778125, 2016. ,
Allosteric post-translational modification codes, Trends Biochem Sci, vol.37, issue.10, p.22884395, 2012. ,
Ubiquitination-induced conformational change within the deiodinase dimer is a switch regulating enzyme activity, Mol Cell Biol, vol.27, issue.13, p.17452445, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00152172
, , p.1951476
Phosphorylation-induced conformational changes in Rap1b: allosteric effects on switch domains and effector loop, J Biol Chem, vol.284, issue.40, pp.27480-27486, 2009. ,
, , p.2785677
Phosphorylation modulates catalytic function and regulation in the cAMP-dependent protein kinase, Biochemistry, vol.34, issue.8, pp.2447-54, 1995. ,
Autoactivation of catalytic (C alpha) subunit of cyclic AMP-dependent protein kinase by phosphorylation of threonine 197, Mol Cell Biol, vol.13, issue.4, p.359554, 1993. ,
Mechanism of CDK activation revealed by the structure of a cyclinA-CDK2 complex, Nature, vol.376, issue.6538, 1995. ,
The Hsp70 interdomain linker is a dynamic switch that enables allosteric communication between two structured domains, J Biol Chem, vol.292, issue.36, p.5592658, 2017. ,
Single mutation in the linker domain confers protein flexibility and camptothecin resistance to human topoisomerase I, J Biol Chem, vol.278, issue.44, p.12904303, 2003. ,
SH2-catalytic domain linker heterogeneity influences allosteric coupling across the SFK family, Biochemistry, vol.53, issue.44, p.4230323, 2014. ,
Allosteric N-WASP activation by an inter-SH3 domain linker in Nck, Proc Natl Acad Sci U S A, vol.112, issue.47, p.4664294, 2015. ,
SCOPe: Structural Classification of Proteins-extended, integrating SCOP and ASTRAL data and classification of new structures, Nucleic Acids Res, vol.42, p.3965108, 2014. ,
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences, Bioinformatics, vol.22, issue.13, pp.1658-1667, 2006. ,
UniProt: the Universal Protein knowledgebase, Nucleic Acids Res, vol.32, p.308865, 2003. ,
TM-align: a protein structure alignment algorithm based on the TM-score, Nucleic Acids Res, vol.33, issue.7, pp.2302-2311, 2005. ,
, , p.1084323
LGA: A method for finding 3D similarities in protein structures, Nucleic Acids Res, vol.31, issue.13, p.168977, 2003. ,
MaxSub: an automated measure for the assessment of protein structure prediction quality, Bioinformatics, vol.16, issue.9, pp.776-85, 2000. ,
Exploring Network Structure, Dynamics, and Function using NetworkX, Proceedings of the 7th Python in Science conference, 2008. ,
GROMACS: fast, flexible, and free, J Comput Chem, vol.26, issue.16, p.16211538, 2005. ,
High-resolution structure prediction and the crystallographic phase problem, Nature, vol.450, issue.7167, p.2504711, 2007. ,
WHAT IF: a molecular modeling and drug design program, J Mol Graph, vol.8, issue.1, pp.52-58, 1990. ,
ProDy: protein dynamics inferred from theory and experiments. Bioinformatics, vol.27, p.3102222, 2011. ,
A Unifying Tool for Linear Multivariate Statistical Methods: The RV-Coefficient, Journal of the Royal Statistical Society Series C (Applied Statistics), vol.25, issue.3, pp.257-65, 1976. ,
Development and current status of the CHARMM force field for nucleic acids, Biopolymers, vol.56, issue.4, pp.257-65, 2000. ,
Interaction Models for Water in Relation to Protein Hydration1981, pp.331-373 ,
Water in protein structure prediction, Proc Natl Acad Sci U S A, vol.101, issue.10, p.373465, 2004. ,