Domains, Motifs, and Scaffolds: The Role of Modular Interactions in the Evolution and Wiring of Cell Signaling Circuits, Annual Review of Biochemistry, vol.75, issue.1, pp.655-680, 2006. ,
DOI : 10.1146/annurev.biochem.75.103004.142710
Evolving specificity from variability for protein interaction domains, Trends in Biochemical Sciences, vol.36, issue.4, pp.183-190, 2011. ,
DOI : 10.1016/j.tibs.2010.12.001
Genome-Wide Analysis of PDZ Domain Binding Reveals Inherent Functional Overlap within the PDZ Interaction Network, PLoS ONE, vol.343, issue.1, p.16047, 2011. ,
DOI : 10.1371/journal.pone.0016047.s018
PDZ Domain Binding Selectivity Is Optimized Across the Mouse Proteome, Science, vol.317, issue.5836, pp.364-369, 2007. ,
DOI : 10.1126/science.1144592
Organization and dynamics of PDZ-domain-related supramodules in the postsynaptic density, Nature Reviews Neuroscience, vol.114, issue.2, pp.87-99, 2009. ,
DOI : 10.1038/sj.emboj.7601860
Allosteric regulation and catalysis emerge via a common route, Nature Chemical Biology, vol.84, issue.8, pp.474-482, 2008. ,
DOI : 10.1038/nchembio.98
On the nature of allosteric transitions: A plausible model, Journal of Molecular Biology, vol.12, issue.1, pp.88-118, 1965. ,
DOI : 10.1016/S0022-2836(65)80285-6
Intrinsic dynamics of an enzyme underlies catalysis, Nature, vol.6, issue.7064, pp.117-121, 2005. ,
DOI : 10.1038/nature04105
Allostery without conformational change, European Biophysics Journal, vol.74, issue.2, pp.103-109, 1984. ,
DOI : 10.1007/BF00276625
Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble, Proceedings of the National Academy of Sciences, vol.97, issue.22, pp.12020-12025, 2000. ,
DOI : 10.1073/pnas.220240297
Dynamically driven protein allostery, Nature Structural & Molecular Biology, vol.28, issue.9, pp.831-838, 2006. ,
DOI : 10.1021/bi9526802
Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play, Journal of Molecular Biology, vol.378, issue.1, pp.1-11, 2008. ,
DOI : 10.1016/j.jmb.2008.02.034
Dynamic activation of an allosteric regulatory protein, Nature, vol.122, issue.7271, pp.368-372, 2009. ,
DOI : 10.1038/nature08560
Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families, Science, vol.286, issue.5438, pp.295-299, 1999. ,
DOI : 10.1126/science.286.5438.295
Evolutionarily conserved networks of residues mediate allosteric communication in proteins, Nature Structural Biology, vol.10, issue.1, pp.59-69, 2003. ,
DOI : 10.1038/nsb881
Signaling pathways of PDZ2 domain: A molecular dynamics interaction correlation analysis, Proteins: Structure, Function, and Bioinformatics, vol.103, issue.1, pp.145-154, 2009. ,
DOI : 10.1002/prot.22139
Mapping of Two Networks of Residues That Exhibit Structural and Dynamical Changes upon Binding in a PDZ Domain Protein, Journal of the American Chemical Society, vol.130, issue.28, pp.8931-8939, 2008. ,
DOI : 10.1021/ja0752080
Reassessing a sparse energetic network within a single protein domain, Proceedings of the National Academy of Sciences, vol.105, issue.12, pp.4679-4684, 2008. ,
DOI : 10.1073/pnas.0711732105
Evaluation of Energetic and Dynamic Coupling Networks in a PDZ Domain Protein, Journal of Molecular Biology, vol.364, issue.3, pp.337-351, 2006. ,
DOI : 10.1016/j.jmb.2006.08.076
Strategy for analysing the co-operativity of intramolecular interactions in peptides and proteins, Journal of Molecular Biology, vol.214, issue.3, pp.613-617, 1990. ,
DOI : 10.1016/0022-2836(90)90275-Q
On the accuracy of inferring energetic coupling between distant sites in protein families from evolutionary imprints: Illustrations using lattice model, Proteins: Structure, Function, and Bioinformatics, vol.374, issue.4, pp.823-831, 2009. ,
DOI : 10.1002/prot.22498
A PDZ domain recapitulates a unifying mechanism for protein folding, Proceedings of the National Academy of Sciences, vol.104, issue.1, pp.128-133, 2007. ,
DOI : 10.1073/pnas.0602770104
Kinetic folding mechanism of PDZ2 from PTP-BL, Protein Engineering Design and Selection, vol.18, issue.8, pp.389-395, 2005. ,
DOI : 10.1093/protein/gzi047
The Kinetics of PDZ Domain-Ligand Interactions and Implications for the Binding Mechanism, Journal of Biological Chemistry, vol.280, issue.41, pp.34805-34812, 2005. ,
DOI : 10.1074/jbc.M506017200
Crystal Structures of a Complexed and Peptide-Free Membrane Protein???Binding Domain: Molecular Basis of Peptide Recognition by PDZ, Cell, vol.85, issue.7, pp.1067-1076, 1996. ,
DOI : 10.1016/S0092-8674(00)81307-0
A Sequential Binding Mechanism in a PDZ Domain, Biochemistry, vol.48, issue.30, pp.7089-7097, 2009. ,
DOI : 10.1021/bi900559k
CRIPT, a Novel Postsynaptic Protein that Binds to the Third PDZ Domain of PSD-95/SAP90, Neuron, vol.20, issue.4, pp.693-707, 1998. ,
DOI : 10.1016/S0896-6273(00)81009-0
The study of bimolecular reactions under non-pseudo-first order conditions, Biophysical Chemistry, vol.116, issue.3, pp.251-256, 2005. ,
DOI : 10.1016/j.bpc.2005.04.006
The use of double mutants to detect structural changes in the active site of the tyrosyl-tRNA synthetase (Bacillus stearothermophilus), Cell, vol.38, issue.3, pp.835-840, 1984. ,
DOI : 10.1016/0092-8674(84)90278-2
Co-operative interactions during protein folding, Journal of Molecular Biology, vol.224, issue.3, pp.733-740, 1992. ,
DOI : 10.1016/0022-2836(92)90557-Z
Rapid, electrostatically assisted association of proteins, Nature Structural Biology, vol.54, issue.5, pp.427-431, 1996. ,
DOI : 10.1107/S0021889891004399
Ligand-dependent Dynamics and Intramolecular Signaling in a PDZ Domain, Journal of Molecular Biology, vol.335, issue.4, pp.1105-1115, 2004. ,
DOI : 10.1016/j.jmb.2003.11.010
??-Value analysis and the nature of protein-folding transition states, Proceedings of the National Academy of Sciences, vol.101, issue.21, pp.7976-7981, 2004. ,
DOI : 10.1073/pnas.0402684101
Solution Structure of the PDZ2 Domain from Cytosolic Human Phosphatase hPTP1E Complexed with a Peptide Reveals Contribution of the ??2?????3 Loop to PDZ Domain???Ligand Interactions, Journal of Molecular Biology, vol.320, issue.4, pp.813-820, 2002. ,
DOI : 10.1016/S0022-2836(02)00544-2
Patterns of nonadditivity between pairs of stability mutations in staphylococcal nuclease, Biochemistry, vol.32, issue.38, pp.10131-10139, 1993. ,
DOI : 10.1021/bi00089a032
The PyMOL Molecular Graphics System, 2002. ,