{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T02:09:36Z","timestamp":1771034976865,"version":"3.50.1"},"reference-count":105,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2022,6,8]],"date-time":"2022-06-08T00:00:00Z","timestamp":1654646400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"NATO Science for Peace and Security Program","award":["G5685"],"award-info":[{"award-number":["G5685"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,11]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Allostery in proteins is an essential phenomenon in biological processes. In this article, we present a computational model to predict paths of maximum information transfer between active and allosteric sites. In this information theoretic study, we use mutual information as the measure of information transfer, where transition probability of information from one residue to its contacting neighbors is proportional to the magnitude of mutual information between the two residues. Starting from a given residue and using a Hidden Markov Model, we successively determine the neighboring residues that eventually lead to a path of optimum information transfer. The Gaussian approximation of mutual information between residue pairs is adopted. The limits of validity of this approximation are discussed in terms of a nonlinear theory of mutual information and its reduction to the Gaussian form.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Predictions of the model are tested on six widely studied cases, CheY Bacterial Chemotaxis, B-cell Lymphoma extra-large (Bcl-xL), Human proline isomerase cyclophilin A (CypA), Dihydrofolate reductase (DHFR), HRas GTPase and Caspase-1. The communication transmission rendering the propagation of local fluctuations from the active sites throughout the structure in multiple paths correlate well with the known experimental data. Distinct paths originating from the active site may likely represent a multi functionality such as involving more than one allosteric site and\/or pre-existence of some other functional states. Our model is computationally fast and simple and can give allosteric communication pathways, which are crucial for the understanding and control of protein functionality.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac380","type":"journal-article","created":{"date-parts":[[2022,6,8]],"date-time":"2022-06-08T12:29:48Z","timestamp":1654691388000},"page":"3590-3599","source":"Crossref","is-referenced-by-count":27,"title":["Prediction of allosteric communication pathways in proteins"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1279-5803","authenticated-orcid":false,"given":"Turkan","family":"Haliloglu","sequence":"first","affiliation":[{"name":"Polymer Research Center and Chemical Engineering Department, Bogazici University , \u0130stanbul 34342, Turkey"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2471-0296","authenticated-orcid":false,"given":"Aysima","family":"Hacisuleyman","sequence":"additional","affiliation":[{"name":"Institute of Bioengineering, Swiss Federal Institute of Technology (EPFL) , Lausanne 1015, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2496-6059","authenticated-orcid":false,"given":"Burak","family":"Erman","sequence":"additional","affiliation":[{"name":"Department of Chemical and Biological Engineering, Koc University , \u0130stanbul 34450, Turkey"}]}],"member":"286","published-online":{"date-parts":[[2022,6,8]]},"reference":[{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1016\/j.str.2020.03.014","article-title":"Distinct allosteric networks underlie mechanistic speciation of ABC transporters","volume":"28","author":"Acar","year":"2020","journal-title":"Structure"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"e41430","DOI":"10.1371\/journal.pone.0041430","article-title":"Mapping the mutual information network of enzymatic families in the protein structure to unveil functional features","volume":"7","author":"Aguilar","year":"2012","journal-title":"PLoS One"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"12477","DOI":"10.1038\/ncomms12477","article-title":"Prediction of allosteric sites and mediating interactions through bond-to-bond propensities","volume":"7","author":"Amor","year":"2016","journal-title":"Nat. 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Biol"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/S1359-0278(97)00024-2","article-title":"Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential","volume":"2","author":"Bahar","year":"1997","journal-title":"Fold Des"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1016\/bs.mie.2016.05.027","article-title":"Detecting allosteric networks using molecular dynamics simulation","volume":"578","author":"Bowerman","year":"2016","journal-title":"Methods Enzymol"},{"key":"2023041405365469500_","volume-title":"Thermodynamics and an Introduction to Thermostatistics","author":"Callen","year":"1985"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"10203","DOI":"10.1073\/pnas.1404220111","article-title":"Cyclophilin a catalyzes proline isomerization by an electrostatic handle mechanism","volume":"111","author":"Camilloni","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1038\/nmeth.1255","article-title":"Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering","volume":"5","author":"Cammarata","year":"2008","journal-title":"Nat. Methods"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1016\/j.jmb.2007.08.047","article-title":"Allosteric communication in dihydrofolate reductase: signaling network and pathways for closed to occluded transition and back","volume":"374","author":"Chen","year":"2007","journal-title":"J. Mol. Biol"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1039\/b717819k","article-title":"Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL","volume":"4","author":"Chennubhotla","year":"2008","journal-title":"Mol. Biosyst"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1006\/jmbi.2000.3595","article-title":"NMR structure of activated CheY","volume":"297","author":"Cho","year":"2000","journal-title":"J. Mol. Biol"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1007\/BF00276625","article-title":"Allostery without conformational change","volume":"11","author":"Cooper","year":"1984","journal-title":"Eur. Biophys. J"},{"key":"2023041405365469500_","volume-title":"Elements of Information Theory","author":"Cover","year":"1999"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"1295","DOI":"10.1110\/ps.03259908","article-title":"Allostery and cooperativity revisited","volume":"17","author":"Cui","year":"2008","journal-title":"Protein Sci"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1002\/prot.21300","article-title":"Local motions in a benchmark of allosteric proteins","volume":"67","author":"Daily","year":"2007","journal-title":"Proteins"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1016\/j.jmb.2008.06.040","article-title":"An allosteric circuit in caspase-1","volume":"381","author":"Datta","year":"2008","journal-title":"J. Mol. Biol"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"7444","DOI":"10.1128\/MCB.18.12.7444","article-title":"Distinct subclasses of small GTPases interact with guanine nucleotide exchange factors in a similar manner","volume":"18","author":"Day","year":"1998","journal-title":"Mol. Cell. Biol"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"1042","DOI":"10.1016\/j.str.2009.06.008","article-title":"The origin of allosteric functional modulation: multiple pre-existing pathways","volume":"17","author":"del Sol","year":"2009","journal-title":"Structure"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"1505","DOI":"10.1110\/ps.035691.108","article-title":"Position-specific residue preference features around the ends of helices and strands and a novel strategy for the prediction of secondary structures","volume":"17","author":"Duan","year":"2008","journal-title":"Protein Sci"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1038\/nature04105","article-title":"Intrinsic dynamics of an enzyme underlies catalysis","volume":"438","author":"Eisenmesser","year":"2005","journal-title":"Nature"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.1002\/prot.21613","article-title":"HingeProt: automated prediction of hinges in protein structures","volume":"70","author":"Emekli","year":"2008","journal-title":"Proteins"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1002\/prot.25535","article-title":"A computational model for controlling conformational cooperativity and function in proteins","volume":"86","author":"Erman","year":"2018","journal-title":"Proteins"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4757-3247-4","volume-title":"Statistical Methods in Bioinformatics","author":"Ewens","year":"2001"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"e4681","DOI":"10.1371\/journal.pone.0004681","article-title":"Computing highly correlated positions using mutual information and graph theory for G protein-coupled receptors","volume":"4","author":"Fatakia","year":"2009","journal-title":"PLoS One"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"5358","DOI":"10.1063\/1.1681888","article-title":"Moments and distribution functions for polymer chains of finite length. I. Theory","volume":"61","author":"Flory","year":"1974","journal-title":"J. Chem. Phys"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/nchembio.1166","article-title":"PUMA binding induces partial unfolding within BCL-xL to disrupt p53 binding and promote apoptosis","volume":"9","author":"Follis","year":"2013","journal-title":"Nat. Chem. Biol"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1038\/nature08615","article-title":"Hidden alternative structures of proline isomerase essential for catalysis","volume":"462","author":"Fraser","year":"2009","journal-title":"Nature"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1038\/nature05959","article-title":"Conformational entropy in molecular recognition by proteins","volume":"448","author":"Frederick","year":"2007","journal-title":"Nature"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1016\/j.jmb.2003.11.010","article-title":"Ligand-dependent dynamics and intramolecular signaling in a PDZ domain","volume":"335","author":"Fuentes","year":"2004","journal-title":"J. Mol. Biol"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"13057","DOI":"10.1021\/jp207500b","article-title":"Direct observation of vibrational energy flow in cytochrome c","volume":"115","author":"Fujii","year":"2011","journal-title":"J. Phys. Chem. B"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"3269","DOI":"10.1021\/jz501882h","article-title":"Observing vibrational energy flow in a protein with the spatial resolution of a single amino acid residue","volume":"5","author":"Fujii","year":"2014","journal-title":"J. Phys. Chem. Lett"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"866","DOI":"10.1016\/j.str.2019.01.014","article-title":"Toward comprehensive allosteric control over protein activity","volume":"27","author":"Guarnera","year":"2019","journal-title":"Structure"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1002\/prot.25272","article-title":"Causality, transfer entropy, and allosteric communication landscapes in proteins with harmonic interactions","volume":"85","author":"Hacisuleyman","year":"2017","journal-title":"Proteins"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"e1005319","DOI":"10.1371\/journal.pcbi.1005319","article-title":"Entropy transfer between residue pairs and allostery in proteins: quantifying allosteric communication in ubiquitin","volume":"13","author":"Hacisuleyman","year":"2017","journal-title":"PLoS Comput. Biol"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1021\/acs.jpcb.0c08409","article-title":"Synchronous and asynchronous response in dynamically perturbed proteins","volume":"125","author":"Hacisuleyman","year":"2021","journal-title":"J. Phys. Chem. B"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"3439","DOI":"10.1074\/jbc.M109.065391","article-title":"BclxL changes conformation upon binding to wild-type but not mutant p53 DNA binding domain","volume":"285","author":"Hagn","year":"2010","journal-title":"J. Biol. Chem"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1002\/(SICI)1097-0134(19991201)37:4<654::AID-PROT15>3.0.CO;2-J","article-title":"Structure-based analysis of protein dynamics: comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data","volume":"37","author":"Haliloglu","year":"1999","journal-title":"Proteins"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"3090","DOI":"10.1103\/PhysRevLett.79.3090","article-title":"Gaussian dynamics of folded proteins","volume":"79","author":"Haliloglu","year":"1997","journal-title":"Phys. Rev. Lett"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"2055","DOI":"10.1529\/biophysj.106.082180","article-title":"Coupling of global and local vibrational modes in dynamic allostery of proteins","volume":"91","author":"Hawkins","year":"2006","journal-title":"Biophys. J"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1002\/(SICI)1520-6343(1996)2:5<277::AID-BSPY2>3.0.CO;2-2","article-title":"Ultrafast infrared spectroscopy in biomolecules: active site dynamics of heme proteins","volume":"2","author":"Hill","year":"1996","journal-title":"Biospectroscopy"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1146\/annurev-biophys-050511-102319","article-title":"Structural and energetic basis of allostery","volume":"41","author":"Hilser","year":"2012","journal-title":"Ann. Rev. Biophys"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"078102","DOI":"10.1103\/PhysRevLett.94.078102","article-title":"Protein structural change upon ligand binding: linear response theory","volume":"94","author":"Ikeguchi","year":"2005","journal-title":"Phys. Rev. Lett"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/0301-0104(93)E0414-Q","article-title":"Complex nonexponential relaxation in myoglobin after photodissociation of MbCO: measurement and analysis from 2 ps to 56 \u03c5s","volume":"180","author":"Jackson","year":"1994","journal-title":"Chem. Phys"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"12981","DOI":"10.1074\/jbc.M117.778886","article-title":"The small GTPases K-Ras, N-Ras, and H-Ras have distinct biochemical properties determined by allosteric effects","volume":"292","author":"Johnson","year":"2017","journal-title":"J. Biol. Chem"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"046005","DOI":"10.1088\/1478-3975\/7\/4\/046005","article-title":"Anharmonicity, mode-coupling and entropy in a fluctuating native protein","volume":"7","author":"Kabak\u00e7\u0131o\u011flu","year":"2010","journal-title":"Phys. Biol"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"W249","DOI":"10.1093\/nar\/gkt284","article-title":"MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues","volume":"41","author":"Kaya","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"748","DOI":"10.1016\/j.sbi.2003.10.008","article-title":"The role of dynamics in allosteric regulation","volume":"13","author":"Kern","year":"2003","journal-title":"Curr. Opin. Struct. Biol"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"1950","DOI":"10.1021\/acs.jpclett.6b00785","article-title":"Importance of atomic contacts in vibrational energy flow in proteins","volume":"7","author":"Kondoh","year":"2016","journal-title":"J. Phys. Chem. Lett"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1021\/bi00865a047","article-title":"Comparison of experimental binding data and theoretical models in proteins containing subunits","volume":"5","author":"Koshland","year":"1966","journal-title":"Biochemistry"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"4734","DOI":"10.1021\/acs.jpcb.1c02511","article-title":"Global dynamics renders protein sites with high functional response","volume":"125","author":"Kutlu","year":"2021","journal-title":"J. Phys. Chem. B"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1007\/s12551-015-0169-3","article-title":"Contrasting roles of dynamics in protein allostery: NMR and structural studies of CheY and the third PDZ domain from PSD-95","volume":"7","author":"Lee","year":"2015","journal-title":"Biophys. Rev"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1126\/science.1159052","article-title":"Surface sites for engineering allosteric control in proteins","volume":"322","author":"Lee","year":"2008","journal-title":"Science"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","DOI":"10.1201\/9781420087048","volume-title":"Proteins: Energy, Heat and Signal Flow","author":"Leitner","year":"2009"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"2895","DOI":"10.3390\/e17052895","article-title":"AIM for allostery: using the ising model to understand information processing and transmission in allosteric biomolecular systems","volume":"17","author":"LeVine","year":"2015","journal-title":"Entropy"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"5036","DOI":"10.1021\/jacs.5b08814","article-title":"Timing correlations in proteins predict functional modules and dynamic allostery","volume":"138","author":"Lin","year":"2016","journal-title":"J. Am. Chem. Soc"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1126\/science.286.5438.295","article-title":"Evolutionarily conserved pathways of energetic connectivity in protein families","volume":"286","author":"Lockless","year":"1999","journal-title":"Science"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"1983","DOI":"10.1007\/s11229-015-0824-z","article-title":"What is shannon information?","volume":"193","author":"Lombardi","year":"2016","journal-title":"Synthese"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1007\/s12551-020-00667-8","article-title":"Allosteric communication in molecular machines via information exchange: what can be learned from dynamical modeling","volume":"12","author":"Loutchko","year":"2020","journal-title":"Biophys. Rev"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"26358","DOI":"10.1016\/S0021-9258(18)47201-8","article-title":"Signal transduction in chemotaxis. A propagating conformation change upon phosphorylation of CheY","volume":"269","author":"Lowry","year":"1994","journal-title":"J. Biol. Chem"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"6607","DOI":"10.1021\/acs.chemrev.5b00542","article-title":"Ras conformational ensembles, allostery, and signaling","volume":"116","author":"Lu","year":"2016","journal-title":"Chem. Rev"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1016\/j.str.2011.06.002","article-title":"Dynamic allostery: linkers are not merely flexible","volume":"19","author":"Ma","year":"2011","journal-title":"Structure"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"2502","DOI":"10.1111\/febs.15826","article-title":"Allosteric communication regulates ligand-specific GPCR activity","volume":"288","author":"Ma","year":"2021","journal-title":"FEBS J"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"2159","DOI":"10.1074\/jbc.M306021200","article-title":"Bcl-XL mutations suppress cellular sensitivity to antimycin A","volume":"279","author":"Manion","year":"2004","journal-title":"J. Biol. Chem"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"2486","DOI":"10.1021\/ct9001812","article-title":"Quantifying correlations between allosteric sites in thermodynamic ensembles","volume":"5","author":"McClendon","year":"2009","journal-title":"J. Chem. Theory Comput"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"e68346","DOI":"10.7554\/eLife.68346","article-title":"Structurally distributed surface sites tune allosteric regulation","volume":"10","author":"McCormick","year":"2021","journal-title":"elife"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"1363","DOI":"10.1016\/j.str.2012.05.008","article-title":"Segmental motions, not a two-state concerted switch, underlie allostery in CheY","volume":"20","author":"McDonald","year":"2012","journal-title":"Structure"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"5032","DOI":"10.1073\/pnas.0500699102","article-title":"Defining the role of active-site loop fluctuations in dihydrofolate reductase catalysis","volume":"102","author":"McElheny","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"044107","DOI":"10.1063\/5.0055662","article-title":"Mutual information analysis of the dynamic correlation between side chains in proteins","volume":"155","author":"Miyashita","year":"2021","journal-title":"J. Chem. Phys"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/S0022-2836(65)80285-6","article-title":"On the nature of allosteric transitions: a plausible model","volume":"12","author":"Monod","year":"1965","journal-title":"J. Mol. Biol"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"E12201","DOI":"10.1073\/pnas.1810452115","article-title":"Eigenvector centrality for characterization of protein allosteric pathways","volume":"115","author":"Negre","year":"2018","journal-title":"Proc. Natl. Acad. Sci. 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Commun"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"18249","DOI":"10.1073\/pnas.0904492106","article-title":"Hidden dynamic allostery in a PDZ domain","volume":"106","author":"Petit","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1038\/nsmb1132","article-title":"Dynamically driven protein allostery","volume":"13","author":"Popovych","year":"2006","journal-title":"Nat. Struct. Mol. Biol"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"7595","DOI":"10.1073\/pnas.0602571103","article-title":"A common allosteric site and mechanism in caspases","volume":"103","author":"Scheer","year":"2006","journal-title":"Proc. Natl. Acad. Sci. 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Biol"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"1190","DOI":"10.1016\/j.bpj.2015.08.011","article-title":"Allosteric dynamic control of binding","volume":"109","author":"Sumbul","year":"2015","journal-title":"Biophys. J"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"3539","DOI":"10.1073\/pnas.1516579113","article-title":"Intramolecular allosteric communication in dopamine D2 receptor revealed by evolutionary amino acid covariation","volume":"113","author":"Sung","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"5407","DOI":"10.1021\/acs.jpcb.0c04772","article-title":"Nonbonded atomic contacts drive ultrafast helix motions in myoglobin","volume":"124","author":"Tahara","year":"2020","journal-title":"J. Phys. Chem. B"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"1905","DOI":"10.1103\/PhysRevLett.77.1905","article-title":"Large amplitude elastic motions in proteins from a single-parameter, atomic analysis","volume":"77","author":"Tirion","year":"1996","journal-title":"Phys. Rev. Lett"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jmb.2008.02.034","article-title":"Allostery: absence of a change in shape does not imply that allostery is not at play","volume":"378","author":"Tsai","year":"2008","journal-title":"J. Mol. Biol"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"e16474","DOI":"10.1371\/journal.pone.0016474","article-title":"Identification of ligand binding sites of proteins using the Gaussian network model","volume":"6","author":"Tuzmen","year":"2011","journal-title":"PLoS One"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1038\/nature08560","article-title":"Dynamic activation of an allosteric regulatory protein","volume":"462","author":"Tzeng","year":"2009","journal-title":"Nature"},{"key":"2023041405365469500_","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/j.coph.2016.07.010","article-title":"Allosteric communication pipelines in G-protein-coupled receptors","volume":"30","author":"Vaidehi","year":"2016","journal-title":"Curr. Opin. 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