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Prediction of allosteric sites and mediating interactions through bond-to-bond propensities
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Document type | Article de périodique (Journal article) – Article de recherche |
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Access type | Accès libre |
Publication date | 2016 |
Language | Anglais |
Journal information | "Nature Communications" - Vol. 7, p. 12477 (August 2016) |
Peer reviewed | yes |
Publisher | Nature Publishing Group ((United Kingdom) London) |
e-issn | 2041-1723 |
Publication status | Publié |
Affiliation | UCL - SST/ICTM/INMA - Pôle en ingénierie mathématique |
Links |
- Monod Jacques, Changeux Jean-Pierre, Jacob François, Allosteric proteins and cellular control systems, 10.1016/s0022-2836(63)80091-1
- Perutz M. F., Mechanisms of cooperativity and allosteric regulation in proteins, 10.1017/s0033583500003826
- Nussinov Ruth, Tsai Chung-Jung, Allostery in Disease and in Drug Discovery, 10.1016/j.cell.2013.03.034
- Frauenfelder H, Sligar S., Wolynes P., The energy landscapes and motions of proteins, 10.1126/science.1749933
- Henzler-Wildman Katherine, Kern Dorothee, Dynamic personalities of proteins, 10.1038/nature06522
- Volkman B. F., Sci. Signal., 291, 2429 (2001)
- Gunasekaran K., Ma Buyong, Nussinov Ruth, Is allostery an intrinsic property of all dynamic proteins?, 10.1002/prot.20232
- Hardy Jeanne A, Wells James A, Searching for new allosteric sites in enzymes, 10.1016/j.sbi.2004.10.009
- Lockless S. W., Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families, 10.1126/science.286.5438.295
- Grant Barry J., Lukman Suryani, Hocker Harrison J., Sayyah Jaqueline, Brown Joan Heller, McCammon J. Andrew, Gorfe Alemayehu A., Novel Allosteric Sites on Ras for Lead Generation, 10.1371/journal.pone.0025711
- Ota Nobuyuki, Agard David A., Intramolecular Signaling Pathways Revealed by Modeling Anisotropic Thermal Diffusion, 10.1016/j.jmb.2005.05.043
- Demerdash Omar N. A., Daily Michael D., Mitchell Julie C., Structure-Based Predictive Models for Allosteric Hot Spots, 10.1371/journal.pcbi.1000531
- Panjkovich Alejandro, Daura Xavier, Exploiting protein flexibility to predict the location of allosteric sites, 10.1186/1471-2105-13-273
- Collier Galen, Ortiz Vanessa, Emerging computational approaches for the study of protein allostery, 10.1016/j.abb.2013.07.025
- Monod Jacque, Wyman Jeffries, Changeux Jean-Pierre, On the nature of allosteric transitions: A plausible model, 10.1016/s0022-2836(65)80285-6
- Koshland D. E., Némethy G., Filmer D., Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits*, 10.1021/bi00865a047
- Hilser Vincent J., Wrabl James O., Motlagh Hesam N., Structural and Energetic Basis of Allostery, 10.1146/annurev-biophys-050511-102319
- del Sol Antonio, Tsai Chung-Jung, Ma Buyong, Nussinov Ruth, The Origin of Allosteric Functional Modulation: Multiple Pre-existing Pathways, 10.1016/j.str.2009.06.008
- Zhuravlev Pavel I., Papoian Garegin A., Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework, 10.1017/s0033583510000119
- Müller-Werkmeister Henrike M., Bredenbeck Jens, A donor–acceptor pair for the real time study of vibrational energy transfer in proteins, 10.1039/c3cp54760d
- Li G., Nat. Commun., 5, 3100 (2014)
- Martínez Leandro, Figueira Ana C. M., Webb Paul, Polikarpov Igor, Skaf Munir S., Mapping the Intramolecular Vibrational Energy Flow in Proteins Reveals Functionally Important Residues, 10.1021/jz200830g
- Fujii Naoki, Mizuno Misao, Ishikawa Haruto, Mizutani Yasuhisa, Observing Vibrational Energy Flow in a Protein with the Spatial Resolution of a Single Amino Acid Residue, 10.1021/jz501882h
- Nguyen Phuong H., Derreumaux Philippe, Stock Gerhard, Energy Flow and Long-Range Correlations in Guanine-Binding Riboswitch: A Nonequilibrium Molecular Dynamics Study, 10.1021/jp902013s
- Gnanasekaran Ramachandran, Agbo Johnson K., Leitner David M., Communication maps computed for homodimeric hemoglobin: Computational study of water-mediated energy transport in proteins, 10.1063/1.3623423
- Gerek Z. Nevin, Ozkan S. Banu, Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning, 10.1371/journal.pcbi.1002154
- Kaya Cihan, Armutlulu Andac, Ekesan Solen, Haliloglu Turkan, MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues, 10.1093/nar/gkt284
- Nakayama Tsuneyoshi, Yakubo Kousuke, Orbach Raymond L., Dynamical properties of fractal networks: Scaling, numerical simulations, and physical realizations, 10.1103/revmodphys.66.381
- Leitner David M., Energy Flow in Proteins, 10.1146/annurev.physchem.59.032607.093606
- del Sol Antonio, Fujihashi Hirotomo, Amoros Dolors, Nussinov Ruth, Residues crucial for maintaining short paths in network communication mediate signaling in proteins, 10.1038/msb4100063
- del Sol Antonio, Araúzo-Bravo Marcos J, Amoros Dolors, Nussinov Ruth, Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages, 10.1186/gb-2007-8-5-r92
- Chennubhotla Chakra, Bahar Ivet, Signal Propagation in Proteins and Relation to Equilibrium Fluctuations, 10.1371/journal.pcbi.0030172
- Amitai Gil, Shemesh Arye, Sitbon Einat, Shklar Maxim, Netanely Dvir, Venger Ilya, Pietrokovski Shmuel, Network Analysis of Protein Structures Identifies Functional Residues, 10.1016/j.jmb.2004.10.055
- Ghosh A., Vishveshwara S., A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis, 10.1073/pnas.0704459104
- Sethi A., Eargle J., Black A. A., Luthey-Schulten Z., Dynamical networks in tRNA:protein complexes, 10.1073/pnas.0810961106
- Ribeiro Andre A. S. T., Ortiz Vanessa, Determination of Signaling Pathways in Proteins through Network Theory: Importance of the Topology, 10.1021/ct400977r
- Ribeiro Andre A. S. T., Ortiz Vanessa, Energy Propagation and Network Energetic Coupling in Proteins, 10.1021/jp509906m
- Delmotte A, Tate E W, Yaliraki S N, Barahona M, Protein multi-scale organization through graph partitioning and robustness analysis: application to the myosin–myosin light chain interaction, 10.1088/1478-3975/8/5/055010
- Amor B., Yaliraki S. N., Woscholski R., Barahona M., Uncovering allosteric pathways in caspase-1 using Markov transient analysis and multiscale community detection, 10.1039/c4mb00088a
- SCHAUB MICHAEL T., LEHMANN JÖRG, YALIRAKI SOPHIA N., BARAHONA MAURICIO, Structure of complex networks: Quantifying edge-to-edge relations by failure-induced flow redistribution, 10.1017/nws.2014.4
- Yu Keming, Lu Zudi, Stander Julian, Quantile regression: applications and current research areas, 10.1111/1467-9884.00363
- Datta Debajyoti, Scheer Justin M., Romanowski Michael J., Wells James A., An Allosteric Circuit in Caspase-1, 10.1016/j.jmb.2008.06.040
- Cook R. Dennis, Influential Observations in Linear Regression, 10.1080/01621459.1979.10481634
- Dyer C. M., Dahlquist F. W., Switched or Not?: the Structure of Unphosphorylated CheY Bound to the N Terminus of FliM, 10.1128/jb.00637-06
- Lee Seok-Yong, Cho Ho. S., Pelton Jeffrey G., Yan Dalai, Berry Edward A., Wemmer David E., Crystal Structure of Activated CheY : COMPARISON WITH OTHER ACTIVATED RECEIVER DOMAINS, 10.1074/jbc.m101002200
- McDonald Leanna R., Boyer Joshua A., Lee Andrew L., Segmental Motions, Not a Two-State Concerted Switch, Underlie Allostery in CheY, 10.1016/j.str.2012.05.008
- Bourret R. B., J. Biol. Chem., 268, 13089 (1993)
- Smith J. G., Latiolais J. A., Guanga G. P., Citineni S., Silversmith R. E., Bourret R. B., Investigation of the Role of Electrostatic Charge in Activation of the Escherichia coli Response Regulator CheY, 10.1128/jb.185.21.6385-6391.2003
- McDonald Leanna R., Whitley Matthew J., Boyer Joshua A., Lee Andrew L., Colocalization of Fast and Slow Timescale Dynamics in the Allosteric Signaling Protein CheY, 10.1016/j.jmb.2013.04.029
- McCormick Frank, Ras-related proteins in signal transduction and growth control, 10.1002/mrd.1080420419
- Buhrman G., Holzapfel G., Fetics S., Mattos C., Allosteric modulation of Ras positions Q61 for a direct role in catalysis, 10.1073/pnas.0912226107
- Murzin A. G., J. Mol. Biol., 247, 536 (1995)
- Daily Michael D., Gray Jeffrey J., Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins, 10.1371/journal.pcbi.1000293
- Zhu X, Amsler C D, Volz K, Matsumura P, Tyrosine 106 of CheY plays an important role in chemotaxis signal transduction in Escherichia coli., 10.1128/jb.178.14.4208-4215.1996
- Bellsolell Lluı́s, Cronet Philippe, Majolero Montserrat, Serrano Luis, Coll Miquel, The Three-dimensional Structure of Two Mutants of the Signal Transduction Protein CheY Suggest its Molecular Activation Mechanism, 10.1006/jmbi.1996.0151
- Buchli B., Waldauer S. A., Walser R., Donten M. L., Pfister R., Blochliger N., Steiner S., Caflisch A., Zerbe O., Hamm P., Kinetic response of a photoperturbed allosteric protein, 10.1073/pnas.1306323110
- Chung Fan, Yau S.-T., Discrete Green's Functions, 10.1006/jcta.2000.3094
- Reuveni S., Granek R., Klafter J., Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure, 10.1073/pnas.1002018107
- Mayo Stephen L., Olafson Barry D., Goddard William A., DREIDING: a generic force field for molecular simulations, 10.1021/j100389a010
- Lin Matthew S., Fawzi Nicolas Lux, Head-Gordon Teresa, Hydrophobic Potential of Mean Force as a Solvation Function for Protein Structure Prediction, 10.1016/j.str.2007.05.004
- Yang L.-W., Rader A. J., Liu X., Jursa C. J., Chen S. C., Karimi H. A., Bahar I., oGNM: online computation of structural dynamics using the Gaussian Network Model, 10.1093/nar/gkl084
- Brooks B. R., Brooks C. L., Mackerell A. D., Nilsson L., Petrella R. J., Roux B., Won Y., Archontis G., Bartels C., Boresch S., Caflisch A., Caves L., Cui Q., Dinner A. R., Feig M., Fischer S., Gao J., Hodoscek M., Im W., Kuczera K., Lazaridis T., Ma J., Ovchinnikov V., Paci E., Pastor R. W., Post C. B., Pu J. Z., Schaefer M., Tidor B., Venable R. M., Woodcock H. L., Wu X., Yang W., York D. M., Karplus M., CHARMM: The biomolecular simulation program, 10.1002/jcc.21287
Bibliographic reference | Amor, B.R.C. ; Schaub, Michael ; Yaliraki, S.N. ; Barahona, M.. Prediction of allosteric sites and mediating interactions through bond-to-bond propensities. In: Nature Communications, Vol. 7, p. 12477 (August 2016) |
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Permanent URL | http://hdl.handle.net/2078.1/178305 |