User menu

Prediction of allosteric sites and mediating interactions through bond-to-bond propensities

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)
Permanent URL
  1. Monod Jacques, Changeux Jean-Pierre, Jacob François, Allosteric proteins and cellular control systems, 10.1016/s0022-2836(63)80091-1
  2. Perutz M. F., Mechanisms of cooperativity and allosteric regulation in proteins, 10.1017/s0033583500003826
  3. Nussinov Ruth, Tsai Chung-Jung, Allostery in Disease and in Drug Discovery, 10.1016/j.cell.2013.03.034
  4. Frauenfelder H, Sligar S., Wolynes P., The energy landscapes and motions of proteins, 10.1126/science.1749933
  5. Henzler-Wildman Katherine, Kern Dorothee, Dynamic personalities of proteins, 10.1038/nature06522
  6. Volkman B. F., Sci. Signal., 291, 2429 (2001)
  7. Gunasekaran K., Ma Buyong, Nussinov Ruth, Is allostery an intrinsic property of all dynamic proteins?, 10.1002/prot.20232
  8. Hardy Jeanne A, Wells James A, Searching for new allosteric sites in enzymes, 10.1016/
  9. Lockless S. W., Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families, 10.1126/science.286.5438.295
  10. 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
  11. Ota Nobuyuki, Agard David A., Intramolecular Signaling Pathways Revealed by Modeling Anisotropic Thermal Diffusion, 10.1016/j.jmb.2005.05.043
  12. Demerdash Omar N. A., Daily Michael D., Mitchell Julie C., Structure-Based Predictive Models for Allosteric Hot Spots, 10.1371/journal.pcbi.1000531
  13. Panjkovich Alejandro, Daura Xavier, Exploiting protein flexibility to predict the location of allosteric sites, 10.1186/1471-2105-13-273
  14. Collier Galen, Ortiz Vanessa, Emerging computational approaches for the study of protein allostery, 10.1016/
  15. Monod Jacque, Wyman Jeffries, Changeux Jean-Pierre, On the nature of allosteric transitions: A plausible model, 10.1016/s0022-2836(65)80285-6
  16. Koshland D. E., Némethy G., Filmer D., Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits*, 10.1021/bi00865a047
  17. Hilser Vincent J., Wrabl James O., Motlagh Hesam N., Structural and Energetic Basis of Allostery, 10.1146/annurev-biophys-050511-102319
  18. 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
  19. Zhuravlev Pavel I., Papoian Garegin A., Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework, 10.1017/s0033583510000119
  20. Müller-Werkmeister Henrike M., Bredenbeck Jens, A donor–acceptor pair for the real time study of vibrational energy transfer in proteins, 10.1039/c3cp54760d
  21. Li G., Nat. Commun., 5, 3100 (2014)
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. Nakayama Tsuneyoshi, Yakubo Kousuke, Orbach Raymond L., Dynamical properties of fractal networks: Scaling, numerical simulations, and physical realizations, 10.1103/revmodphys.66.381
  29. Leitner David M., Energy Flow in Proteins, 10.1146/annurev.physchem.59.032607.093606
  30. 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
  31. 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
  32. Chennubhotla Chakra, Bahar Ivet, Signal Propagation in Proteins and Relation to Equilibrium Fluctuations, 10.1371/journal.pcbi.0030172
  33. 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
  34. 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
  35. Sethi A., Eargle J., Black A. A., Luthey-Schulten Z., Dynamical networks in tRNA:protein complexes, 10.1073/pnas.0810961106
  36. Ribeiro Andre A. S. T., Ortiz Vanessa, Determination of Signaling Pathways in Proteins through Network Theory: Importance of the Topology, 10.1021/ct400977r
  37. Ribeiro Andre A. S. T., Ortiz Vanessa, Energy Propagation and Network Energetic Coupling in Proteins, 10.1021/jp509906m
  38. 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
  39. 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
  40. 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
  41. Yu Keming, Lu Zudi, Stander Julian, Quantile regression: applications and current research areas, 10.1111/1467-9884.00363
  42. Datta Debajyoti, Scheer Justin M., Romanowski Michael J., Wells James A., An Allosteric Circuit in Caspase-1, 10.1016/j.jmb.2008.06.040
  43. Cook R. Dennis, Influential Observations in Linear Regression, 10.1080/01621459.1979.10481634
  44. 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
  45. 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
  46. 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
  47. Bourret R. B., J. Biol. Chem., 268, 13089 (1993)
  48. 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
  49. 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
  50. McCormick Frank, Ras-related proteins in signal transduction and growth control, 10.1002/mrd.1080420419
  51. Buhrman G., Holzapfel G., Fetics S., Mattos C., Allosteric modulation of Ras positions Q61 for a direct role in catalysis, 10.1073/pnas.0912226107
  52. Murzin A. G., J. Mol. Biol., 247, 536 (1995)
  53. Daily Michael D., Gray Jeffrey J., Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins, 10.1371/journal.pcbi.1000293
  54. 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
  55. 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
  56. 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
  57. Chung Fan, Yau S.-T., Discrete Green's Functions, 10.1006/jcta.2000.3094
  58. Reuveni S., Granek R., Klafter J., Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure, 10.1073/pnas.1002018107
  59. Mayo Stephen L., Olafson Barry D., Goddard William A., DREIDING: a generic force field for molecular simulations, 10.1021/j100389a010
  60. 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
  61. 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
  62. 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