ASD v3.0: Unraveling Allosteric regulation with structural mechanisms and biological networks

Nucleic Acids Research

Volumn 44, Issue D1, 2016, Pages D527-D535

  Shen, Qiancheng ^a   Wang, Guanqiao ^a   Li, Shuai ^a   Liu, Xinyi ^a   Lu, Shaoyong ^a   Chen, Zhongjie ^a   Song, Kun ^a   Yan, Junhao ^b   Geng, Lv ^a   Huang, Zhimin ^a   Huang, Wenkang ^a   Chen, Guoqiang ^a   Zhang, Jian ^a  

^a SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE   (China)

^b SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE   (China)

Author keywords

[No Author keywords available]

Indexed keywords

G PROTEIN COUPLED RECEPTOR; PROTEIN KINASE; PROTEIN;

ACCESS TO INFORMATION; ALLOSTERIC DATABASE; ALLOSTERISM; ARTICLE; CALCIUM SIGNALING; COMPUTER INTERFACE; CONFORMATIONAL TRANSITION; DATA BASE; DATA MINING; INTERNET; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; CHEMISTRY; DRUG DEVELOPMENT; HUMAN; METABOLISM; PROTEIN DATABASE; SIGNAL TRANSDUCTION;

ALLOSTERIC REGULATION; DATABASES, PROTEIN; DRUG DISCOVERY; HUMANS; INTERNET; PROTEIN KINASES; PROTEINS; RECEPTORS, G-PROTEIN-COUPLED; SIGNAL TRANSDUCTION;

EID: 84976873372     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv902     Document Type: Article

References (68)

1. Goodey, N. M. and Benkovic, S. J. (2008) Allosteric regulation and catalysis emerge via a common route. Nat. Chem. Biol., 4, 474-482.
2. Changeux, J.-P. and Edelstein, S. J. (2005) Allosteric mechanism of signal transduction. Science, 308, 1424-1428.
3. Changeux, J.-P. (2010) Allosteric receptors: from electric orange to cognition. Annu. Rev. Pharmacol. Toxicol., 50, 1-38.
4. Fenton, A. W. (2008) Allostery: an illustrated definition for the 'second secret of life'. Trends Biochem. Sci., 33, 420-425.
5. Motlagh, H. N., Wrabl, J. O., Li, J. and Hilser, V. J. (2014) The ensemble nature of allostery. Nature, 508, 331-339.
6. Lu, S., Huang, W. and Zhang, J. (2014) Recent computational advances in the identification of allosteric sites in proteins. Drug Discov. Today, 19, 1595-1600.
7. Nussinov, R. and Tsai, C.-J. (2013) Allostery in disease and in drug discovery. Cell, 153, 293-305.
8. Lu, S., Li, S. and Zhang, J. (2014) Harnessing allostery: a novel approach to drug discovery. Med. Res. Rev., 34, 1242-1285.
9. Raman, S., Taylor, N., Genuth, N., Fields, S. and Church, G. N. (2014) Engineering allostery. Trends Genet., 30, 521-528.
10. De Smet, F., Christopoulos, A. and Carmeliet, P. (2014) Allosteric targeting of receptor tyrosine kinases. Nat. Biotechnol., 32, 1113-1120.
11. Peracchi, A. and Mozzarelli, A. (2011) Exploring and exploiting allostery: models, evolution, and drug targeting. Biochem. Biophys. Acta, 1814, 922-933.
12. Gunasekaran, K., Ma, B. and Nussinov, R. (2004) Is allostery an intrinsic property of all dynamic proteins? Proteins, 57, 433-443.
13. Tsai, C.-J. and Nussinov, R. (2014) A unified view of "how allostery works". PLoS Comput. Biol., 10, e1003394.
14. Kaya, C., Armutlulu, A., Ekesan, S. and Haliloglu, T. (2013) MCPath: monte carlo path generation approach to predict likely allosteric pathways and functional residues. Nucleic Acids Res., 41, W249-W255.
15. Goncearenco, A., Mitternacht, S., Yong, T., Eisenhaber, B., Eisenhaber, F. and Berezovsky, I. N. (2013) SPACER: server for predicting allosteric communication and effects of regulation. Nucleic Acids Res., 41, W266-W272.
16. Das, A., Gur, M., Cheng, M. H., Jo, S., Bahar, I. and Roux, B. (2014) Exploring the conformational transition of biological systems using a simple two-state anisotropic network model. PLoS Comput. Biol., 10, e1003521.
17. General, I. J., Liu, Y., Balckburn, M., Mao, W., Gierasch, L. and Bahar, I. (2014) ATPase subdomain IA is a mediator of interdomain allostery in Hsp70 molecular chaperones. PLoS Comput. Biol., 10, e1003624.
18. Link, H., Kochanowski, K. and Sauer, U. (2013) Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo. Nat. Biotechnol., 4, 357-361.
19. Nussinov, R. (2013) The spatial structure of cell signaling systems. Phys. Biol., 10, 045004.
20. Nussinov, R., Tsai, C.-J. and Ma, B. (2013) The underappreciated role of allostery in the cellular network. Annu. Rev. Biophys., 42, 169-189.
21. Nussinov, R., Tsai, C.-J. and Liu, J. (2014) Principles of allosteric interactions in cell signaling. J. Am. Chem. Soc., 136, 17692-17701.
22. Hubbard, P. A., Moody, C. L. and Murali, R. (2014) Allosteric modulation of Ras and the PI3K/AKT/mTOR pathway: emerging therapeutic opportunities. Front. Physiol., 5, 478.
23. Nussinov, R. and Tsai, C.-J. (2014) Unraveling structural mechanisms of allosteric drug action. Trends Pharmacol. Sci., 35, 256-264.
24. Cowan-Jacob, S. W., Jahnke, W. and Knapp, S. (2014) Novel approaches for targeting kinases: allosteric inhibition, allosteric activation and pseudokinases. Future Med. Chem., 6, 541-561.
25. Foda, Z. H. and Seeliger, M. A. (2014) An allosteric add-on. Nat. Chem. Biol., 10, 796-797.
26. Langmead, C. J. and Christopoulos, A. (2014) Functional and structural perspectives on allosteric modulation of GPCRs. Curr. Opin. Cell Biol., 27, 94-101.
27. Christopoulos, A. (2014) Advances in G protein-coupled receptor allostery: from function to structure. Mol. Pharmacol., 86, 463-487.
28. Kruse, A. C., Ring, A. M., Manglik, A., Hu, J., Hu, K., Eitel, K., Hübner, H., Pardon, E., Valant, C., Sexton, P. M. et al. (2013) Activation and allosteric modulation of a muscarinic acetylcholine receptor. Nature, 504, 101-106.
29. Tan, Q., Zhu, Y., Li, J., Chen, Z., Han, G. W., Kufareva, I., Li, T., Ma, L., Fenalti, G., Li, J. et al. (2013) Structure of the CCR5 chemokine receptor|HIV entry inhibitor maraviroc complex. Science, 341, 1387-1390.
30. Hollenstein, K., Kean, J., Bortolato, A., Cheng, R. K. Y., Doré, A. S., Jazayeri, A., Cooke, R. M., Weir, M. and Marshall, F. H. (2013) Structure of class B GPCR corticotrophin-releasing factor receptor 1. Nature, 499, 438-443.
31. Wu, H., Wang, C., Gregory, K. J., Han, G. W., Cho, H. P., Xia, Y., Niswender, C. M., Katritch, V., Meiler, J., Cherezov, V. et al. (2014) Structure of a class C GPCR metabotropic glutamate receptor 1 bound to an allosteric modulator. Science, 344, 58-64.
32. Srivastava, A., Yano, J., Hirozane, Y., Kefala, G., Gruswitz, F., Snell, G., Lane, W., Ivetac, A., Aertgeerts, K., Nguyen, J. et al. (2014) High-resolution structure of the human GPR40 receptor bound to allosteric agonist TAK-875. Nature, 513, 124-127.
33. Lee, C.-H., Lü, W., Michel, J. C., Goehring, A., Du, J., Song, X. and Gouaux, E. (2014) NMDA receptor structures reveal subunit arrangement and pore architecture. Nature, 511, 191-197.
34. Zhang, D., Gao, Z.-G., Zhang, K., Kiselev, E., Crane, S., Wang, J., Paoletta, S., Yi, C., Ma, L., Zhang, W. et al. (2015) Two disparate ligand-binding sites in the human P2Y1 receptor. Nature, 520, 317-321.
35. Ostrem, J. M., Peters, U., Sos, M. L., Wells, J. A. and Shokat, K. M. (2013) K-Ras (G12C) inhibitors allosterically control GTP affinity and effector interactions. Nature, 503, 548-551.
36. Feldman, T., Kabaleeswaran, V., Jang, S. B., Antczak, C., Djaballah, H., Wu, H. and Jiang, X. (2012) A class of allosteric caspase inhibitors identified by high-throughput screening. Mol. Cell, 47, 585-595.
37. Jahnke, W., Rondeau, J.-M., Cotesta, S., Marzinzik, A., Pellé, X., Geiser, M., Strauss, A., Götte, M., Bitsch, F., Hemmig, R. et al. (2010) Allosteric non-bisphosphonate FPPS inhibitors identified by ferment-based discovery. Nat. Chem. Biol., 6, 660-666.
38. Taly, A., Corringer, P. J., Guedin, D., Lestage, P. and Changeux, J. P. (2009) Nicotinic receptors: allosteric transitions and therapeutic targets in the nervous system. Nat. Rev. Drug Discov., 8, 733-750.
39. Müller, C. E., Schiedel, A. C. and Baqi, Y. (2012) Allosteric modulators of rhodopsin-like G protein-coupled receptors: opportunities in drug development. Pharmacol. Ther., 135, 292-315.
40. Wootten, D., Christopoulos, A. and Sexton, P. M. (2013) Emerging paradigms in GPCR allostery: implications for drug discovery. Nat. Rev. Drug. Discov., 12, 630-644.
41. Matschinsky, F. M. (2009) Assessing the potential of glucokinase activator in diabetes therapy. Nat. Rev. Drug Discov., 8, 399-416.
42. Shonberg, J., Lopez, L., Scammells, P. J., Christopoulos, A., Capuano, B. and Lane, J. R. (2014) Biased agonism at G protein-coupled receptors: the promise and the challenges|a medicinal chemistry perspective. Med. Res. Rev., 34, 1286-1330.
43. Fang, Z., Grütter, C. and Rauh, D. (2013) Strategies for the selective regulation of kinases with allosteric modulators: exploiting exclusive structural features. ACS Chem. Biol., 8, 58-70.
44. Huang, Z., Zhu, L., Cao, Y., Wu, G., Liu, X., Chen, Y., Wang, Q., Shi, T., Zhao, Y., Wang, Y. et al. (2011) ASD: a comprehensive database of allosteric proteins and modulators. Nucleic Acids Res., 39, D663-D669.
45. Huang, Z., Mou, L., Shen, Q., Lu, S., Li, C., Liu, X., Wang, G., Li, S., Geng, L., Liu, Y. et al. (2014) ASD v2.0: updated context and novel features focusing on allosteric regulation. Nucleic Acids Res., 42, D510-D516.
46. Rydberg, E. H., Li, C., Maurus, R., Overall, C. M., Brayer, G. D. and Withers, S. G. (2002) Mechanistic analyses of catalysis in human pancreatic alpha-amylase: detailed kinetic and structural studies of mutants of three conserved carboxylic acids. Biochemistry, 41, 4492-4502.
47. Johnson, L. N. (1992) Glycogen phosphorylase: control by phosphorylation and allosteric effectors. FASEB J., 6, 2274-2282.
48. Tsitsanou, K. E., Skamnaki, V. T. and Oikonomakos, N. G. (2000) Structural basis of the synergistic inhibition of glycogen phosphorylase a by caffeine and a potential antidiabetic drug. Arch. Biochem. Biophys., 384, 245-254.
49. Huang, W., Wang, G., Shen, Q., Liu, X., Lu, S., Geng, L., Huang, Z. and Zhang, J. (2015) ASBench: benchmarking sets for allosteric discovery. Bioinformatics, 31, 2598-2600.
50. Huang, W., Lu, S., Huang, Z., Liu, X., Mou, L., Luo, Y., Zhao, Y., Liu, Y., Chen, Z., Hou, T. and Zhang, J. (2013) Allosite: a method for predicting allosteric sites. Bioinformatics, 29, 2357-2359.
51. Daily, M. D. and Gray, J. J. (2007) Local motions in a benchmark of allosteric proteins. Proteins, 67, 385-399.
52. Chang, D. T., Yao, T. J., Fan, C. Y., Chiang, C. Y. and Bai, Y. H. (2012) AH-DB: collecting protein structure pairs before and after binding. Nucleic Acids Res., 40, D472-D478.
53. Lu, S., Huang, W., Wang, Q., Shen, Q., Li, S., Nussinov, R. and Zhang, J. (2014) The structural basis of ATP as an allosteric modulator. PLoS Comput. Biol., 10, e1003831.
54. George, A. and Bell, J. E. (1980) Effects of adenosine 5'-diphosphate on bovine glutamate dehydrogenase: diethyl pyrocarbonate modification. Biochemistry, 19, 6057-6061.
55. Li, C., Li, M., Chen, P., Narayan, S., Matschinsky, F. M., Bennett, M. J., Stanley, C. A. and Smith, T. J. (2011) Green tea polyphenols control dysregulated glutamate dehydrogenase in transgenic mice by hijacking the ADP activation site. J. Biol. Chem., 286, 34164-34174.
56. Nussinov, R., Ma, B., Tsai, C. J. and Csermely, P. (2014) Allosteric conformational barcodes direct signaling in the cell. Structure, 21, 1509-1521.
57. Korcsmáros, T., Farkas, I. J., Szalay, M. S., Rovó, P., Fazekas, D., Spiró, Z., Böde, C., Lenti, K., Vellai, T. and Csermely, P. (2010) Uniformly curated signaling pathways reveal tissue-specific cross-talks and support drug target discovery. Bioinformatics, 26, 2042-2050.
58. Nussinov, R., Ma, B. and Tsai, C. J. (2013) A broad view of scaffolding suggests that scaffolding proteins can actively control regulation and signaling of multienzyme complexes through allostery. Biochim. Biophys. Acta, 1834, 820-829.
59. Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. and Tanabe, M. (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res., 40, D109-D114.
60. Kanehisa, M., Goto, S., Sato, Y., Kawashima, M., Furumichi, M. and Tanabe, M. (2014) Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res., 42, D199-D205.
61. Nadeau, O. W., Anderson, D. W., Yang, Q., Artigues, A., Paschall, J. E., Wyckoff, G. J., McClintock, J. L. and Carlson, G. M. (2007) Evidence for the location of the allosteric activation switch in the multisubunit phosphorylase kinase complex from mass spectrometric identification of chemically crosslinked peptides. J. Mol. Biol., 365, 1429-1445.
62. MacEwan, D. J., Mitchell, R., Johnson, M. S., Thomson, F. J., Lutz, E. M., Clegg, R. A. and Connor, K. (1993) Evidence that protein kinase C alpha has reduced affinity towards 1, 2-dioctanoyl-sn-glycerol: the effects of lipid activators on phorbol ester binding and kinase activity. Eur. J. Pharmacol., 246, 9-18.
63. Hedlund, P. B., Carson, M. J., Sutcliffe, J. G. and Thomas, E. A. (1999) Allosteric regulation by oleamide of the binding properties of 5-hydroxytryptamine7 receptors. Biochem. Pharmacol., 58, 1807-1813.
64. Jones, G. A. and Carpenter, G. (1993) The regulation of phospholipase C-gamma 1 by phosphatidic acid. Assessment of kinetic parameters. J. Biol. Chem., 268, 20845-20850.
65. Wu, Y., Perisic, O., Williams, R. L., Katan, M. and Roberts, M. F. (1997) Phosphoinositide-specific phospholipase C delta1 activity toward micellar substrates, inositol 1, 2-cyclic phosphate, and other water-soluble substrates: a sequential mechanism and allosteric activation. Biochemistry, 36, 11223-11233.
66. Conn, P. J., Christopoulos, A. and Lindsley, C. W. (2009) Allosteric modulators of GPCRs: a novel approach for the treatment of CNS disorders. Nat. Rev. Drug Discov., 8, 41-54.
67. Lewis, J. A., Lebois, E. P. and Lindsley, C. W. (2008) Allosteric modulation of kinases and GPCRs: design principles and structural diversity. Curr. Opin. Chem. Biol., 12, 269-280.
68. UniProt Consortium. (2015) UniProt: a hub for protein information. Nucleic Acids Res., 43, D204-D212.