ASD v2.0: Updated content and novel features focusing on allosteric regulation

Nucleic Acids Research

Volumn 42, Issue D1, 2014, Pages

  Huang, Zhimin ^a   Mou, Linkai ^b   Shen, Qiancheng ^a   Lu, Shaoyong ^a   Li, Chuangang ^b   Liu, Xinyi ^a   Wang, Guanqiao ^a   Li, Shuai ^a   Geng, Lv ^a   Liu, Yaqin ^a   Wu, Jiawei ^a   Chen, Guoqiang ^a   Zhang, Jian ^a  

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

^b DALIAN MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALLOSTERIC PROTEIN; PROTEIN; UNCLASSIFIED DRUG; CELL NUCLEUS RECEPTOR; ION CHANNEL; PEPTIDASE; PHOSPHATASE; PHOSPHOTRANSFERASE; TRANSCRIPTION FACTOR;

ALLOSTERIC DATABASE V2.0; ALLOSTERISM; ARTICLE; BINDING SITE; BIOENGINEERING; COMPUTER INTERFACE; CONFORMATIONAL TRANSITION; MOLECULAR MECHANICS; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN DATABASE; X RAY CRYSTALLOGRAPHY; ALLOSTERIC DATABASE; CRYSTAL STRUCTURE; DRUG DEVELOPMENT; HUMAN; NONHUMAN; PROTEIN INTERACTION; PROTEIN STRUCTURE; REGULATORY MECHANISM; SEARCH ENGINE; SIGNAL TRANSDUCTION; WEB BROWSER; CHEMISTRY; INTERNET; METABOLISM;

ALLOSTERIC REGULATION; ALLOSTERIC SITE; DATABASES, PROTEIN; DRUG DISCOVERY; INTERNET; PROTEINS;

EID: 84891778690     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1247     Document Type: Article

References (55)

1. Eisenberg, D., Marcotte, E.M., Xenarios, I. and Yeates, T.O. (2000) Protein function in the post-genomic era. Nature, 405, 823-826.
2. Csermely, P., Palotai, R. and Nussinov, R. (2010) Induced fit, conformational selection and independent dynamics segments: an extended view of binding events. Trends Biochem. Sci., 35, 539-546.
3. Cui, Q. and Karplus, M. (2008) Allostery and cooperativity revisited. Protein Sci., 17, 1295-1307.
4. Pan, Y.P., Tsai, C.J., Ma, B.Y. and Nussinov, R. (2010) Mechanism of transcription factor selectivity. Trends Genet., 26, 75-83.
5. Sinha, N. and Nussinov, R. (2001) Point mutations and sequence variability in proteins: redistributions of preexisting populations. Proc. Natl Acad. Sci. USA, 98, 3130-3144.
6. Goodey, N.M. and Benkovic, S.J. (2008) Allosteric regulation and catalysis emerge via a common route. Nat. Chem. Biol., 4, 474-482.
7. Nussinov, R., Tsai, C.J., Xin, F. and Radivojac, P. (2012) Allosteric post-translational modification codes. Trends Biochem. Sci., 37, 447-455.
8. 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.
9. Munro, G., Ahring, P.K. and Mirza, N.R. (2009) Developing analgesics by enhancing spinal inhibition after injury: GABAA receptor subtypes as novel targets. Trends Pharmacol. Sci., 30, 453-459.
10. Matschinsky, F.M. (2009) Assessing the potential of glucokinase activator in diabetes therapy. Nat. Rev. Drug Discov., 8, 399-416.
11. Kar, G., Keskin, O., Gursoy, A. and Nussinov, R. (2010) Allostery and population shift in drug discovery. Curr. Opin. Pharmacol., 10, 715-722.
12. Fang, Z., Grutter, 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.
13. Nussinov, R. and Tsai, C.J. (2013) Allostery in disease and in drug discovery. Cell, 153, 293-305.
14. Nussinov, R. and Tsai, C.J. (2012) The different ways through which specificity works in orthosteric and allosteric drugs. Curr. Pharm. Des., 18, 1311-1316.
15. Palmieri, L. and Rastelli, G. (2013) aC helix displacement as a general approach for allosteric modulation of protein kinases. Drug Discov. Today, 18, 407-414.
16. 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.
17. Hardy, J.A. and Wells, J.A. (2004) Searching for new allosteric sites in enzymes. Curr. Opin. Struct. Biol., 14, 706-715.
18. Tzeng, S.R. and Kalodimos, C.G. (2011) Protein dynamics and allostery: an NMR view. Curr. Opin. Struct. Biol., 21, 62-27.
19. Prasannan, C.B., Villar, M.T., Artigues, A. and Fenton, A.W. (2013) Identification of regions of rabbit muscle pyruvate kinase important for allosteric regulation by phenylalanine, detected by H/D exchange mass spectrometry. Biochemistry, 52, 1998-2006.
20. Wu, S., Vysotskaya, Z.V., Xu, X., Xie, C., Liu, Q. and Zhou, L. (2011) State-dependent cAMP binding to functioning HCN channels studied by patch-clamp fluorometry. Biophys. J., 100, 1226-1232.
21. Wang, X., Horswill, J.G., Whalley, B.J. and Stephens, G.J. (2011) Effects of the allosteric antagonist 1-(4-Chlorophenyl)-3-[3-(6-pyrrolidin-1-ylpyridin- 2-yl)phenyl]urea (PSNCBAM-1) on CB1 receptor modulation in the cerebellum. Mol. Pharmacol., 79, 758-767.
22. Monod, J., Wyman, J. and Changeux, J.P. (1965) On the nature of allosteric transitions: a plausible model. J. Mol. Biol., 12, 88-118.
23. Koshland, D.E., Nemethy, G. and Filmer, D. (1966) Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry, 5, 365-385.
24. Jaffe, E.K. (2005) Morpheeins-A new structural paradigm for allosteric regulation. Trends Biochem. Sci., 30, 490-497.
25. Selwood, T. and Jaffe, E.K. (2012) Dynamic dissociating homo-oligomers and the control of protein function. Arch. Biochem. Biophys., 519, 131-143.
26. Semenova, G. and Chernoff, J. (2012) PKM2 enters the morpheein academy. Mol. Cell, 45, 583-584.
27. del Sol, A., Tsai, C.J., Ma, B. and Nussinov, R. (2009) The origin of allosteric functional modulation: multiple pre-existing pathways. Structure, 17, 1042-1050.
28. Zhu, F., Shi, Z., Qin, C., Tao, L., Liu, X., Xu, F., Zhang, L., Song, Y., Liu, X., Zhang, J. et al. (2012) Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery. Nucleic Acids Res., 40, D1128-D1136.
29. Knox, C., Law, V., Jewison, T., Liu, P., Ly, S., Frolkis, A., Pon, A., Banco, K., Mak, C., Neveu, V. et al. (2011) DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res., 39, D1035-D1041.
30. Jaffe, E.K. (2013) Impact of quaternary structure dynamics on allosteric drug discovery. Curr. Top. Med. Chem., 13, 55-63.
31. van der Klein, P.A.M., Kourounakis, A.P. and IJzerman, A.P. (1999) Allosteric modulation of the adenosine A1 receptor: synthesis and biological evaluation of novel 2-amino-3-benzoylthiophenes as allosteric enhancers of agonist binding. J. Med. Chem., 42, 3629-3635.
32. Wombacher, H. (1982) Theophylline effect on the cyclic AMP degrading multienzyme sequence. Biochem. Pharmacol., 31, 3441-3446.
33. Wallden, K., Stenmark, P., Nyman, T., Flodin, S., Graslund, S., Loppnau, P., Bianchi, V. and Nordlund, P. (2007) Crystal structure of human cytosolic 5'-Nucleotidase II: insights into allosteric regulation and substrate recognition. J. Biol. Chem., 282, 17828-17836.
34. Lukacs, C.M., Oikonomakos, N.G., Crowther, R.L., Hong, L.N., Kammlott, R.U., Lein, W., Li, S., Liu, C.M., Lucas-McGady, D., Pietranico, S. et al. (2006) The crystal structure of human muscle glycogen phosphorylase a with bound glucose and AMP: an intermediate conformation with T-state and R-state feature. Proteins, 63, 1123-1126.
35. Stevens, R.C., Gouaux, J.E. and Lipscomb, W.N. (1990) Structural consequences of effector binding to the T state of aspartate carbamoyltransferase; crystal structures of the unligated and ATP-and CTP-complexed enzymes at 2.6 A resolution. Biochemistry, 29, 7691-7701.
36. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242.
37. Zhang, Y. (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 36, 40.
38. Panjkovich, A. and Daura, X. (2012) Exploiting protein flexibility to predict the location of allosteric sites. BMC Bioinformatics, 13, 273.
39. DeLano, W.L. (2002) The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA.
40. Kufareva, I., Ilatovskiy, A.V. and Abagyan, R. (2012) Pocketome: an encyclopedia of small-molecule binding sites in 4D. Nucleic Acids Res., 40, D535-D540.
41. Porter, C.T., Bartlett, G.J. and Thornton, J.M. (2004) The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res., 32, D129-D133.
42. Yang, J., Roy, A. and Zhang, Y. (2013) BioLIP: a semi-manually curated database for biologically relevant ligand-protein interactions. Nucleic Acids Res., 41, D1096-D1103.
43. Schmidtke, P., Le Guilloux, V., Maupetit, J. and Tuffery, P. (2010) fpocket: online tools for protein ensemble pocket detection and tracking. Nucleic Acids Res., 38, W582-W589.
44. 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.
45. Laine, E., Auclair, C. and Tchertanov, L. (2012) Allosteric communication across the native and mutated KIT receptor tyrosine kinase. PLoS Comput. Biol., 8, e1002661.
46. Chennubhotla, C. and Bahar, I. (2006) Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES. Mol. Syst. Biol., 2, 36.
47. Vijayabaskar, M.S. and Vishveshwara, S. (2010) Interaction energy based protein structure networks. Biophys. J., 99, 3704-3715.
48. Cilia, E., Vuister, G.W. and Lenaerts, T. (2012) Accurate prediction of the dynamical changes within the second PDZ domain of PTP1e. PLoS Comput. Biol., 8, e1002794.
49. Wang, Q., Zheng, M., Huang, Z., Liu, X., Zhou, H., Chen, Y., Shi, T. and Zhang, J. (2012) Toward understanding the molecular basis for chemical allosteric modulator design. J. Mol. Graph. Model., 39, 324-333.
50. Huang, W., Lu, S., Huang, Z., Liu, X., Mou, L., Luo, Y., Zhao, Y., Liu, Y., Chen, Z., Hou, T. et al. (2013) Allosite: a method for predicting allosteric sites. Bioinformatics, 29, 2357-2359.
51. Li, X., Chen, Y., Lu, S., Huang, Z., Liu, X., Wang, Q., Shi, T. and Zhang, J. (2013) Toward an understanding of the sequence and structural basis of allosteric proteins. J. Mol. Graph. Model., 40, 30-49.
52. Namboodiri, S., Giuliani, A., Nair, A.S. and Dhar, P.K. (2012) Looking for a sequence based allostery definition: a statistical journey at different resolution scales. J. Theor. Biol., 304, 211-218.
53. Yang, J.S., Seo, S.W., Jang, S., Jung, G.Y. and Kim, S. (2012) Rational engineering of enzyme allosteric regulation through sequence evolution analysis. PLoS Comput. Biol., 8, e1002612.
54. Nussinov, R., Tsai, C.J. and Csermely, P. (2011) Allo-network drugs: harnessing allostery in cellular networks. Trends Pharmacol. Sci., 32, 686-693.
55. Nussinov, R., Tsai, C.J. and Ma, B. (2013) The underappreciated role of allostery in the cellular network. Annu. Rev. Biophys., 42, 169-189.