Relative motions between left flipper and dorsal fin domains favour P2X4 receptor activation

Nature Communications

Volumn 5, Issue , 2014, Pages

  Zhao, Wen Shan ^a,b   Wang, Jin ^a   Ma, Xiao Juan ^a,b   Yang, Yang ^a   Liu, Yan ^a   Huang, Li Dong ^a   Fan, Ying Zhe ^d   Cheng, Xiao Yang ^a   Chen, Hong Zhuan ^a   Wang, Rui ^b   Yu, Ye ^a,c  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b LANZHOU UNIVERSITY   (China)

^c HUNAN AGRICULTURAL UNIVERSITY   (China)

^d SHANGHAI UNIVERSITY OF TRADITIONAL CHINESE MEDICINE   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; PURINERGIC P2X4 RECEPTOR; ZINC;

CHEMICAL BINDING; HYDROPHOBICITY; PHYSIOLOGICAL RESPONSE;

ALLOSTERISM; ARTICLE; BINDING SITE; CHANNEL GATING; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CROSS LINKING; CRYSTAL STRUCTURE; DISULFIDE BOND; DORSAL FIN; ELECTROPHYSIOLOGICAL PROCEDURES; HYDROPHOBICITY; LEFT FLIPPER; MOLECULAR WEIGHT; MOTION; MUTAGENESIS; MUTATION; NONHUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRINCIPAL COMPONENT ANALYSIS; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FUNCTION; WESTERN BLOTTING; ANIMAL; CHEMICAL PHENOMENA; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; METABOLISM; PROTEIN MOTIF; PROTEIN TERTIARY STRUCTURE; RAT;

ADENOSINE TRIPHOSPHATE; ALLOSTERIC REGULATION; AMINO ACID MOTIFS; ANIMALS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MODELS, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; RATS; RECEPTORS, PURINERGIC P2X4;

EID: 84903145837     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms5189     Document Type: Article

References (33)

1. Surprenant, A. & North, R. A. Signaling at purinergic P2X receptors. Annu. Rev. Physiol. 71, 333-359 (2009).
2. Browne, L. E., Jiang, L. H. & North, R. A. New structure enlivens interest in P2X receptors. Trends Pharmacol. Sci. 31, 229-237 (2010).
3. Coddou, C., Yan, Z., Obsil, T., Huidobro-Toro, J. P. & Stojilkovic, S. S. Activation and Regulation of Purinergic P2X Receptor Channels. Pharmacol. Rev. 63, 641-683 (2011).
4. Kawate, T., Michel, J. C., Birdsong, W. T. & Gouaux, E. Crystal structure of the ATP-gated P2X(4) ion channel in the closed state. Nature 460, 592-598 (2009).
5. Hattori, M. & Gouaux, E. Molecular mechanism of ATP binding and ion channel activation in P2X receptors. Nature 485, 207-212 (2012).
6. Shinozaki, Y. et al. Direct observation of ATP-Induced conformational changes in single P2X4 Receptors. PLoS Biol. 7, e103 (2009).
7. Du, J., Dong, H. & Zhou, H. X. Gating mechanism of a P2X4 receptor developed from normal mode analysis andmolecular dynamics simulations. Proc. Natl Acad. Sci. USA 109, 4140-4145 (2012).
8. Jiang, R. et al. Tightening of the ATP-binding sites induces the opening of P2X receptor channels. EMBO J. 31, 2134-2143 (2012).
9. Lorinczi, E. et al. Involvement of the cysteine-rich head domain in activation and desensitization of the P2X1 receptor. Proc. Natl Acad. Sci. USA 109, 11396-11401 (2012).
10. Roberts, J. A. et al. Agonist binding evokes extensive conformational changes in the extracellulardomain of the ATP-gated human P2X1 receptor ion channel. Proc. Natl Acad. Sci. USA 109, 4663-4667 (2012).
11. Li, M., Kawate, T., Silberberg, S. D. & Swartz, K. J. Pore-opening mechanism in trimeric P2X receptor channels. Nat. Commun. 1, 1-7 (2010).
12. Heymann, G. et al. Inter-and intrasubunit interactions between transmembrane helices in the open state of P2X receptor channels. Proc. Natl Acad. Sci. USA 110, E4045-E4054 (2013).
13. Baconguis, I., Hattori, M. & Gouaux, E. Unanticipated parallels in architecture and mechanism between ATP-gated P2X receptors and acid sensing ion channels. Curr. Opin. Struct. Biol. 23, 277-284 (2013).
14. Yu, Y. et al. Atomic-level characterization of the nonproton ligand sensing domain of ASIC3 channels. J. Biol. Chem. 286, 24996-25006 (2011).
15. Careaga, C. L. & Falke, J. J. Thermal motions of surface alpha-helices in the D-galactose chemosensory receptor. Detection by disulfide trapping. J. Mol. Biol. 226, 1219-1235 (1992).
16. Jiang, L. H. et al. Subunit arrangement in P2X receptors. J. Neurosci. 23, 8903-8910 (2003).
17. Van Wart, H. E. SHA. Raman spectra of strained disulfides Effect of rotation about sulfur-sulfur bonds on sulfur-sulfur stretching frequencies. J. Phys. Chem. 80, 1823-1832 (1976).
18. Alberts, I. L., Nadassy, K. & Wodak, S. J. Analysis of zinc binding sites in protein crystal structures. Protein Sci. 7, 1700-1716 (1998). (Pubitemid 29133175)
19. Laio, A. & Gervasio, F. L. Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science. Rep. Prog. Phys. 71, 126601 (2008).
20. Jiang, L. H., Rassendren, F., Surprenant, A. & North, R. A. Identification of amino acid residues contributing to the ATP-binding site of a purinergic P2X receptor. J. Biol. Chem. 275, 34190-34196 (2000).
21. Jiang, R., Taly, A. & Grutter, T. Moving through the gate in ATP-activated P2X receptors. Trends Biochem. Sci. 38, 20-29 (2012).
22. Yu, Y. et al. A nonproton ligand sensor in the acid-sensing ion channel. Neuron 68, 61-72 (2010).
23. Lewis, C. J. & Evans, R. J. Lack of run-down of smooth muscle P2X receptor currents recorded with the amphotericin permeabilized patch technique, physiological and pharmacological characterization of the properties of mesenteric artery P2X receptor ion channels. Br. J. Pharmacol. 131, 1659-1666 (2000). (Pubitemid 32056432)
24. Yang, Y. et al. Highly conserved salt bridge stabilizes rigid signal patch at extracellular loop critical for surface expression of acid-sensing ion channels. J. Biol. Chem. 287, 14443-14455 (2012).
25. Shaw, D. E. A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions. J. Comput. Chem. 26, 1318-1328 (2005). (Pubitemid 41454622)
26. Banks, J. L. et al. Integrated Modeling Program, Applied Chemical Theory (IMPACT). J. Comput. Chem. 26, 1752-1780 (2005). (Pubitemid 43076184)
27. Morris, G. M. et al. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comput. Chem. 30, 2785-2791 (2009).
28. Smart, O. S., Neduvelil, J. G., Wang, X., Wallace, B. A. & Sansom, M. S. HOLE: a program for the analysis of the pore dimensions of ion channel structural models. J. Mol. Graph. 14, 354-360 (1996). (Pubitemid 27302826)
29. Bakan, A., Meireles, L. M. & Bahar, I. ProDy: protein dynamics inferred from theory and experiments. Bioinformatics 27, 1575-1577 (2011).
30. Sali, A. & Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815 (1993). (Pubitemid 24007801)
31. Gadakar, P. K., Phukan, S., Dattatreya, P. & Balaji, V. N. Pose prediction accuracy in docking studies and enrichment of actives in the active site of GSK-3beta. J. Chem. Inf. Model. 47, 1446-1459 (2007). (Pubitemid 47210048)
32. Limongelli, V. et al. Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition. Proc. Natl Acad. Sci. USA 107, 5411-5416 (2010).
33. Laio, A., Rodriguez-Fortea, A., Gervasio, F. L., Ceccarelli, M. & Parrinello, M. Assessing the accuracy of metadynamics. J. Phys. Chem. B 109, 6714-6721 (2005). (Pubitemid 40538439)