Unpicking allosteric mechanisms of homo-oligomeric proteins by determining their successive ligand binding constants

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 373, Issue 1749, 2018, Pages

  Gruber, Ranit ^a   Horovitz, Amnon ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

Chaperonins; Cooperativity; Native mass spectrometry; Ring shaped oligomers; Single molecule techniques

Indexed keywords

CHEMICAL BINDING; LIGAND; MASS SPECTROMETRY; MOLECULAR ANALYSIS; PROBABILITY; PROTEIN;

LIGAND; PROTEIN BINDING;

ALLOSTERISM; CHEMISTRY; HUMAN; MOLECULAR MODEL; PROTEIN SUBUNIT;

ALLOSTERIC REGULATION; HUMANS; LIGANDS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN SUBUNITS;

EID: 85046822154     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2017.0176     Document Type: Review

References (20)

1. Cui Q, Karplus M. 2008 Allostery and cooperativity revisited. Protein Sci. 17, 1295–1307. (doi:10.1110/ps.03259908)
2. Monod J, Wyman J, Changeux JP. 1965 On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12, 88–118. (doi:10.1016/S0022-2836(65)80285-6)
3. Koshland Jr DE, Némethy G, Filmer D. 1966 Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5, 365–385. (doi:10.1021/bi00865a047)
4. Perutz MF. 1989 Mechanisms of cooperativity and allosteric regulation in proteins. Q. Rev. Biophys. 22, 139–237. (doi:10.1017/S0033583500003826)
5. Rivenzon-Segal D, Wolf SG, Shimon L, Willison KR, Horovitz A. 2005 Sequential ATP-induced allosteric transitions of the cytoplasmic chaperonin containing TCP-1 revealed by EM analysis. Nat. Struct. Mol. Biol. 12, 233–237. (doi:10.1038/nsmb901)
6. Danziger O, Rivenzon-Segal D, Wolf SG, Horovitz A. 2003 Conversion of the allosteric transition of GroEL from concerted to sequential by the single mutation Asp-155→Ala. Proc. Natl Acad. Sci. USA 100, 13797–13802. (doi:10.1073/pnas. 2333925100)
7. Papo N, Kipnis Y, Haran G, Horovitz A. 2008 Concerted release of substrate domains from GroEL by ATP is demonstrated with FRET. J. Mol. Biol. 380, 717–725. (doi:10.1016/j.jmb.2008.05.021)
8. Gruber R, Horovitz A. 2016 Allosteric mechanisms in chaperonin machines. Chem. Rev. 116, 6588–6606. (doi:10.1021/acs.chemrev.5b00556)
9. Liu S, Chistol G, Bustamante C. 2014 Mechanical operation and intersubunit coordination of ring-shaped molecular motors: insights from single-molecule studies. Biophys. J. 106, 1844–1858. (doi:10.1016/j.bpj.2014.03.029)
10. Dyachenko A, Gruber R, Shimon L, Horovitz A, Sharon M. 2013 Allosteric mechanisms can be distinguished using structural mass spectrometry. Proc. Natl Acad. Sci. USA 110, 7235–7239. (doi:10. 1073/pnas.1302395110)
11. Sharon M, Horovitz A. 2015 Probing allosteric mechanisms using native mass spectrometry. Curr. Opin. Struct. Biol. 34, 7–16. (doi:10.1016/j.sbi. 2015.05.002)
12. Jiang Y, Douglas NR, Conley NR, Miller EJ, Frydman J, Moerner WE. 2011 Sensing cooperativity in ATP hydrolysis for single multisubunit enzymes in solution. Proc. Natl Acad. Sci. USA 108, 16962–16967. (doi:10.1073/pnas.1112244108)
13. Duke TA, Le Novère N, Bray D. 2001 Conformational spread in a ring of proteins: a stochastic approach to allostery. J. Mol. Biol. 308, 541–553. (doi:10.1006/jmbi.2001.4610)
14. Cooper A, Dryden DT. 1984 Allostery without conformational change. A plausible model. Eur. Biophys. J. 11, 103–109. (doi:10.1007/BF00276625)
15. Popovych N, Sun S, Ebright RH, Kalodimos CG. 2006 Dynamically driven protein allostery. Nat. Struct. Mol. Biol. 13, 831–838. (doi:10.1038/nsmb1132)
16. McLeish TC, Cann MJ, Rodgers TL. 2015 Dynamic transmission of protein allostery without structural change: spatial pathways or global modes? Biophys. J. 109, 1240–1250. (doi:10.1016/j.bpj.2015.08.009)
17. Heddle JG, Okajima T, Scott DJ, Akashi S, Park SY, Tame JR. 2007 Dynamic allostery in the ring protein TRAP. J. Mol. Biol. 371, 154–167. (doi:10.1016/j. jmb.2007.05.013)
18. Viappiani C, Abbruzzetti S, Ronda L, Bettati S, Henry ER, Mozzarelli A, Eaton WA. 2014 Experimental basis for a new allosteric model for multisubunit proteins. Proc. Natl Acad. Sci. USA 111, 12 758–12 763. (doi:10.1073/pnas.1413566111)
19. Gruber R, Levitt M, Horovitz A. 2017 Sequential allosteric mechanism of ATP hydrolysis by the CCT/ TRiC chaperone is revealed through Arrhenius analysis. Proc. Natl Acad. Sci. USA 114, 5189–5194. (doi:10.1073/pnas.1617746114)
20. Ma J, Sigler PB, Xu Z, Karplus M. 2000 A dynamic model for the allosteric mechanism of GroEL. J. Mol. Biol. 302, 303–313. (doi:10.1006/jmbi.2000.4014)