Cooperative Binding

PLoS Computational Biology

Volumn 9, Issue 6, 2013, Pages

  Stefan, Melanie I ^a   Le Novère, Nicolas ^b  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b BABRAHAM INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; NUCLEIC ACIDS;

A-STABLE; BINDING-SITES; BIOCHEMICAL PROCESS; COOPERATIVE BINDING; COOPERATIVITY; LIGAND CONCENTRATION; MOLECULAR BINDING; NONLINEAR FUNCTIONS; PHYSIOLOGICAL PROCESS;

LIGANDS;

ADAIR EQUATION; ARTICLE; BINDING KINETICS; BINDING SITE; CHEMICAL BINDING; CONCEPTUAL FRAMEWORK; CONFORMATIONAL TRANSITION; COOPERATIVE BINDING; GENETIC TRANSCRIPTION; HILL EQUATION; KLOTZ EQUATION; LIGAND BINDING; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MATHEMATICAL PARAMETERS; MOLECULAR INTERACTION; MWC MODEL; NUCLEIC ACID ANALYSIS; PAULING EQUATION;

EID: 84879545398     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003106     Document Type: Article

References (38)

1. Bohr C, Hasselbalch K, Krogh A, (1904) Ueber einen in biologischer Beziehung wichtigen Einfluss, den die Kohlensäurespannung des Blutes auf dessen Sauerstoffbindung übt. Skandinavisches. Arch Physiol 16: 402-412.
2. Wyman J, Gill SJ (1990) Binding and linkage. Functional chemistry of biological molecules. Mill Valley: University Science Books.
3. Hill AV, (1910) The possible effects of the aggregation of the molecules of haemoglobin on its dissociation curves. J Physiol 40: iv-vii.
4. Adair GS, (1925) The hemoglobin system. IV. The oxygen dissociation curve of hemoglobin. J Biol Chem 63: 529-545.
5. Klotz IM, (1946) The application of the law of mass action to binding by proteins; interactions with calcium. Arch Biochem 9: 109-117.
6. Klotz IM, (2004) Ligand-receptor complexes: origin and development of the concept. J Biol Chem 279: 1-12.
7. Pauling L, (1935) The oxygen equilibrium of hemoglobin and its structural interpretation. Proc Natl Acad Sci U S A 21: 186-191.
8. Koshland DE, Némethy G, Filmer D, (1966) Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5: 365-385.
9. Koshland DE, (1958) Application of a theory of enzyme specificity to protein synthesis. Proc Natl Acad Sci U S A 44: 98-104.
10. Monod J, Wyman J, Changeux JP, (1965) On the nature of allosteric transitions: a plausible model. J Mol Biol 12: 88-118.
11. Rubin MM, Changeux JP, (1966) On the nature of allosteric transitions: implications of non-exclusive ligand binding. J Mol Biol 21: 265-274.
12. Cluzel P, Surette M, Leibler S, (2000) An ultrasensitive bacterial motor revealed by monitoring signaling proteins in single cells. Science 287: 1652-1655.
13. Sourjik V, Berg HC, (2002) Binding of the Escherichia coli response regulator CheY to its target measured in vivo by fluorescence resonance energy transfer. Proc Natl Acad Sci U S A 99: 12669-12674.
14. Edelstein SJ, Schaad O, Henry E, Bertrand D, Changeux JP, (1996) A kinetic mechanism for nicotinic acetylcholine receptors based on multiple allosteric transitions. Biol Cybern 75: 361-379.
15. Mello BA, Tu Y, (2005) An allosteric model for heterogeneous receptor complexes: understanding bacterial chemotaxis responses to multiple stimuli. Proc Natl Acad Sci U S A 102: 17354-17359.
16. Najdi TS, Yang CR, Shapiro BE, Hatfield GW, Mjolsness ED, (2006) Application of a generalized MWC model for the mathematical simulation of metabolic pathways regulated by allosteric enzymes. J Bioinform Comput Biol 4: 335-355.
17. Stefan MI, Edelstein SJ, Le Novère N, (2009) Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters. BMC Syst Biol 3: 68.
18. Perutz MF, Rossmann MG, Cullis AF, Muirhead H, Will G, et al. (1960) Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5-A. resolution, obtained by X-ray analysis. Nature 185: 416-422.
19. Changeux JP, (1961) The feedback control mechanisms of biosynthetic L-threonine deaminase by L-isoleucine. Cold Spring Harb Symp Quant Biol 26: 313-318.
20. Changeux JP, (1963) Allosteric interactions on biosynthetic L-threonine deaminase from E. coli K12. Cold Spring Harb Symp Quant Biol 28: 497-504.
21. Gallagher DT, Gilliland GL, Xiao G, Zondlo J, Fisher KE, et al. (1998) Structure and control of pyridoxal phosphate dependent allosteric threonine deaminase. Structure 6: 465-475.
22. Gerhart JC, Pardee AB, (1962) The enzymology of control by feedback inhibition. J Biol Chem 237: 891-896.
23. Changeux JP, Rubin MM, (1968) Allosteric interactions in aspartate transcarbamylase. 3. Interpretation of experimental data in terms of the model of Monod, Wyman, and Changeux. Biochemistry 7: 553-561.
24. Honzatko RB, Crawford JL, Monaco HL, Ladner JE, Ewards BF, et al. (1982) Crystal and molecular structures of native and CTP-liganded aspartate carbamoyltransferase from Escherichia coli. J Mol Biol 160: 219-263.
25. Karlin A, (1967) On the application of "a plausible model" of allosteric proteins to the receptor for acetylcholine. J Theor Biol 16: 306-320.
26. Changeux JP, Kasai M, Lee CY, (1970) Use of a snake venom toxin to characterize the cholinergic receptor protein. Proc Natl Acad Sci U S A 67: 1241-1247.
27. Brejc K, van Dijk WJ, Klaassen RV, Schuurmans M, van Der Oost J, et al. (2001) Crystal structure of an ACh-binding protein reveals the ligand-binding domain of nicotinic receptors. Nature 411: 269-276.
28. Meyer T, Holowka D, Stryer L, (1988) Highly cooperative opening of calcium channels by inositol 1,4,5-trisphosphate. Science 240: 653-656.
29. Seo MD, Velamakanni S, Ishiyama N, Stathopulos PB, Rossi AM, et al. (2012) Structural and functional conservation of key domains in InsP3 and ryanodine receptors. Nature 483: 108-112.
30. Teo TS, Wang JH, (1973) Mechanism of activation of a cyclic adenosine 3′:5′-monophosphate phosphodiesterase from bovine heart by calcium ions. Identification of the protein activator as a Ca2+ binding protein. J Biol Chem 248: 5950-5955.
31. Babu YS, Sack JS, Greenhough TJ, Bugg CE, Means AR, et al. (1985) Three-dimensional structure of calmodulin. Nature 315: 37-40.
32. Ptashne M, Jeffrey A, Johnson AD, Maurer R, Meyer BJ, et al. (1980) How the lambda repressor and cro work. Cell 19: 1-11.
33. Ackers GK, Johnson AD, Shea MA, (1982) Quantitative model for gene regulation by lambda phage repressor. Proc Natl Acad Sci U S A 79: 1129-1133.
34. Krell T, Terán W, López Mayorga O, Rivas G, Jiménez M, et al. (2007) Optimization of the palindromic order of the TtgR operator enhances binding cooperativity. J Mol Biol 369: 1188-1199.
35. Aramaki H, Kabata H, Takeda S, Itou H, Nakayama H, et al. (2011) Formation of repressor-inducer-operator ternary complex: negative cooperativity of d-camphor binding to CamR. Genes Cells 16: 1200-1207.
36. Changeux JP, Thiéry J, Tung Y, Kittel C, (1967) On the cooperativity of biological membranes. Proc Natl Acad Sci U S A 57: 335-341.
37. Wyman J, (1969) Possible allosteric effects in extended biological systems. J Mol Biol 39: 523-538.
38. 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.