Allosteric modulation of monomeric proteins

Biochemistry and Molecular Biology Education

Volumn 33, Issue 3, 2005, Pages 169-176

  Ascenzi, Paolo ^a,b   Bocedi, Alessio ^a,b   Bolli, Alessandro ^a   Fasano, Mauro ^c   Notari, Stefania ^b   Polticelli, Fabio ^a  

^a ROMA TRE UNIVERSITY   (Italy)

^b NATIONAL INSTITUTE FOR INFECTIOUS DISEASES L SPALLANZANI   (Italy)

^c UNIVERSITY OF INSUBRIA   (Italy)

Author keywords

Albumin; Allostery; Monomeric proteins; Myoglobin; Thrombin

Indexed keywords

BINDING PROTEIN; LACTIC ACID; LIGAND; MONOMERIC PROTEIN; MULTIMERIC PROTEIN; MYOGLOBIN; SERUM ALBUMIN; SODIUM; THROMBIN; UNCLASSIFIED DRUG;

ALLOSTERISM; ANTICOAGULATION; MOLECULAR MODEL; REVIEW; SPERM;

CETACEA; PHYSETER CATODON;

EID: 18844382948     PISSN: 14708175     EISSN: None     Source Type: Journal    
DOI: 10.1002/bmb.2005.494033032470     Document Type: Review

References (100)

1. J. T. Edsall, J. Wyman (1958) Biophysical Chemistry, pp. 653-662, Academic Press, Inc., New York.
2. J. Wyman (1964) Linked functions and reciprocal effects in hemoglobin: A second look, Adv. Protein Chem. 19, 223-286.
3. J. Monod, J. Wyman, J. P. Changeux (1965) On the nature of allosteric transitions: A plausibile model, J. Mol. Biol. 12, 88-118.
4. J. A. Todhunter (1979) Reversible enzyme inhibition, Methods Enzymol. 63, 383-411.
5. E. Di Cera (1994) Linkage thermodynamics, Methods Enzymol. 232, 655-683.
6. L. H. Janssen, M. T. Van Wilgenburg, J. Wilting (1981) Human serum albumin as an allosteric two-state protein. Evidence from effects of calcium and warfarin on proton binding behaviour, Biochim. Biophys. Acta 669, 244-250.
7. J. Wyman, S. J. Gill (1990) Binding and Linkage, University Science Books, Mill Valley, CA.
8. B. Giardina, P. Ascenzi, M. E. Clementi, G. De Sanctis, M. Rizzi, M. Coletta (1996) Functional modulation by lactate of myoglobin. A monomeric allosteric hemoprotein, J. Biol. Chem. 271, 16999-17001.
9. E. J. Duffy, H. Angliker, B. F. Le Bonniec, S. R. Stone (1997) Allosteric modulation of the activity of thrombin, Biochem. J. 321, 361-365.
10. L. L. Leung, C. S. Gibbs (1997) Modulation of thrombin's procoagulant and anticoagulant properties, Thromb. Haemost. 78, 577-580.
11. E. Di Cera (1998) Anticoagulant thrombins, Trends Cardiovasc. Med. 8, 340-350.
12. S. Baroni, M. Mattu, A. Vannini, R. Cipollone, S. Aime, P. Ascenzi, M. Fasano (2001) Effect of ibuprofen and warfarin on the allosteric properties of haem-human serum albumin. A spectroscopic study, Eur. J. Biochem. 268, 6214-6220.
13. H. Frauenfelder, B. H. McMahon, R. H. Austin, K. Chu, J. T. Groves (2001) The role of structure, energy landscape, dynamics, and allostery in the enzymatic function of myoglobin, Proc. Natl. Acad. Sci. U. S. A. 98, 2370-2374.
14. V. T. G. Chuang, M. Otagiri (2002) How do fatty acids cause allosteric binding of drugs to human serum albumin? Pharm. Res. 19, 1458-1464.
15. I. Fitos, J. Visy, J. Kardos (2002) Stereoselective kinetics of warfarin binding to human serum albumin: Effect of an allosteric interaction, Chirality 14, 442-448.
16. M. Brunori, D. Bourgeois, B. Vallone (2004) The structural dynamics of myoglobin, J. Struct. Biol. 147, 223-234.
17. J. Chen, D. S. Hage (2004) Quantitative analysis of allosteric drug-protein binding by biointeraction chromatography, Nat. Biotechnol. 22, 1445-1448.
18. E. Di Cera (2004) Thrombin: A paradigm for enzymes allosterically activated by monovalent cations, C. R. Biol. 327, 1065-1076.
19. J. B. Wittenberg (1970) Myoglobin-facilitated oxygen diffusion: role of myoglobin in oxygen entry into muscle, Physiol. Rev. 50, 559-636.
20. B. A. Wittenberg, J. B. Wittenberg (1989) Transport of oxygen in muscle, Annu. Rev. Physiol. 51, 857-878.
21. J. B. Wittenberg, B. A. Wittenberg (1990) Mechanisms of cytoplasmic hemoglobin and myoglobin function, Annu. Rev. Biophys. Biophys. Chem. 19, 217-241.
22. M. Brunori (2001) Nitric oxide moves myoglobin centre stage, Trends Biochem. Sci. 26, 209-210.
23. M. W. Merx, U. Flögel, T. Stumpe, A. Gödecke, U. K. Decking, J. Schrader (2001) Myoglobin facilitates oxygen diffusion, FASEB J. 15, 1077-1079.
24. U. Flögel, M. W. Merx, A. Gödecke, U. K. Decking, J. Schrader (2001) Myoglobin: A scavenger of bioactive NO, Proc. Natl. Acad. Sci. U. S. A. 98, 735-740; erratum in Proc. Natl. Acad. Sci. U. S. A. 98, 4276.
25. J. B. Wittenberg, B. A. Wittenberg (2003) Myoglobin function reassessed, J. Exp. Biol. 206, 2011-2020.
26. U. Flögel, A. Gödecke, L. O. Klotz, J. Schrader, (2004) Role of myoglobin in the antioxidant defense of the heart, FASEB J. 18, 1156-1158.
27. M. Brunori, Q. H. Gibson (2001) Cavities and packing defects in the structural dynamics of myoglobin, EMBO Rep. 2, 674-679.
28. H. Frauenfelder, B. H. McMahon, P. W. Fenimore (2003) Myoglobin: The hydrogen atom of biology and a paradigm of complexity, Proc. Natl. Acad. Sci. U. S. A. 100, 8615-8617.
29. Y. Seno, N. Gô (1990) Deoxymyoglobin studied by the conformational normal mode analysis. II. The conformational change upon oxygenation, J. Mol. Biol. 216, 111-126.
30. M. Coletta, P. Ascenzi, T. G. Traylor, M. Brunori (1985) Kinetics of carbon monoxide binding to monomeric hemoproteins. Role of the proximal histidine, J. Biol. Chem. 260, 4151-4155.
31. A. Ansari, C. M. Jones, E. R. Henry, J. Hofrichter, W. A. Eaton (1994) Conformational relaxation and ligand binding in myoglobin, Biochemistry 33, 5128-5145.
32. F. Polizio, G. De Sanctis, P. Ascenzi, M. Coletta (1998) Anion- and pH-linked effects on the heme iron-geometry in ferrous nitrosylated monomeric myoglobins, J. Biol. Inorg. Chem. 3, 458-462.
33. M. F. Perutz (1979) Regulation of oxygen affinity of hemoglobin: Influence of structure of the globin on the heme iron, Annu. Rev. Biochem. 48, 327-386.
34. M. F. Perutz (1990) Mechanisms regulating the reactions of human hemoglobin with oxygen and carbon monoxide, Annu. Rev. Physiol. 52, 1-25.
35. M. Brunori (1999) Hemoglobin is an honorary enzyme, Trends Biochem. Sci. 24, 158-161.
36. K. Imai (1999) The haemoglobin enzyme, Nature 401, 437-439.
37. 2 affinity, cooperativity, and Bohr effect by heterotropic allosteric effectors, J. Biol. Chem. 277, 34508-34520.
38. P. W. Hochachka, G. N. Somero (1984) Biochemical Adaptation, pp. 182-203, Princeton University Press, Princeton, NJ.
39. S. E. Phillips (1980) Structure and refinement of oxymyoglobin at 1.6 Å resolution, J. Mol. Biol. 142, 531-554.
40. M. F. Perutz (1989) Myoglobin and haemoglobin: Role of distal residues in reactions with haem ligands, Trends Biochem. Sci. 14, 42-44.
41. A. Brancaccio, F. Cutruzzolà, C. Travaglini Allocatelli, M. Brunori, S. J. Smerdon, A. J. Wilkinson, Y. Dou, D. Keenan, M. Ikeda-Saito, R. E. Brantley Jr., J. S. Olson (1994) Structural factors governing azide and cyanide binding to mammalian metmyoglobins, J. Biol. Chem. 269, 13843-13853.
42. B. A. Springer, S. G. Sligar, J. S. Olson, G. N. Phillips (1994) Mechanisms of ligand recognition in myoglobin, Chem. Rev. 94, 699-714.
43. C. L. Milligan, S. S. Girard (1993) Lactate metabolism in rainbow trout, J. Exp. Biol. 180, 175-193.
44. A. A. Spector (1975) Fatty acid binding to plasma albumin, J. Lipid Res. 16, 165-179.
45. G. Sudlow, D. J. Birkett, D. N. Wade (1975) The characterization of two specific drug binding sites on human serum albumin, Mol. Pharmacol. 11, 824-832.
46. 13C NMR study, Proc. Natl. Acad. Sci. U. S. A. 81, 3718-3722.
47. X. He, D. C. Carter (1992) Atomic structure and chemistry of human serum albumin, Nature 358, 209-215.
48. T. Peters Jr. (1996) All About Albumin: Biochemistry, Genetics and Medical Applications, Academic Press, Orlando, FL.
49. I. Petitpas, C. E. Petersen, C. E. Ha, A. A. Bhattacharya, P. A. Zunszain, J. Ghuman, N. V. Bhagavan, S. Curry (2003) Structural basis of albumin-thyroxine interactions and familial dysalbuminemic hyperthyroxinemia, Proc. Natl. Acad. Sci. U. S. A. 100, 6440-6445.
50. P. A. Zunszain, J. Ghuman, T. Komatsu, E. Tsuchida, S. Curry (2003) Crystal structural analysis of human serum albumin complexed with hemin and fatty acid, BMC Struct. Biol. 3, 6.
51. F. J. Diana, K. Veronich, A. L. Kapoor (1989) Binding of nonsteroidal anti-inflammatory agents and their effect on binding of racemic warfarin and its enantiomers to human serum albumin, J. Pharm. Sci. 78, 195-199.
52. S. Curry, H. Mandelkow, P. Brick, N. Franks (1998) Crystal structure of human complexed with fatty acid reveals an asymmetric distribution of binding sites, Nat. Struct. Biol. 5, 751-753.
53. A. A. Bhattacharya, T. Grüne, S. Curry (2000) Crystallographic analysis reveals common modes of binding of medium and long chain fatty acids to human serum albumin, J. Mol. Biol. 303, 721-732.
54. M. Wardell, Z. Wang, J. X. Ho, J. Robert, F. Ruker, J. Ruble, D. C. Carter (2002) The atomic structure of human methemalbumin at 1.9 Å, Biochem. Biophys. Res. Commun. 291, 813-819.
55. I. Fitos, J. Visy, M. Simonyi, J. Hermansson (1999) Stereoselective allosteric binding interaction on human serum albumin between ibuprofen and lorazepam acetate, Chirality 11, 115-120.
56. V. T. G. Chuang, M. Otagiri (2001) Flunitrazepam, a 7-nitro-1,4- benzodiazepine that is unable to bind to the indole-benzodiazepine site of human serum albumin, Biochim. Biophys. Acta 1546, 337-345.
57. J. Chen, C. Ohnmacht, D. S. Hage (2004) Studies of phenytoin binding to human serum albumin by high-performance affinity chromatography, J. Chromatogr. B 809, 137-145.
58. H. S. Kim, D. S. Hage (2005) Chromatographic analysis of carbamazepine binding to human serum albumin, J. Chromatogr. B 816, 57-66.
59. V. Sampath, X. J. Zhao, W. S. Caughey (2001) Anesthetic-like interactions of nitric oxide with albumin and hemeproteins. A mechanism for control of protein function, J. Biol. Chem. 276, 13635-13643.
60. A. A. Bhattacharya, S. Curry, N. P. Franks (2000) Binding of the general anesthetics propofol and halothane to human serum albumin. High resolution crystal structures, J. Biol. Chem. 275, 38731-38738.
61. I. Petitpas, A. A. Bhattacharya, S. Twine, M. East, S. Curry (2001) Crystal structure analysis of warfarin binding to human serum albumin: anatomy of drug site I, J. Biol. Chem. 276, 22804-22809.
62. J. Wilting, W. F. van der Giesen, L. H. M. Janssen, M. M. Weideman, M. Otagiri (1980) The effect of albumin conformation on the binding of warfarin to human serum albumin, J. Biol. Chem. 255, 3032-3037.
63. K. Yamasaki, T. Maruyama, K. Yoshimoto, Y. Tsutsumi, R. Narazaki, A. Fukuhara, U. Kragh-Hansen, M. Otagiri (1999) Interactive binding to the two principal ligand binding sites of human serum albumin: Effect of the neutral-to-base transition, Biochim. Biophys. Acta 1432, 313-323.
64. M. Fasano, S. Baroni, A. Vannini, P. Ascenzi, S. Aime (2001) Relaxometric characterization of human hemalbumin, J. Biol. Inorg. Chem. 6, 650-658.
65. M. Mattu, A. Vannini, M. Coletta, M. Fasano, P. Ascenzi (2001) Effect of bezafibrate and clofibrate on the heme-iron geometry of ferrous nitrosylated heme-human serum albumin: an EPR study, J. Inorg. Biochem. 84, 293-296.
66. T. Sakai, K. Yamasaki, T. Sako, U. Kragh-Hansen, A. Suenaga, M. Otagiri (2001) Interaction mechanism between indoxyl sulfate, a typical uremic toxin bound to site II, and ligands bound to site I of human serum albumin, Pharm. Res. 18, 520-524.
67. M. Fasano, M. Mattu, M. Coletta, P. Ascenzi (2002) The heme-iron geometry of ferrous nitrosylated heme-serum lipoproteins, hemopexin, and albumin: a comparative EPR study, J. Inorg. Biochem. 91, 487-490.
68. M. T. Stubbs, W. Bode (1993) A player of many parts: The spotlight falls on thrombin's structure, Thromb. Res. 69, 1-58.
69. M. T. Stubbs, W. Bode (1994) Coagulation factors and their inhibitors, Curr. Opin. Struct. Biol. 4, 823-832.
70. M. T. Stubbs, W. Bode (1995) The clot thickens. Clues provided by thrombin structure, Trends Biochem. Sci. 20, 23-28.
71. C. T. Esmon (2000) Regulation of blood coagulation, Biochim. Biophys. Acta 1477, 349-360.
72. K. G. Mann, ed. (2003) Thrombin: Physiology and pathophysiology, Chest 124, Suppl. 4, 1-68.
73. R. L. Lundblad, R. A. Bradshaw, D. Gabriel, T. L. Ortel, J. Lawson, K. G. Mann (2004) A review of the therapeutic uses of thrombin, Thromb. Haemost. 91, 851-860.
74. A. J. Barrett, N. D. Rawlings, J. F. Woessner, eds. (2004) Handbook of Proteolytic Enzymes, Academic Press, London and San Diego.
75. + activated enzyme, Biochemistry 31, 11721-11730.
76. E. Di Cera, Q. D. Dang, Y. M. Ayala (1997) Molecular mechanisms of thrombin function, Cell. Mol. Life Sci. 53, 701-730.
77. S. W. Hall, C. S. Gibbs, L. L. Leung, (1997) Strategies for development of novel antithrombotics: Modulating thrombin's procoagulant and anticoagulant properties, Cell. Mol. Life. Sci. 53, 731-736.
78. L. L. K. Leung, S. W. Hall (2000) Dissociation of thrombin's substrate interactions using site-directed mutagenesis, Trends Cardiovasc. Med. 10, 89-92.
79. E. Di Cera, A. M. Cantwell (2001) Determinants of thrombin specificity, Ann. N. Y. Acad. Sci. 936, 133-146.
80. Q. D. Dang, E. R. Guinto, E. Di Cera (1997) Rational engineering of activity and specificity in a serine protease, Nat. Biotechnol. 15, 146-149.
81. Q. D. Dang, A. Vindigni, E. Di Cera (1995) An allosteric switch controls the procoagulant and anticoagulant activities of thrombin, Proc. Natl. Acad. Sci. U. S. A. 92, 5977-5981.
82. E. R. Guinto, A. Vindigni, Y. M. Ayala, Q. D. Dang, E. Di Cera (1995) Identification of residues linked to the slow→fast transition of thrombin, Proc. Natl. Acad. Sci. U. S. A. 92, 11185-11189.
83. E. R. Guinto, S. Caccia, T. Rose, K. Futterer, G. Waksman, E. Di Cera (1999) Unexpected crucial role of residue 225 in serine proteases, Proc. Natl. Acad. Sci. U. S. A. 96, 1852-1857.
84. + binding site of thrombin, J. Biol. Chem. 270, 22089-22092.
85. + binding site of thrombin, Biophys. Chem. 63, 185-200.
86. + binding, Proteins 30, 34-42.
87. + binding to thrombin, J. Biol. Chem. 279, 31842-31853.
88. +-induced allosteric regulation of catalytic activity in serine proteases, Proc. Natl. Acad. Sci. U. S. A. 93, 10653-10656.
89. M. M. Krem, T. Rose, E. Di Cera (2000) Sequence determinants of function and evolution in serine proteases, Trends Cardiovasc. Med. 10, 171-176.
90. A. R. Rezaie, S. T. Cooper, F. C. Church, C. T. Esmon (1995) Protein C inhibitor is a potent inhibitor of the thrombin-thrombomodulin complex, J. Biol. Chem. 270, 25336-25339.
91. A. R. Rezaie, X. He, C. T. Esmon (1998) Thrombomodulin increases the rate of thrombin inhibition by BPTI, Biochemistry 37, 693-699.
92. R. De Cristofaro, R. Landolfi (1999) Allosteric modulation of BPTI interaction with human α- and ζ-thrombin, Eur. J. Biochem. 260, 97-102.
93. P. Fuentes-Prior, Y. Iwanaga, R. Huber, R. Pagila, G. Rumennik, M. Seto, J. Morser, D. R. Light, W. Bode (2000) Structural basis for the anticoagulant activity of the thrombin-thrombomodulin complex, Nature 404, 518-525.
94. M. E. Nesheim (1983) A simple rate law that describes the kinetics of the heparin-catalyzed reaction between antithrombin III and thrombin, J. Biol. Chem. 258, 14708-14717.
95. C. W. Pratt, F. C. Church (1992) Heparin binding to protein C inhibitor, J. Biol. Chem. 267, 8789-8794.
96. S. R. Stone, B. F. Le Bonniec (1997) Inhibitory mechanism of serpins. Identification of steps involving the active-site serine residue of the protease, J. Mol. Biol. 265, 344-362.
97. G. Guntas, M. Ostermeier (2004) Creation of an allosteric enzyme by domain insertion, J. Mol. Biol. 336, 263-273.
98. S. E. Phillips, B. P. Schoenborn (1981) Neutron diffraction reveals oxygen-histidine hydrogen bond in oxymyoglobin, Nature 292, 81-82.
99. J. Kuriyan, S. Wilz, M. Karplus, G. A. Petsko (1986) X-ray structure and refinement of carbon-monoxy (Fe II)-myoglobin at 1.5 Å resolution, J. Mol. Biol. 192, 133-154.
100. A. Nicholls, K. A. Sharp, B. Honig (1991) Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons, Proteins 11, 281-296.