Structural model of human α1-microglobulin: Proposed scheme for the interaction with the Gla domain of anticoagulant protein C

Blood Coagulation and Fibrinolysis

Volumn 11, Issue 3, 2000, Pages 261-275

  Villoutreix, Bruno O ^a,b   Akerstrom B ^a   Lindqvist, A ^a  

^a LUND UNIVERSITY   (Sweden)

^b INSERM   (France)

Author keywords

1 microglobulin; Coagulation; Lipocalin; Protein C; Protein modelling

Indexed keywords

ALPHA 1 MICROGLOBULIN; PROTEIN C;

ARTICLE; INFORMATION SCIENCE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE;

AMINO ACID SEQUENCE; HUMANS; MEMBRANE GLYCOPROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN C; PROTEIN CONFORMATION; STRUCTURE-ACTIVITY RELATIONSHIP; TRYPSIN INHIBITOR, KUNITZ SOYBEAN;

EID: 0034036722     PISSN: 09575235     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (87)

1. 1. Pervaiz S, Brew K. Homology of β-lactoglobulin, serum retinol-binding protein and protein HC. Science 1985; 228: 335-337.
2. 2. Flower DR. The lipocalin protein family: structure and function. Biochem J 1996; 318: 1-14.
3. 3. Cowan SW, Newcomer ME, Jones TA. Crystallographic refinement of human serum retinol-binding protein at 2 Å resolution. Proteins 1990; 8: 44-61.
4. 4. Papiz MZ, Sawyer L, Eliopoulos EE, North ACT, Findlay JBC, et al. The structure of β-lactoglobulin and its similarity to plasma retinol-binding protein. Nature 1986; 324: 383-385.
5. 5. Holden HM, Rypniewski WR, Law JH, Rayment I. The molecular structure of insecticyanin from the hemolymph of the tobacco hornworm Manduca sexta. L. at 2.6 A resolution. EMBO J 1987; 6: 1565-1570.
6. 6. Huber R, Schneider M, Mayr I, Muller R, Deutzmann R, Suter F, et al. Molecular structure of the bilin binding protein (BBP) from Pieris brassicae after refinement at 2.0 Å resolution. J Mol Biol 1987; 198: 499-513.
7. 7. Böcskei Zs, Groom CR, Flower DR, Wright CE, Phillips SEV, Cavaggioni A, et al. Pheromone binding to two rodent urinary proteins revealed by X-ray crystallography. Nature 1992; 360: 186-188.
8. 8. Bianchet MA, Bains G, Pelosi P, Pevsner J, Snyder SH, Monaco HL, et al. The three-dimensional structure of bovine odorant-binding protein and its mechanism of odour recognition. Nat Struct Biol 1996; 3: 934-939.
9. 9. Tegoni M, Ramoni R, Bignetti E, Spinelli S, Cambillau C. Domain swapping creates a third putative combining site in bovine odorant binding protein dimer. Nat Struct Biol 1996; 3: 863-867.
10. 10. Newcomer ME. Structure of the epididymal retinoic acid binding protein at 2.1 Å resolution. Structure 1993; 1: 7-18.
11. 11. Coles M, Diercks T, Muehlenweg B, Bartsch S, Zolzer V, Tschesche H, et al. The solution structure and dynamics of human neutrophil gelatinase-associated lipocalin. J Mol Biol 1999; 2891: 139-157.
12. 12. Rouvinen J, Rautiainen J, Virtanen T, Zeiler T, Kauppinen J, Taivainen A, et al Probing the molecular basis of allergy: three-dimensional structure of the bovine lipocalin allergen Bos d 2. J Biol Chem 1999; 274: 2337-2343.
13. 1-glycoprotein of low molecular weight: isolation and some properties. Biochem Biophys Res Commun 1975; 65: 1427-1433.
14. 1-microglobulin: purification procedure, chemical and physicochemical properties. J Biol Chem 1977; 252: 8048-8057.
15. 15. Tejler L, Grubb AO, A complex-forming glycoprotein heterogeneous in charge and present in human plasma, urine and cerebrospinal fluid. Biochim Biophys Acta 1976; 439: 82-94.
16. 1-microglobulin is 5-8 kDa larger in primates. J Biol Chem 1985; 260: 4839-4844.
17. 1-microglobulin/bikunin protein. Gene 1994; 147: 297-298.
18. 1-microglobulin/bikunin mRNA: cloning of a cDNA from plaice (Pleuronectes platessa). Comp Biochem Physiol 1994; 108B: 275-281.
19. 1-microglobulin/bikunin precursor (AMBP) gene expression during amphibian metamorphosis. Dev Genes Evol 1997; 206: 355-362.
20. 1-microglobulin. Scand J Immunol 1981; 13: 383-390.
21. 21. Mendez E, Fernandez-Luna JL, Grubb AO, Leyva-Cobian F. Human protein HC and its IgA complex are inhibitors of neutrophil chemotaxis. Proc Natl Acad Sci USA 1986; 83: 1472-1475.
22. 1-microglobulin on T lymphocytes. Inhibition of antigen-induced interleukin-2 production. Scand J Immunol 1998; 48: 1-7.
23. 1-microglobulin. Trends Biochem Sci 1990; 15: 240-243.
24. 1-microglobulin: conservation of structure and chromophore. Biochim Biophys Acta 1999; 1430: 222-233.
25. 25. Escribano J, Lopez-Otin C, Hjerpe A, Grubb A, Mendez E. Location and characterization of the three carbohydrate prosthetic groups of human protein HC. FEBS Lett 1990; 266: 167-170.
26. 1-Microglobulin chromophores are located to three lysine residues semiburied in the lipocalin pocket and associated with a novel lipophilic compound. Protein Sci 1999; 8: 2611-2620.
27. 27. Grubb A, Mendez E, Fernandez-Luna JL, Lopez C, Mihaesco E, Vaerman J-P. The molecular organization of the protein HC-IgA complex (HC-IgA). J Biol Chem 1986; 261: 14313-14320.
28. 1-microglobulin in human plasma. Eur J Biochem 1997; 245: 676-683.
29. 2-macroglobulin homologue. J Biol Chem 1990; 265: 16150-16157.
30. 1-microglobulin complex in rat plasma. Isolation and characterization. Biochem J 1994; 301: 745-751.
31. 1-microglobulin and the inability to form a calcium-induced conformation. Biochem J 1995; 311: 753-759.
32. 1-microglobulin. Thromb Haemost 1996; 75: 70-75.
33. 33. Esmon CT, Gu JM, Xu J, Qu D, Stearns-Kurosawa DJ, Kurosawa S. Regulation and functions of the protein C anticoagulant pathway. Haematologica 1999; 84: 363-368.
34. 2+ ion and membrane binding structure of the Gla domain of Ca-prothrombin fragment 1. Biochemistry 1992; 31: 2554-2566.
35. 2+ binding to the first Egf domain. A combined NMR-small angle X-ray scattering study. Biochemistry 1996; 35: 11547-11559.
36. 36. Fischer D, Eisenbcrg D. Protein fold recognition using sequence-derived predictions. Protein Sci 1996; 5: 947-955.
37. 37. Bernstein FC, Koetzle TF, Williams GJB, Meyer EFJr, Brice MD, Rodgers JR, et al. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977; 112: 535-542.
38. 38. Ponder JW, Richards FM. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol 1987; 193: 775-791.
39. 39. Jones T, Thirup S. Using known substructures in protein model building and crystallography. EMBO J 1986; 5: 819-822.
40. 40. Hobohm U, Sander C. Enlarged representative set of protein structures. Protein Sci 1994; 3: 522-524.
41. 41. Villoutreix BO, Teleman O, Dahlbäck B. A theoretical model for the Gla-TSR-EGF-1 region of the anticoagulant cofactor protein S: from biostructural pathology to species-specific cofactor activity. J Comput Aided Mol Des 1997; 11: 293-304
42. 42. Mackay DHL, Cross AJ, Hagler AT. The role of energy minimization in simulation strategies of bio-molecular systems. In: Fasman GD (editor): Prediction of protein structure and the principles of protein conformation. New York: Plenum; 1989. pp. 317-358.
43. 43. Sharp KA, Honig B. Electrostatic interactions in macromolecules: theory and applications Annu Rev Biophys Chem 1990; 19: 301-332.
44. 44. Klapper I, Hagstrom R, Fine R, Sharp K, Honig B. Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification. Proteins 1986; 1: 47-59
45. 45. Lüthy R, Bowie JU, Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature 1992; 356: 83-85.
46. 46. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983; 22: 2577-2637.
47. 47. Greer J. Comparative modeling of homologous proteins. Methods Enzymol 1991; 202: 239-252.
48. 48. Branden CI, Tooze J. Introduction to protein structure, Second edition. Garland Publishing, New York; 1999. Chapter 17.
49. 49. Kochl P, Levitt M. A brighter future for protein structure prediction. Nat Struct Biol 1999; 6: 108-111.
50. 50. Russel RB, Saqi MAS, Bates PA, Sayle RA, Stenberg MJE. Recognition of analogous and homologous protein folds-assessment of prediction success and associated alignment accuracy using empirical substitution matrices. Prot Eng 1998; 11: 1-9.
51. 51. Martin ACR, MacArthur MW, Thornton JM. Assessment of comparative modeling in CASP2. Proteins 1997; Suppl 1: 14-28.
52. 52. Smith LJ, Redfield C, Smith RAG, Dobson CM, Clore GM, Gronenborn AM, et al. Comparison of four independently determined tructures of human recombinant interleukin-4. Nat Struct Biol 1994; 1: 301-310.
53. 53. Sali A. 100 000 protein structures for the biologist. Nat Struct Biol 1998; 5: 1029-1032.
54. 54. Villoutreix BO, Härdig Y, Wallqvist A, Covell DG, García de Frutos P, Dahlbäck B Structural investigation of human C4b-binding protein by molecular modeling: localization of putative binding sites. Proteins 1998; 31: 391-405.
55. 55. Villoutreix BO, Dahlbäck B. Molecular model for the lectin domain of human thrombomodulin. J Mol Model 1998; 4: 310-322.
56. 56. Villoutreix BO, Bucher P, Hofmann K, Baumgartner S, Dahlbäck B. Molecular models for the two discoidin domains of human blood coagulation factor V. J Mol Model 1998; 4: 268-275.
57. 57. Blom AM, Webb J, Villoutreix BO, Dahlbäck B. A cluster of positively charged amino acids in the C4BP alpha-chain is crucial for C4b binding and factor I cofactor function. J Biol Chem 1999; 274: 19237-19245.
58. 2+. Eur J Biochem 1999; 262: 522-533
59. 59. Nicolaes GA, Villoutreix BO, Dahlbäck B. Partial glycosylation of Asn2181 in human factor V as a cause of molecular and functional heterogeneity. Modulation of glycosylation efficiency by mutagenesis of the consensus sequence for N-linked glycosylation. Biochemistry 1999; 38: 13584-13591.
60. 60. Nicolaes GAF, Villoutreix BO, Dahlbäck B. Mutations in a potential phospholipid binding loop in the C2 domain of factor V affecting the assembly of the prothrombinase complex. Blood Coag Fibrinol 2000; 11:89-100.
61. 61. Pratt KP, Fujikawa K, Takeshima K, Davic EW, Stoddard BS. Crystal structure of the factor VIII C2 domain (abstract). Thromb Haemost 1999; Suppl: 234.
62. 62. Santa H, Saarela JTA, Laatikainen R, Rautianen J, Virtanen T, Rytkönen M, et al. A bovine dander allergen, comparative modeling and similarities and differences in folding with related proteins. J Prot Chem 1998; 17: 657-662.
63. 63. Rouvinen J, Rautiainen J, Virtanen T, Zeiler T, Kauppinen J, Taivaincn A, et al. Probing the molecular basis of allergy, three-dimensional structure of the bovine lipcalin allergen Bos d 2. J Biol Chem 1999; 274: 2337-2343.
64. 64. Smirnov MD, Safa O, Regan L, Mather T, Stearns-Kurosawa DJ, Kurosawa S, et al. A chimeric protein C containing the prothrombin Gla domain exhibits increased anticoagulant activity and altered phospholipid specificity. J Biol Chem 1998; 273: 9031-9040.
65. 65. Brandstetter H, Bauer M, Huber R, Lollar P, Bode W. X-ray structure of clotting factor IXa: active site and module structure related to Xase activity and hemophilia B. Proc Natl Acad Sci USA 1995; 92: 9796-9800.
66. 66. Sabharwal AK, Padmanabhan K, Tulinsky A, Mathur A, Gorka J, Bajaj SP. Interaction of calcium with native and decarboxylated human factor X. J Biol Chem 1997; 272: 22037-22045.
67. 67. Banner DW, D'Arcy A, Chene C, Winkler FK, Guha A, Konigsberg WH, et al. The crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor. Nature 1996; 380: 41-46.
68. 68. Bogan AA, Thorn KS. Anatomy of hot spots in protein interfaces. J Mol Biol 1998; 280: 1-9.
69. 69. Young L, Jernigan RL, Covell DG. A role for surface hydrophobicity in protein-protein recognition. Prot Sci 1994; 3: 717-729.
70. 70. Honig B, Nicholls A. Classical electrostatics in biology and chemistry. Science 1995; 268: 1144-1149.
71. 2-)-free Gla domain sheds light on membrane binding of blood coagulation proteins. Nat Struct Biol 1995; 2: 504-509.
72. 72. Bashford D. Electrostatic effects in biological molecules. Curr Opin Struct Biol 1991; 1: 175-184.
73. 73. Laberge M. Intrinsic protein electric fields: basic non-covalent interactions and relationship to protein-induced Stark effects. Biocbem Biophys Acta 1998; 1386: 305-330.
74. 74. Warwicker J. Improving pKa calculations with consideration of hydration entropy. Protein Eng 1997; 10: 809-814.
75. 75. Simonson T, Archontis G, Karplus M. A Poisson-Boltzmann study of charge insertion in an enzyme active site: the effect of dielectric relaxation. J Phy Chem 1999; 103: 6142-6156.
76. 76. McKay EJ, Laurell C-B. The interaction of heparin with plasma proteins. J Lab Clin Med 1980; 95: 69-80.
77. 77. Fromm JR, Hileman RE, Caldwell EE, Weiler JM, Linhardt RJ. Differences in the interaction of heparin with arginine and lysine and the importance of these basic amino acids in the binding of heparin to acidic fibroblast growth factor. Arch Biochem Biophys 1995; 323: 279-287.
78. 78. Nelsestuen GL, Ostrowski BG. Membrane association with multiple calcium ions: vitamin K-dependent proteins, annexins and pentraxins. Curr Opin Struct Biol 1999; 9: 433-437.
79. 79. Selzer T, Schreiber G. Predicting the rate enhancement of protein complex formation from the electrostatic energy of interaction. J Mol Biol 1999; 287: 409-419.
80. 80. Dill KA. Dominant forces in protein folding. Biochemistry 1990; 29: 7133-7155.
81. 81. Betts MJ, Sternberg MJE. An analysis of conformational changes on protein-protein association: implications for predictive docking. Prot Eng 1999; 12: 271-283.
82. 82. Janin J. Principles of protein-protein recognition from structure to thermodynamics. Biochimie 1995; 77: 497-505.
83. 83. Janin J. Elusive affinities. Proteins 1995; 21: 30-39.
84. 84. Mian IS, Bradwell AR, Olson AJ. Structure, function and properties of antibody binding sites. J Mol Biol 1991; 217: 133-151.
85. 85. Dougherty DA. Cation-pi interactions in chemistry and biology: a new view of benzene, Phe, Tyr and Trp. Science 1996; 271: 163-168.
86. 86. Yau W-M, Wimley WC, Gawrisch K, White SH. The preference of tryptophan for membrane interfaces. Biochemistry 1998; 37: 14713-14718.
87. 87. Richardson J. The anatomy and taxonomy of protein structure. Adv Prot Chem 1981; 34: 167-339.