Alpha-1-proteinase inhibitor is a heparin binding serpin: Molecular interactions with the Lys rich cluster of helix-F domain

Biochimie

Volumn 90, Issue 5, 2008, Pages 749-761

  Gupta, Vivek Kumar ^a   Gowda, Lalitha R ^a  

^a CENTRAL FOOD TECHNOLOGICAL RESEARCH INSTITUTE   (India)

Author keywords

Antithrombin; Association rate; Binding constant; Molecular docking; pH stability

Indexed keywords

ALPHA 1 ANTITRYPSIN; ANTITHROMBIN; ELASTASE; HEPARIN; LYSINE; SERINE PROTEINASE INHIBITOR;

AFFINITY CHROMATOGRAPHY; ARTICLE; CHEMICAL MODIFICATION; ENZYME ACTIVE SITE; ENZYME STABILITY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOLECULAR DOCKING; MOLECULAR WEIGHT; PH; PHYLOGENY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; SEQUENCE ANALYSIS; ZYMOGRAPHY;

ALGORITHMS; ALPHA 1-ANTITRYPSIN; AMINO ACID SEQUENCE; ANIMALS; CHROMATOGRAPHY, AFFINITY; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HEPARIN; HUMANS; HYDROGEN-ION CONCENTRATION; LYSINE; MOLECULAR SEQUENCE DATA; SEQUENCE HOMOLOGY, AMINO ACID; SERPINS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

MAMMALIA; OVIS; SUS;

EID: 42649132051     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2008.01.004     Document Type: Article

References (49)

1. Fagerhol M.K., and Cox D.W. The Pi polymorphism: genetic, biochemical and clinical aspects of human alpha-1-antitrypsin. Adv. Hum. Genet. 11 (1981) 1-62 371-372
2. Lisowska-Myjak B. AAT as a diagnostic tool. Clin. Chim. Acta. 352 (2005) 1-13
3. Gettins P.G.W. Serpin structure, mechanism and function. Chem. Rev. 102 (2002) 4751-4803
4. Olson S.T., and Bjork I. Predominant contribution of surface approximation to the mechanism of heparin acceleration of the antithrombin-thrombin reaction. J. Biol. Chem. 266 (1990) 6353-6364
5. Pike R.N., Buckle A.M., Le Bonniec B.F., and Church F.C. Control of the coagulation system by serpins. Getting with a little help from glycosaminoglycans. FEBS J. 272 (2005) 4842-4851
6. Linhardt R.J., and Gunay N.S. Production and chemical processing of low molecular weight heparins. Sem. Thromb. Hem. 3 (1999) 5-16
7. Guyton A.C., and Hall J.E. Textbook of Medical Physiology. eleventh ed (2006), Elsevier Saunders, USA 464
8. Frommherz K.J., Faller B., and Bieth J.G. Heparin strongly decreases the rate of inhibition of neutrophil elastase by alpha-1-proteinase inhibitor. J. Biol. Chem. 266 (1991) 15356-15362
9. Peterson B., Claudia M.N., Jill M.P., Frank C.C., and Michael N.B. Identification of a Lysyl residue in antithrombin, which is essential for heparin binding. J. Biol. Chem. 262 (1987) 8061-8065
10. Bjork I., and Nordenman B. Acceleration of the reaction between thrombin and antithrombin III by non-stoichiometric amounts of heparin. Eur. J. Biochem. 68 (1976) 507-511
11. Seegers W.H., Warner E.D., Brinkhous K.M., and Smith H.P. Heparin and the antithrombic activity of plasma. Science 96 (1942) 300-301
12. Jin L., Abrahams J.P., Skinner R., Petitous M., Pike R.N., and Carrell R.W. The anticoagulant activation of antithrombin by heparin. Proc. Natl. Acad. Sci. U.S.A. 94 (1997) 14683-14688
13. Kakade M.M., Simons N., and Leiner I.E. An evaluation of natural vs. synthetic substrates for measuring the antitryptic activity of soybean samples. Cereal Chem. 46 (1969) 518-526
14. Laemmeli U.K. Cleavage of structural proteins during the assembly of the head of Bacteriophage T4. Nature 227 (1970) 680
15. Bradford M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72 (1976) 248-254
16. Djie M.Z., Le Bonnie B.F., Hopkins P.C., Hipler K., and Stone S.R. Role of the P2 residue in determining the specificity of serpins. Biochemistry 35 (1996) 11461-11469
17. 2 terminal peptide segment of Myosin ATPase associated with ATP hydrolysis. J. Biol. Chem. 265 (1990) 18786-18790
18. Dixon H.B.F., and Perham R.N. Reversible blocking of amino groups with citraconic anhydride. Biochem. J. 109 (1968) 312-314
19. Carrell R.W., Stein P.E., Fermi G., and Wardell M.R. Biological implications of a 3 Å structure of dimeric antithrombin. Structure 2 (1994) 257-270
20. Higgins D.G., Thompson J.D., and Gidson T.J. Using CLUSTAL for multiple sequence alignments. Methods Enzymol. 266 (1996) 383-402
21. Higgins D., Thompson J., Gibson T., Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
22. Nicholas K.B., Nicholas Jr. H.B., and Deerfield D.W. GeneDoc: analysis and visualization of genetic variation. Embnew News 14 (1997)
23. Goodstadt L., and Ponting C.P. CHROMA: consensus-based coloring of multiple alignments for publication. Bioinformatics 17 (2001) 845-846
24. Kim S.J., Woo J.R., Seo E.J., Yu M.H., and Ryu S.E. A 2.1 Å resolution structure of an uncleaved α1-antitrypsin shows variability of the reactive centre and other loops. J. Mol. Biol. 306 (2001) 109-119
25. Schuettelkopf A.W., and van Aalten D.M.F. PRODRG- a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. D60 (2004) 1355-1363
26. Chang D.T., Oyang Y., and Lin J. MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm. Nucleic Acids Res. 33 (2005) W233-W238
27. Hyvarinen A., Karhunen J., and Oja E. Independent Component Analysis (2001), J. Wiley, New York
28. Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereo chemical quality of protein structures. J. Appl. Cryst. 26 (1993) 283-291
29. Vriend G. WHATIF: a molecular modeling and drug design program. J. Mol. Graph. 8 (1990) 52-56
30. Humphrey W., Dalke A., and Schulten K. VMD-visual molecular dynamics. J. Mol. Graph. 14 (1996) 33-38
31. Gettins P.G.W., Fan B., Crews B.C., Turko I.V., Olson S.T., and Streusand V.J. Transmission of conformational change from the heparin-binding site to the reactive center of antithrombin. Biochemistry 32 (1993) 8385-8389
32. Lundell N., and Schreitmuller T. Sample preparation for peptide mapping. A pharmaceutical quality control perspective. Anal. Biochem. 266 (1999) 31-47
33. Long G.L., Chandra T., Woo S.L.C., Davie E.W., and Kurachi K. Complete sequence of the cDNA for human alpha-1-antitrypsin and the gene for the S-variant. Biochemistry 23 (1984) 4828-4837
34. Chao S., Chai K.X., Chao L., and Chao J. Molecular cloning and primary structure of rat alpha-1-antitrypsin. Biochemistry 29 (1990) 323-329
35. Archibald A.L., Couper W.S., Mellink C.H.M., Lahbib M.Y., and Gellin J. Porcine alpha-1-antitrypsin (PI): cDNA sequence, polymorphism and assignment to chromosome 7q 2.4-q2.6. Anim. Genet. 27 (1996) 85-89
36. Brown W.M., Dziegielewska K.D., Foreman R.C., Saunders N.R., and Wu Y. Nucleotide and deduced amino acid sequence of sheep alpha 1-antitrypsin. Nucleic Acids Res. 17 (1989) 6398
37. Tersariol I.L., Pimenta D.C., Chagas J.R., and Almeida P.C. Proteinase activity regulation by glycosaminoglycans. Braz. J. Med. Biol. Res. 35 (2002) 135-144
38. Nader H.B., Lopes C.C., Rocha H.A., Santos E.A., and Dietrich C.P. Heparins and heparinoids: occurrence, structure and mechanism of antithrombotic and hemorrhagic activities. Curr. Pharm. Des. 10 (2004) 951-966
39. Kress L.F., and Catanese J.J. Identification of the cleavage sites resulting from enzymatic inactivation of human antithrombin III by Croatalus adamanteus proteinase II in the presence and absence of heparin. Biochemistry 20 (1981) 7432-7438
40. Olson S.T., Bjork I., Craig P.A., Shore J.D., and Choay J. Role of the antithrombin binding penta-saccharide in heparin acceleration of antithrombin-proteinase reactions. Resolution of the antithrombin conformational change contribution to heparin rate enhancement. J. Biol. Chem. 267 (1992) 12528-12538
41. Olson S.T., and Chuang Y.J. Heparin activates antithrombin anticoagulant function by generating new interaction sites (exosites) for blood clotting proteinases. Trends Cardiovasc. Med. 12 (2002) 331-338
42. Li W., Johnson D.J.D., Esmon C.T., and Huntington J.A. Structure of the antithrombin-thrombin-heparin ternary complex reveals the antithrombotic mechanism of heparin. Nat. Struct. Mol. Biol. 11 (2004) 857-862
43. Spencer J.L., Stone P.J., and Nugent M.A. New insights into the inhibition of human neutrophil elastase by heparin. Biochemistry 45 (2006) 9104-9120
44. Shirk R.A., Elisen G.L.M., Meijers J.C.M., and Church F.C. Role of the H-helix in heparin binding to protein C inhibitor. J. Biol. Chem. 269 (1994) 28690-28695
45. Blinder M.A., and Tollefsen D.M. Site directed mutagenesis of arginine 103 and lysine 185 in the proposed glycosaminoglycan binding site of heparin co-factor II. J. Biol. Chem. 265 (1990) 286-291
46. Carrell R.W. How serpins are shaping up. Science 285 (1999) 1861
47. Yamasaki M., Arii Y., Mikami B., and Hirose M. Loop inserted and thermostabilized structure of P1-P1′ cleaved ovalbumin mutant R339T. J. Mol. Biol. 315 (2002) 113-120
48. Cardin A.D., and Weintraub H.I.R. Molecular modeling of protein-glycosaminoglycan interactions. Arteriosclerosis 9 (1989) 21-32
49. Tjong S., Chen T., Huang W., and Wu W. Structure of heparin-derived tetrasaccharide bound to cobra cardiotoxins: heparin binding at a single protein site with diverse side chain interactions. Biochemistry 46 (2007) 9941-9952