1b3k Citations

The active conformation of plasminogen activator inhibitor 1, a target for drugs to control fibrinolysis and cell adhesion.

Abstract

Background

Plasminogen activator inhibitor 1 (PAI-1) is a serpin that has a key role in the control of fibrinolysis through proteinase inhibition. PAI-1 also has a role in regulating cell adhesion processes relevant to tissue remodeling and metastasis; this role is mediated by its binding to the adhesive glycoprotein vitronectin rather than by proteinase inhibition. Active PAI-1 is metastable and spontaneously transforms to an inactive latent conformation. Previous attempts to crystallize the active conformation of PAI-1 have failed.

Results

The crystal structure of a stable quadruple mutant of PAI-1(Asn150-->His, Lys154-->Thr, Gln319-->Leu, Met354-->Ile) in its active conformation has been solved at a nominal 3 A resolution. In two of four independent molecules within the crystal, the flexible reactive center loop is unconstrained by crystal-packing contacts and is disordered. In the other two molecules, the reactive center loop forms intimate loop-sheet interactions with neighboring molecules, generating an infinite chain within the crystal. The overall conformation resembles that seen for other active inhibitory serpins.

Conclusion

The structure clarifies the molecular basis of the stabilizing mutations and the reduced affinity of PAI-1, on cleavage or in the latent form, for vitronectin. The infinite chain of linked molecules also suggests a new mechanism for the serpin polymerization associated with certain diseases. The results support the concept that the reactive center loop of an active serpin is flexible and has no defined conformation in the absence of intermolecular contacts. The determination of the structure of the active form constitutes an essential step for the rational design of PAI-1 inhibitors.

Reviews - 1b3k mentioned but not cited (3)

  1. An overview of the serpin superfamily. Law RH, Zhang Q, McGowan S, Buckle AM, Silverman GA, Wong W, Rosado CJ, Langendorf CG, Pike RN, Bird PI, Whisstock JC. Genome Biol 7 216 (2006)
  2. Plasminogen Activator Inhibitor-1 in Cancer: Rationale and Insight for Future Therapeutic Testing. Placencio VR, DeClerck YA. Cancer Res 75 2969-2974 (2015)
  3. Targeting PAI-1 in Cardiovascular Disease: Structural Insights Into PAI-1 Functionality and Inhibition. Sillen M, Declerck PJ. Front Cardiovasc Med 7 622473 (2020)

Articles - 1b3k mentioned but not cited (11)

  1. Protein-protein docking benchmark version 4.0. Hwang H, Vreven T, Janin J, Weng Z. Proteins 78 3111-3114 (2010)
  2. Structural basis for recognition of urokinase-type plasminogen activator by plasminogen activator inhibitor-1. Lin Z, Jiang L, Yuan C, Jensen JK, Zhang X, Luo Z, Furie BC, Furie B, Andreasen PA, Huang M. J Biol Chem 286 7027-7032 (2011)
  3. Crystal Structure of the Michaelis Complex between Tissue-type Plasminogen Activator and Plasminogen Activators Inhibitor-1. Gong L, Liu M, Zeng T, Shi X, Yuan C, Andreasen PA, Huang M. J Biol Chem 290 25795-25804 (2015)
  4. Extending the capabilities of targeted molecular dynamics: simulation of a large conformational transition in plasminogen activator inhibitor 1. Krüger P, Verheyden S, Declerck PJ, Engelborghs Y. Protein Sci 10 798-808 (2001)
  5. Modeling of loops in proteins: a multi-method approach. Jamroz M, Kolinski A. BMC Struct Biol 10 5 (2010)
  6. Structural differences between active forms of plasminogen activator inhibitor type 1 revealed by conformationally sensitive ligands. Li SH, Gorlatova NV, Lawrence DA, Schwartz BS. J Biol Chem 283 18147-18157 (2008)
  7. Heparin Binds Lamprey Angiotensinogen and Promotes Thrombin Inhibition through a Template Mechanism. Wei H, Cai H, Wu J, Wei Z, Zhang F, Huang X, Ma L, Feng L, Zhang R, Wang Y, Ragg H, Zheng Y, Zhou A. J Biol Chem 291 24900-24911 (2016)
  8. Specific interactions of serpins in their native forms attenuate their conformational transitions. Na YR, Im H. Protein Sci 16 1659-1666 (2007)
  9. An In Silico Approach towards the Prediction of Druglikeness Properties of Inhibitors of Plasminogen Activator Inhibitor1. Subramanian U, Sivapunniyam A, Pudukadu Munusamy A, Sundaram R. Adv Bioinformatics 2014 385418 (2014)
  10. 1.45 Å resolution structure of SRPN18 from the malaria vector Anopheles gambiae. Meekins DA, Zhang X, Battaile KP, Lovell S, Michel K. Acta Crystallogr F Struct Biol Commun 72 853-862 (2016)
  11. The Importance of N186 in the Alpha-1-Antitrypsin Shutter Region Is Revealed by the Novel Bologna Deficiency Variant. Ronzoni R, Ferrarotti I, D'Acunto E, Balderacchi AM, Ottaviani S, Lomas DA, Irving JA, Miranda E, Fra A. Int J Mol Sci 22 5668 (2021)


Reviews citing this publication (9)

  1. Serpins in thrombosis, hemostasis and fibrinolysis. Rau JC, Beaulieu LM, Huntington JA, Church FC. J Thromb Haemost 5 Suppl 1 102-115 (2007)
  2. Conformational pathology of the serpins: themes, variations, and therapeutic strategies. Gooptu B, Lomas DA. Annu Rev Biochem 78 147-176 (2009)
  3. The molecular basis for anti-proteolytic and non-proteolytic functions of plasminogen activator inhibitor type-1: roles of the reactive centre loop, the shutter region, the flexible joint region and the small serpin fragment. Wind T, Hansen M, Jensen JK, Andreasen PA. Biol Chem 383 21-36 (2002)
  4. Unravelling the twists and turns of the serpinopathies. Roussel BD, Irving JA, Ekeowa UI, Belorgey D, Haq I, Ordóñez A, Kruppa AJ, Duvoix A, Rashid ST, Crowther DC, Marciniak SJ, Lomas DA. FEBS J 278 3859-3867 (2011)
  5. Old dogs and new tricks: proteases, inhibitors, and cell migration. Stefansson S, Lawrence DA. Sci STKE 2003 pe24 (2003)
  6. Serpin polymerization and its role in disease--the molecular basis of alpha1-antitrypsin deficiency. Knaupp AS, Bottomley SP. IUBMB Life 61 1-5 (2009)
  7. Twenty years of polymers: a personal perspective on alpha-1 antitrypsin deficiency. Lomas DA. COPD 10 Suppl 1 17-25 (2013)
  8. Bugs in the system. Menachery VD, Baric RS. Immunol Rev 255 256-274 (2013)
  9. Serpin crystal structure and serpin polymer structure. Marszal E, Shrake A. Arch Biochem Biophys 453 123-129 (2006)

Articles citing this publication (56)

  1. How vitronectin binds PAI-1 to modulate fibrinolysis and cell migration. Zhou A, Huntington JA, Pannu NS, Carrell RW, Read RJ. Nat Struct Biol 10 541-544 (2003)
  2. Crystal structures of native and thrombin-complexed heparin cofactor II reveal a multistep allosteric mechanism. Baglin TP, Carrell RW, Church FC, Esmon CT, Huntington JA. Proc Natl Acad Sci U S A 99 11079-11084 (2002)
  3. Topography of a 2.0 A structure of alpha1-antitrypsin reveals targets for rational drug design to prevent conformational disease. Elliott PR, Pei XY, Dafforn TR, Lomas DA. Protein Sci 9 1274-1281 (2000)
  4. Plasminogen activator inhibitor 1. Structure of the native serpin, comparison to its other conformers and implications for serpin inactivation. Nar H, Bauer M, Stassen JM, Lang D, Gils A, Declerck PJ. J Mol Biol 297 683-695 (2000)
  5. Serpin Inhibition Mechanism: A Delicate Balance between Native Metastable State and Polymerization. Khan MS, Singh P, Azhar A, Naseem A, Rashid Q, Kabir MA, Jairajpuri MA. J Amino Acids 2011 606797 (2011)
  6. Localization of epitopes for monoclonal antibodies to urokinase-type plasminogen activator: relationship between epitope localization and effects of antibodies on molecular interactions of the enzyme. Petersen HH, Hansen M, Schousboe SL, Andreasen PA. Eur J Biochem 268 4430-4439 (2001)
  7. Differential detection of PAS-positive inclusions formed by the Z, Siiyama, and Mmalton variants of alpha1-antitrypsin. Janciauskiene S, Eriksson S, Callea F, Mallya M, Zhou A, Seyama K, Hata S, Lomas DA. Hepatology 40 1203-1210 (2004)
  8. The vitronectin binding area of plasminogen activator inhibitor-1, mapped by mutagenesis and protection against an inactivating organochemical ligand. Jensen JK, Wind T, Andreasen PA. FEBS Lett 521 91-94 (2002)
  9. Importance of the amino-acid composition of the shutter region of plasminogen activator inhibitor-1 for its transitions to latent and substrate forms. Hansen M, Busse MN, Andreasen PA. Eur J Biochem 268 6274-6283 (2001)
  10. The 2.1-A crystal structure of native neuroserpin reveals unique structural elements that contribute to conformational instability. Takehara S, Onda M, Zhang J, Nishiyama M, Yang X, Mikami B, Lomas DA. J Mol Biol 388 11-20 (2009)
  11. Interaction of plasminogen activator inhibitor type-1 (PAI-1) with vitronectin. Arroyo De Prada N, Schroeck F, Sinner EK, Muehlenweg B, Twellmeyer J, Sperl S, Wilhelm OG, Schmitt M, Magdolen V. Eur J Biochem 269 184-192 (2002)
  12. Structural insight into inactivation of plasminogen activator inhibitor-1 by a small-molecule antagonist. Lin Z, Jensen JK, Hong Z, Shi X, Hu L, Andreasen PA, Huang M. Chem Biol 20 253-261 (2013)
  13. The reactive-center loop of active PAI-1 is folded close to the protein core and can be partially inserted. Hägglöf P, Bergström F, Wilczynska M, Johansson LB, Ny T. J Mol Biol 335 823-832 (2004)
  14. Characterization of a small molecule PAI-1 inhibitor, ZK4044. Liang A, Wu F, Tran K, Jones SW, Deng G, Ye B, Zhao Z, Snider RM, Dole WP, Morser J, Wu Q. Thromb Res 115 341-350 (2005)
  15. Mechanisms of conversion of plasminogen activator inhibitor 1 from a suicide inhibitor to a substrate by monoclonal antibodies. Komissarov AA, Declerck PJ, Shore JD. J Biol Chem 277 43858-43865 (2002)
  16. The structural basis of serpin polymerization studied by hydrogen/deuterium exchange and mass spectrometry. Tsutsui Y, Kuri B, Sengupta T, Wintrode PL. J Biol Chem 283 30804-30811 (2008)
  17. Crystal structure of plasminogen activator inhibitor-1 in an active conformation with normal thermodynamic stability. Jensen JK, Thompson LC, Bucci JC, Nissen P, Gettins PG, Peterson CB, Andreasen PA, Morth JP. J Biol Chem 286 29709-29717 (2011)
  18. Biochemical mechanism of action of a diketopiperazine inactivator of plasminogen activator inhibitor-1. Einholm AP, Pedersen KE, Wind T, Kulig P, Overgaard MT, Jensen JK, Bødker JS, Christensen A, Charlton P, Andreasen PA. Biochem J 373 723-732 (2003)
  19. Intrinsic fluorescence changes and rapid kinetics of proteinase deformation during serpin inhibition. Tew DJ, Bottomley SP. FEBS Lett 494 30-33 (2001)
  20. Mechanistic characterization and crystal structure of a small molecule inactivator bound to plasminogen activator inhibitor-1. Li SH, Reinke AA, Sanders KL, Emal CD, Whisstock JC, Stuckey JA, Lawrence DA. Proc Natl Acad Sci U S A 110 E4941-9 (2013)
  21. Structural dynamics associated with intermediate formation in an archetypal conformational disease. Nyon MP, Segu L, Cabrita LD, Lévy GR, Kirkpatrick J, Roussel BD, Patschull AO, Barrett TE, Ekeowa UI, Kerr R, Waudby CA, Kalsheker N, Hill M, Thalassinos K, Lomas DA, Christodoulou J, Gooptu B. Structure 20 504-512 (2012)
  22. Characterization of a site on PAI-1 that binds to vitronectin outside of the somatomedin B domain. Schar CR, Jensen JK, Christensen A, Blouse GE, Andreasen PA, Peterson CB. J Biol Chem 283 28487-28496 (2008)
  23. Protein conformational change delayed by steric hindrance from an N-linked glycan. Bager R, Johansen JS, Jensen JK, Stensballe A, Jendroszek A, Buxbom L, Sørensen HP, Andreasen PA. J Mol Biol 425 2867-2877 (2013)
  24. Mutational analysis of plasminogen activator inhibitor-1. Wind T, Jensen JK, Dupont DM, Kulig P, Andreasen PA. Eur J Biochem 270 1680-1688 (2003)
  25. Novel inhibitors of plasminogen activator inhibitor-1: development of new templates from diketopiperazines. Wang S, Golec J, Miller W, Milutinovic S, Folkes A, Williams S, Brooks T, Hardman K, Charlton P, Wren S, Spencer J. Bioorg Med Chem Lett 12 2367-2370 (2002)
  26. Local transient unfolding of native state PAI-1 associated with serpin metastability. Trelle MB, Madsen JB, Andreasen PA, Jørgensen TJ. Angew Chem Int Ed Engl 53 9751-9754 (2014)
  27. Binding areas of urokinase-type plasminogen activator-plasminogen activator inhibitor-1 complex for endocytosis receptors of the low-density lipoprotein receptor family, determined by site-directed mutagenesis. Skeldal S, Larsen JV, Pedersen KE, Petersen HH, Egelund R, Christensen A, Jensen JK, Gliemann J, Andreasen PA. FEBS J 273 5143-5159 (2006)
  28. Characterising the association of latency with α(1)-antitrypsin polymerisation using a novel monoclonal antibody. Tan L, Perez J, Mela M, Miranda E, Burling KA, Rouhani FN, DeMeo DL, Haq I, Irving JA, Ordóñez A, Dickens JA, Brantly M, Marciniak SJ, Alexander GJ, Gooptu B, Lomas DA. Int J Biochem Cell Biol 58 81-91 (2015)
  29. Metals affect the structure and activity of human plasminogen activator inhibitor-1. I. Modulation of stability and protease inhibition. Thompson LC, Goswami S, Ginsberg DS, Day DE, Verhamme IM, Peterson CB. Protein Sci 20 353-365 (2011)
  30. Additivity in effects of vitronectin and monoclonal antibodies against alpha-helix F of plasminogen activator inhibitor-1 on its reactions with target proteinases. Komissarov AA, Andreasen PA, Bødker JS, Declerck PJ, Anagli JY, Shore JD. J Biol Chem 280 1482-1489 (2005)
  31. Identification of the disulfide bonds in the recombinant somatomedin B domain of human vitronectin. Kamikubo Y, Okumura Y, Loskutoff DJ. J Biol Chem 277 27109-27119 (2002)
  32. Plasminogen activator inhibitor-1 polymers, induced by inactivating amphipathic organochemical ligands. Pedersen KE, Einholm AP, Christensen A, Schack L, Wind T, Kenney JM, Andreasen PA. Biochem J 372 747-755 (2003)
  33. A structural basis for loop C-sheet polymerization in serpins. Zhang Q, Law RH, Bottomley SP, Whisstock JC, Buckle AM. J Mol Biol 376 1348-1359 (2008)
  34. Two latent and two hyperstable polymeric forms of human neuroserpin. Ricagno S, Pezzullo M, Barbiroli A, Manno M, Levantino M, Santangelo MG, Bonomi F, Bolognesi M. Biophys J 99 3402-3411 (2010)
  35. Intrahepatic heteropolymerization of M and Z alpha-1-antitrypsin. Laffranchi M, Elliston EL, Miranda E, Perez J, Ronzoni R, Jagger AM, Heyer-Chauhan N, Brantly ML, Fra A, Lomas DA, Irving JA. JCI Insight 5 135459 (2020)
  36. Discovery and characterisation of an antibody that selectively modulates the inhibitory activity of plasminogen activator inhibitor-1. Vousden KA, Lundqvist T, Popovic B, Naiman B, Carruthers AM, Newton P, Johnson DJD, Pomowski A, Wilkinson T, Dufner P, de Mendez I, Mallinder PR, Murray C, Strain M, Connor J, Murray LA, Sleeman MA, Lowe DC, Huntington JA, Vaughan TJ. Sci Rep 9 1605 (2019)
  37. High-affinity binding of plasminogen-activator inhibitor 1 complexes to LDL receptor-related protein 1 requires lysines 80, 88, and 207. Migliorini M, Li SH, Zhou A, Emal CD, Lawrence DA, Strickland DK. J Biol Chem 295 212-222 (2020)
  38. Metals affect the structure and activity of human plasminogen activator inhibitor-1. II. Binding affinity and conformational changes. Thompson LC, Goswami S, Peterson CB. Protein Sci 20 366-378 (2011)
  39. Purification of recombinant plasminogen activator inhibitor-1 in the active conformation by refolding from inclusion bodies. Lee HJ, Im H. Protein Expr Purif 31 99-107 (2003)
  40. E. coli trp repressor forms a domain-swapped array in aqueous alcohol. Lawson CL, Benoff B, Berger T, Berman HM, Carey J. Structure 12 1099-1108 (2004)
  41. High quality structure of cleaved PAI-1-stab. Dewilde M, Strelkov SV, Rabijns A, Declerck PJ. J Struct Biol 165 126-132 (2009)
  42. Molecular bases of neuroserpin function and pathology. Caccia S, Ricagno S, Bolognesi M. Biomol Concepts 1 117-130 (2010)
  43. Study of recombinant antibody fragments and PAI-1 complexes combining protein-protein docking and results from site-directed mutagenesis. Novoa de Armas H, Dewilde M, Verbeke K, De Maeyer M, Declerck PJ. Structure 15 1105-1116 (2007)
  44. Comparison between the clot-protecting activity of a mutant plasminogen activator inhibitor-1 with a very long half-life and 6-aminocaproic acid. Kindell DG, Keck RW, Jankun J. Exp Ther Med 9 2339-2343 (2015)
  45. The loss of tryptophan 194 in antichymotrypsin lowers the kinetic barrier to misfolding. Pearce MC, Cabrita LD, Ellisdon AM, Bottomley SP. FEBS J 274 3622-3632 (2007)
  46. The pH sensitivity of murine heat shock protein 47 (HSP47) binding to collagen is affected by mutations in the breach histidine cluster. Abdul-Wahab MF, Homma T, Wright M, Olerenshaw D, Dafforn TR, Nagata K, Miller AD. J Biol Chem 288 4452-4461 (2013)
  47. Collapse of a long axis: single-molecule Förster resonance energy transfer and serpin equilibrium unfolding. Liu L, Werner M, Gershenson A. Biochemistry 53 2903-2914 (2014)
  48. Conjugation of polymers to proteins through an inhibitor-derived peptide: taking up the inhibitor "berth". Tang Z, Li D, Luan Y, Zhu L, Du H, Tao Y, Wang Y, Haddleton DM, Chen H. Chem Commun (Camb) 51 10099-10102 (2015)
  49. Distinct encounter complexes of PAI-1 with plasminogen activators and vitronectin revealed by changes in the conformation and dynamics of the reactive center loop. Qureshi T, Goswami S, McClintock CS, Ramsey MT, Peterson CB. Protein Sci 25 499-510 (2016)
  50. Polymerization of human angiotensinogen: insights into its structural mechanism and functional significance. Stanley P, Serpell LC, Stein PE. Biochem J 400 169-178 (2006)
  51. Probing nanosecond motions of plasminogen activator inhibitor-1 by time-resolved fluorescence anisotropy. Ko CW, Wei Z, Marsh RJ, Armoogum DA, Nicolaou N, Bain AJ, Zhou A, Ying L. Mol Biosyst 5 1025-1031 (2009)
  52. PAI-1 is a potential transcriptional silencer that supports bladder cancer cell activity. Furuya H, Sasaki Y, Chen R, Peres R, Hokutan K, Murakami K, Kim N, Chan OTM, Pagano I, Dyrskjøt L, Jensen JB, Malmstrom PU, Segersten U, Sun Y, Arab A, Goodarzi H, Goodison S, Rosser CJ. Sci Rep 12 12186 (2022)
  53. Dissecting molecular details and functional effects of the high-affinity copper binding site in plasminogen activator Inhibitor-1. Chu Y, Bucci JC, Peterson CB. Protein Sci 30 597-612 (2021)
  54. Distal hinge of plasminogen activator inhibitor-1 involves its latency transition and specificities toward serine proteases. Wang Q, Shaltiel S. BMC Biochem 4 5 (2003)
  55. Crystal structure of cleaved vaspin (serpinA12). Pippel J, Kuettner EB, Ulbricht D, Daberger J, Schultz S, Heiker JT, Sträter N. Biol Chem 397 111-123 (2016)
  56. Enthalpy measurement using calorimetry shows a significant difference in potential energy between the active and latent conformations of PAI-1. Sherman WA, Blouse GE, Perron MJ, Tran T, Shore JD, Gafni A. Biol Chem 386 111-116 (2005)