Ingrid M. Verhamme, Ph.D.

Research Associate Professor

ingrid.verhamme@vanderbilt.edu
Faculty Appointments
Research Associate Professor of Pathology, Microbiology and Immunology
Education
Ph.D., Biochemistry, Universiteit Gent, Ghent, BelgiumM.S., Pharmacy, Universiteit Gent, Ghent, BelgiumB.S., Pharmacy, Universiteit Gent, Ghent, Belgium
Office Address
C3321A Medical Center North
Nashville, TN 37232
Research Description
Our mechanism-based studies involve inactivation of the central clotting protease, thrombin, by the serine proteinase inhibitors (SERPINs) heparin cofactor II (HCII), antithrombin (AT) and plasminogen activator inhibitor-1 (PAI-1). These irreversible inactivation reactions are selectively accelerated by glycosaminoglycans (GAGs) such as heparin, dermatan sulfate, heparan sulfate, and in the case of PAI-1, also by vitronectin. Regulation of these reactions is important in controlling thrombosis and reocclusion.
Thrombin localized on fibrin, and on the cell surface GAGs reacts mainly with HCII and platelet PAI-1 at the injury site, in GAG-accelerated mechanisms different from AT. Subendothelial dermatan sulfate selectively enhances covalent T-HCII formation. Only HCII, in the presence of dermatan sulfate, inhibits fibrin-bound thrombin, by an unknown mechanism, and HCII has been identified as an important inhibitor of arterial thrombosis.
Thrombin possesses two Arg- and Lys-rich exosites, I and II. Exosite I is thought to bind HCII and PAI-1 directly, whereas exosite II - heparin interactions may modulate HCII and PAI-1 turnover as thrombin substrates. These mechanism steps are absent in the thrombin - AT reaction. PAI-1 stabilizes arterial thrombi, but paradoxically, may also promote embolization after atherosclerotic plaque rupture. Selective PAI-1 inhibitory vs. substrate activity toward localized thrombin may be a regulatory mechanism for modulating thrombin activity in arterial clots.

Our lab studies the mechanisms important in thrombin localization, inhibitory and substrate serpin recognition, and the mechanisms by which GAGs act as molecular switches for inhibiting or promoting serpin-mediated inactivation of fibrin-bound thrombin. In collaborative studies, we recently expanded our interests to factor XIa and XIIa interactions with AT and PAI-1, and to serpin-independent anticoagulant and profibrinolytic effects of GAGs, at the level of inhibition of prothrombinase activity, and enhancement of plasminogen activation by tPA and uPA.

Rapid and steady-state kinetics, and equilibrium binding with native and mutant proteins are used to characterize enzyme inactivation, serpin substrate pathway modulation, preferred pathways of productive complex formation, and regulation by fibrinogen and fibrin. These techniques allow quantitation of protein-protein and protein-GAG affinities, and conformational and chemical reaction steps. The combined approaches are aimed at quantitating the HCII and PAI-1 mechanisms of thrombin interaction in the presence of GAGs, and the effect of fibrin on these mechanisms. The goal of these studies is to understand differential HCII and PAI-1 regulation of clot-localized, thrombin-dependent processes in arterial thrombosis and reocclusion.
Research Keywords
Regulation of blood coagulation proteolytic enzymes
Publications
Mohammed BM, Matafonov A, Ivanov I, Sun MF, Cheng Q, Dickeson SK, Li C, Sun D, Verhamme IM, Emsley J, Gailani D. An update on factor XI structure and function. Thromb. Res [print-electronic]. 2018 Jan; 161: 94-105. PMID: 29223926, PMCID: PMC5776729, PII: S0049-3848(17)30524-8, DOI: 10.1016/j.thromres.2017.10.008, ISSN: 1879-2472.

Mohammed BM, Matafonov A, Ivanov I, Sun MF, Cheng Q, Dickeson SK, Li C, Sun D, Verhamme IM, Emsley J, Gailani D. An update on factor XI structure and function. Thromb. Res [print-electronic]. 2018 Jan; 161: 94-105. PMID: 29223926, PMCID: PMC5776729, PII: S0049-3848(17)30524-8, DOI: 10.1016/j.thromres.2017.10.008, ISSN: 1879-2472.

Verhamme IM. A novel antithrombin domain dictates the journey's end of a proteinase. J. Biol. Chem. 2017 Oct 10/6/2017; 292(40): 16521-2. PMID: 28986431, PMCID: PMC5633113, PII: 292/40/16521, DOI: 10.1074/jbc.H117.787325, ISSN: 1083-351X.

Verhamme IM. A novel antithrombin domain dictates the journey's end of a proteinase. J. Biol. Chem. 2017 Oct 10/6/2017; 292(40): 16521-2. PMID: 28986431, PMCID: PMC5633113, PII: 292/40/16521, DOI: 10.1074/jbc.H117.787325, ISSN: 1083-351X.

Woodruff RS, Ivanov I, Verhamme IM, Sun MF, Gailani D, Sullenger BA. Generation and characterization of aptamers targeting factor XIa. Thromb. Res [print-electronic]. 2017 Aug; 156: 134-41. PMID: 28644959, PMCID: PMC5697752, PII: S0049-3848(17)30379-1, DOI: 10.1016/j.thromres.2017.06.015, ISSN: 1879-2472.

Woodruff RS, Ivanov I, Verhamme IM, Sun MF, Gailani D, Sullenger BA. Generation and characterization of aptamers targeting factor XIa. Thromb. Res [print-electronic]. 2017 Aug; 156: 134-41. PMID: 28644959, PMCID: PMC5697752, PII: S0049-3848(17)30379-1, DOI: 10.1016/j.thromres.2017.06.015, ISSN: 1879-2472.

Ivanov I, Matafonov A, Sun MF, Cheng Q, Dickeson SK, Verhamme IM, Emsley J, Gailani D. Proteolytic properties of single-chain factor XII: a mechanism for triggering contact activation. Blood [print-electronic]. 2017 Mar 3/16/2017; 129(11): 1527-37. PMID: 28069606, PMCID: PMC5356457, PII: blood-2016-10-744110, DOI: 10.1182/blood-2016-10-744110, ISSN: 1528-0020.

Ivanov I, Matafonov A, Sun MF, Cheng Q, Dickeson SK, Verhamme IM, Emsley J, Gailani D. Proteolytic properties of single-chain factor XII: a mechanism for triggering contact activation. Blood [print-electronic]. 2017 Mar 3/16/2017; 129(11): 1527-37. PMID: 28069606, PMCID: PMC5356457, PII: blood-2016-10-744110, DOI: 10.1182/blood-2016-10-744110, ISSN: 1528-0020.

Verhamme IM, Panizzi PR, Bock PE. Pathogen activators of plasminogen. J. Thromb. Haemost. 2015 Jun; 13 Suppl 1: S106-14. PMID: 26149011, PMCID: PMC4498406, DOI: 10.1111/jth.12939, ISSN: 1538-7836.

Jacobson R, Mignemi N, Rose K, O'Rear L, Sarilla S, Hamm HE, Barnett JV, Verhamme IM, Schoenecker J. The hyperglycemic byproduct methylglyoxal impairs anticoagulant activity through covalent adduction of antithrombin III. Thromb. Res [print-electronic]. 2014 Dec; 134(6): 1350-7. PMID: 25307422, PMCID: PMC4337957, PII: S0049-3848(14)00523-4, DOI: 10.1016/j.thromres.2014.09.038, ISSN: 1879-2472.

Verhamme IM, Bock PE. Rapid binding of plasminogen to streptokinase in a catalytic complex reveals a three-step mechanism. J. Biol. Chem [print-electronic]. 2014 Oct 10/3/2014; 289(40): 28006-18. PMID: 25138220, PMCID: PMC4183831, PII: M114.589077, DOI: 10.1074/jbc.M114.589077, ISSN: 1083-351X.

Gailani D, Geng Y, Verhamme I, Sun MF, Bajaj SP, Messer A, Emsley J. The mechanism underlying activation of factor IX by factor XIa. Thromb. Res. 2014 May; 133 Suppl 1: S48-51. PMID: 24759143, PMCID: PMC4017667, PII: S0049-3848(14)00145-5, DOI: 10.1016/j.thromres.2014.03.020, ISSN: 1879-2472.

Matafonov A, Cheng Q, Geng Y, Verhamme IM, Umunakwe O, Tucker EI, Sun MF, Serebrov V, Gruber A, Gailani D. Evidence for factor IX-independent roles for factor XIa in blood coagulation. J. Thromb. Haemost. 2013 Dec; 11(12): 2118-27. PMID: 24152424, PMCID: PMC3947433, DOI: 10.1111/jth.12435, ISSN: 1538-7836.

Geng Y, Verhamme IM, Smith SA, Cheng Q, Sun M, Sheehan JP, Morrissey JH, Gailani D. Factor XI anion-binding sites are required for productive interactions with polyphosphate. J. Thromb. Haemost. 2013 Nov; 11(11): 2020-8. PMID: 24118982, PMCID: PMC3865764, DOI: 10.1111/jth.12414, ISSN: 1538-7836.

Geng Y, Verhamme IM, Sun MF, Bajaj SP, Emsley J, Gailani D. Analysis of the factor XI variant Arg184Gly suggests a structural basis for factor IX binding to factor XIa. J. Thromb. Haemost. 2013 Jul; 11(7): 1374-84. PMID: 23617568, PMCID: PMC4158700, DOI: 10.1111/jth.12275, ISSN: 1538-7836.

Geng Y, Verhamme IM, Smith SB, Sun MF, Matafonov A, Cheng Q, Smith SA, Morrissey JH, Gailani D. The dimeric structure of factor XI and zymogen activation. Blood [print-electronic]. 2013 May 5/9/2013; 121(19): 3962-9. PMID: 23515926, PMCID: PMC3650707, PII: blood-2012-12-473629, DOI: 10.1182/blood-2012-12-473629, ISSN: 1528-0020.

Geng Y, Verhamme IM, Messer A, Sun MF, Smith SB, Bajaj SP, Gailani D. A sequential mechanism for exosite-mediated factor IX activation by factor XIa. J. Biol. Chem [print-electronic]. 2012 Nov 11/2/2012; 287(45): 38200-9. PMID: 22961984, PMCID: PMC3488089, PII: M112.376343, DOI: 10.1074/jbc.M112.376343, ISSN: 1083-351X.

Verhamme IM. Fluorescent reporters of thrombin, heparin cofactor II, and heparin binding in a ternary complex. Anal. Biochem [print-electronic]. 2012 Feb 2/15/2012; 421(2): 489-98. PMID: 22206940, PMCID: PMC3461310, PII: S0003-2697(11)00753-6, DOI: 10.1016/j.ab.2011.11.021, ISSN: 1096-0309.

Matafonov A, Sarilla S, Sun MF, Sheehan JP, Serebrov V, Verhamme IM, Gailani D. Activation of factor XI by products of prothrombin activation. Blood [print-electronic]. 2011 Jul 7/14/2011; 118(2): 437-45. PMID: 21527525, PMCID: PMC3138693, PII: blood-2010-10-312983, DOI: 10.1182/blood-2010-10-312983, ISSN: 1528-0020.

Sarilla S, Habib SY, Tollefsen DM, Friedman DB, Arnett DR, Verhamme IM. Glycosaminoglycan-binding properties and kinetic characterization of human heparin cofactor II expressed in Escherichia coli. Anal. Biochem [print-electronic]. 2010 Nov 11/15/2010; 406(2): 166-75. PMID: 20670608, PMCID: PMC2952836, PII: S0003-2697(10)00470-7, DOI: 10.1016/j.ab.2010.07.024, ISSN: 1096-0309.

Sarilla S, Habib SY, Kravtsov DV, Matafonov A, Gailani D, Verhamme IM. Sucrose octasulfate selectively accelerates thrombin inactivation by heparin cofactor II. J. Biol. Chem [print-electronic]. 2010 Mar 3/12/2010; 285(11): 8278-89. PMID: 20053992, PMCID: PMC2832979, PII: M109.005967, DOI: 10.1074/jbc.M109.005967, ISSN: 1083-351X.

Verhamme IM, Bock PE. Rapid-reaction kinetic characterization of the pathway of streptokinase-plasmin catalytic complex formation. J. Biol. Chem [print-electronic]. 2008 Sep 9/19/2008; 283(38): 26137-47. PMID: 18658146, PMCID: PMC2533780, PII: M804038200, DOI: 10.1074/jbc.M804038200, ISSN: 0021-9258.

Smith SB, Verhamme IM, Sun MF, Bock PE, Gailani D. Characterization of Novel Forms of Coagulation Factor XIa: independence of factor XIa subunits in factor IX activation. J. Biol. Chem [print-electronic]. 2008 Mar 3/14/2008; 283(11): 6696-705. PMID: 18192270, PMCID: PMC2633474, PII: M707234200, DOI: 10.1074/jbc.M707234200, ISSN: 0021-9258.

Bock PE, Panizzi P, Verhamme IM. Exosites in the substrate specificity of blood coagulation reactions. J. Thromb. Haemost. 2007 Jul; 5 Suppl 1: 81-94. PMID: 17635714, PMCID: PMC2291348, PII: JTH2496, DOI: 10.1111/j.1538-7836.2007.02496.x, ISSN: 1538-7933.

Panizzi P, Boxrud PD, Verhamme IM, Bock PE. Binding of the COOH-terminal lysine residue of streptokinase to plasmin(ogen) kringles enhances formation of the streptokinase.plasmin(ogen) catalytic complexes. J. Biol. Chem [print-electronic]. 2006 Sep 9/15/2006; 281(37): 26774-8. PMID: 16857686, PMCID: PMC2291350, PII: C600171200, DOI: 10.1074/jbc.C600171200, ISSN: 0021-9258.

Ogawa T, Verhamme IM, Sun MF, Bock PE, Gailani D. Exosite-mediated substrate recognition of factor IX by factor XIa. The factor XIa heavy chain is required for initial recognition of factor IX. J. Biol. Chem [print-electronic]. 2005 Jun 6/24/2005; 280(25): 23523-30. PMID: 15829482, PMCID: PMC2292466, PII: M500894200, DOI: 10.1074/jbc.M500894200, ISSN: 0021-9258.

Bean RR, Verhamme IM, Bock PE. Role of the streptokinase alpha-domain in the interactions of streptokinase with plasminogen and plasmin. J. Biol. Chem [print-electronic]. 2005 Mar 3/4/2005; 280(9): 7504-10. PMID: 15623524, PMCID: PMC2292463, PII: M411637200, DOI: 10.1074/jbc.M411637200, ISSN: 0021-9258.

Boxrud PD, Verhamme IM, Bock PE. Resolution of conformational activation in the kinetic mechanism of plasminogen activation by streptokinase. J. Biol. Chem [print-electronic]. 2004 Aug 8/27/2004; 279(35): 36633-41. PMID: 15215240, PII: M405264200, DOI: 10.1074/jbc.M405264200, ISSN: 0021-9258.

Verhamme IM, Bock PE, Jackson CM. The preferred pathway of glycosaminoglycan-accelerated inactivation of thrombin by heparin cofactor II. J. Biol. Chem [print-electronic]. 2004 Mar 3/12/2004; 279(11): 9785-95. PMID: 14701814, PII: M313962200, DOI: 10.1074/jbc.M313962200, ISSN: 0021-9258.

Friedrich R, Panizzi P, Fuentes-Prior P, Richter K, Verhamme I, Anderson PJ, Kawabata S, Huber R, Bode W, Bock PE. Staphylocoagulase is a prototype for the mechanism of cofactor-induced zymogen activation. Nature. 2003 Oct 10/2/2003; 425(6957): 535-9. PMID: 14523451, PII: nature01962, DOI: 10.1038/nature01962, ISSN: 1476-4687.

Verhamme IM, Olson ST, Tollefsen DM, Bock PE. Binding of exosite ligands to human thrombin. Re-evaluation of allosteric linkage between thrombin exosites I and II. J. Biol. Chem [print-electronic]. 2002 Mar 3/1/2002; 277(9): 6788-98. PMID: 11724802, PII: M110257200, DOI: 10.1074/jbc.M110257200, ISSN: 0021-9258.

Olson ST, Swanson R, Day D, Verhamme I, Kvassman J, Shore JD. Resolution of Michaelis complex, acylation, and conformational change steps in the reactions of the serpin, plasminogen activator inhibitor-1, with tissue plasminogen activator and trypsin. Biochemistry. 2001 Oct 10/2/2001; 40(39): 11742-56. PMID: 11570875, PII: bi0107290, ISSN: 0006-2960.

Boxrud PD, Verhamme IM, Fay WP, Bock PE. Streptokinase triggers conformational activation of plasminogen through specific interactions of the amino-terminal sequence and stabilizes the active zymogen conformation. J. Biol. Chem [print-electronic]. 2001 Jul 7/13/2001; 276(28): 26084-9. PMID: 11369771, PII: M101966200, DOI: 10.1074/jbc.M101966200, ISSN: 0021-9258.

Verhamme I, Kvassman JO, Day D, Debrock S, Vleugels N, Declerck PJ, Shore JD. Accelerated conversion of human plasminogen activator inhibitor-1 to its latent form by antibody binding. J. Biol. Chem. 1999 Jun 6/18/1999; 274(25): 17511-7. PMID: 10364183, ISSN: 0021-9258.

Kvassman JO, Verhamme I, Shore JD. Inhibitory mechanism of serpins: loop insertion forces acylation of plasminogen activator by plasminogen activator inhibitor-1. Biochemistry. 1998 Nov 11/3/1998; 37(44): 15491-502. PMID: 9799512, PII: bi9814787, DOI: 10.1021/bi9814787, ISSN: 0006-2960.

Gibson A, Baburaj K, Day DE, Verhamme I, Shore JD, Peterson CB. The use of fluorescent probes to characterize conformational changes in the interaction between vitronectin and plasminogen activator inhibitor-1. J. Biol. Chem. 1997 Feb 2/21/1997; 272(8): 5112-21. PMID: 9030577, ISSN: 0021-9258.

Bock PE, Day DE, Verhamme IM, Bernardo MM, Olson ST, Shore JD. Analogs of human plasminogen that are labeled with fluorescence probes at the catalytic site of the zymogen. Preparation, characterization, and interaction with streptokinase. J. Biol. Chem. 1996 Jan 1/12/1996; 271(2): 1072-80. PMID: 8557633, ISSN: 0021-9258.

Lawrence DA, Ginsburg D, Day DE, Berkenpas MB, Verhamme IM, Kvassman JO, Shore JD. Serpin-protease complexes are trapped as stable acyl-enzyme intermediates. J. Biol. Chem. 1995 Oct 10/27/1995; 270(43): 25309-12. PMID: 7592687, ISSN: 0021-9258.

Sherman PM, Lawrence DA, Verhamme IM, Paielli D, Shore JD, Ginsburg D. Identification of tissue-type plasminogen activator-specific plasminogen activator inhibitor-1 mutants. Evidence that second sites of interaction contribute to target specificity. J. Biol. Chem. 1995 Apr 4/21/1995; 270(16): 9301-6. PMID: 7721851, ISSN: 0021-9258.

Shore JD, Day DE, Francis-Chmura AM, Verhamme I, Kvassman J, Lawrence DA, Ginsburg D. A fluorescent probe study of plasminogen activator inhibitor-1. Evidence for reactive center loop insertion and its role in the inhibitory mechanism. J. Biol. Chem. 1995 Mar 3/10/1995; 270(10): 5395-8. PMID: 7890653, ISSN: 0021-9258.

Verhamme IM, Van Dedem GW, Lauwers AR. Ionic-strength-dependent substrate inhibition of the lysis of Micrococcus luteus by hen egg-white lysozyme. Eur. J. Biochem. 1988 Mar 3/15/1988; 172(3): 615-20. PMID: 3350016, ISSN: 0014-2956.

Den Tandt WR, Inaba T, Verhamme I, Overdyk B, Brouwer J, Prieur D. Non-identity of human plasma lysozyme and 4-methylumbelliferyl-tetra-N-acetyl-beta-D-chitotetraoside hydrolase. Int. J. Biochem. 1988; 20(7): 713-9. PMID: 3181601, ISSN: 0020-711X.