The thrombin-thrombomodulin (TM) interaction is critical for the cessation of blood clotting and maintenance of hemostasis. Structures of both proteins are now available, but much still needs to be learned about the dynamics of this important interaction. A comprehensive structure-function study is proposed in which each protein will be studied individually (Aims 1 and 2), the mechanism of their association will be analyzed (Aim 3) and finally, the activity of the thrombin-TM complex towards protein C will be probed (Aim 4).
In Aim 1, we shall study how the two essential EGF-like domains (EGF4 and EGF5) work together to cause anticoagulant cofactor activity. Our hypothesis is that the two domains of TM, a non-globular protein, communicate via structural and dynamic effects and are tightly coupled. The solution structure and backbone dynamics will be correlated with specific kinetic parameters (KM for thrombin, KM for protein C, kcat for protein C activation). The role of the 6th domain, which aids in thrombin binding, shall also be explored.
In Aim 2, conformational changes in thrombin that occur when TM binds will be studied to see whether they are important for catalysis of protein C activation. Our recently developed method for probing changes in backbone amide exchange has revealed beta-sheets within thrombin that tighten upon TM binding, and these """"""""transmission lines"""""""" connect the TM binding site to the active site. Various substrate analogs and TM fragments devoid of cofactor activity will be used to discover which transmission lines correlate with anticoagulant activity.
In Aim 3, the thermodynamic and kinetic driving forces for thrombin-TM association will be probed using surface plasmon resonance on mutants of both proteins.
In Aim 4, protein C activation by the thrombin-TM complex will be probed. Our hypothesis is that TM does more than provide a binding scaffold for protein C. A panel of mutants will be analyzed to determine which residues cause specific defects (KM for thrombin, KM for protein C, kcat for thrombin activation of protein C). Those that show kcat defects will be used to further delineate which transmission lines in thrombin are important for anticoagulant cofactor activity.

Agency
National Institute of Health (NIH)
Institute
National Heart, Lung, and Blood Institute (NHLBI)
Type
Research Project (R01)
Project #
1R01HL070999-01
Application #
6534878
Study Section
Hematology Subcommittee 2 (HEM)
Program Officer
Link, Rebecca P
Project Start
2002-07-01
Project End
2007-06-30
Budget Start
2002-07-01
Budget End
2003-06-30
Support Year
1
Fiscal Year
2002
Total Cost
$327,606
Indirect Cost
Name
University of California San Diego
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
077758407
City
La Jolla
State
CA
Country
United States
Zip Code
92093
Peacock, Riley B; Davis, Jessie R; Markwick, Phineus R L et al. (2018) Dynamic Consequences of Mutation of Tryptophan 215 in Thrombin. Biochemistry 57:2694-2703
Handley, Lindsey D; Fuglestad, Brian; Stearns, Kyle et al. (2017) NMR reveals a dynamic allosteric pathway in thrombin. Sci Rep 7:39575
Handley, Lindsey D; Treuheit, Nicholas A; Venkatesh, Varun J et al. (2015) Thrombomodulin Binding Selects the Catalytically Active Form of Thrombin. Biochemistry 54:6650-8
Boechi, Leonardo; Pierce, Levi; Komives, Elizabeth A et al. (2014) Trypsinogen activation as observed in accelerated molecular dynamics simulations. Protein Sci 23:1550-8
Fuglestad, Brian; Gasper, Paul M; McCammon, J Andrew et al. (2013) Correlated motions and residual frustration in thrombin. J Phys Chem B 117:12857-63
Fuglestad, Brian; Gasper, Paul M; Tonelli, Marco et al. (2012) The dynamic structure of thrombin in solution. Biophys J 103:79-88
Gasper, Paul M; Fuglestad, Brian; Komives, Elizabeth A et al. (2012) Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities. Proc Natl Acad Sci U S A 109:21216-22
Treuheit, Nicholas A; Beach, Muneera A; Komives, Elizabeth A (2011) Thermodynamic compensation upon binding to exosite 1 and the active site of thrombin. Biochemistry 50:4590-6
Koeppe, Julia R; Beach, Muneera A; Baerga-Ortiz, Abel et al. (2008) Mutations in the fourth EGF-like domain affect thrombomodulin-induced changes in the active site of thrombin. Biochemistry 47:10933-9
Truhlar, Stephanie M E; Croy, Carrie H; Torpey, Justin W et al. (2006) Solvent accessibility of protein surfaces by amide H/2H exchange MALDI-TOF mass spectrometry. J Am Soc Mass Spectrom 17:1490-7

Showing the most recent 10 out of 15 publications