We propose to leverage recent advances in computer technology and algorithm development, together with the growing database of three-dimensional (3D) structures of Vitamin K-dependent (VKD) proteins and their complexes, to build reliable 3D complexes in electrically neutral solvent and with structural water molecules in place. It is our hypothesis that theoretical techniques are now at a level of sophistication and accuracy to warrant the judicious application to key coagulation systems: the prothrombin-prothombinase complex, which provides the penultimate step in the cascade (formation of thrombin) and the extrinsic tenase complex, which initiates the extrinsic blood coagulation cascade. We propose to provide solvent-equilibrated models for these systems. The plan:
AIM I : To model the prothrombinase-prothrombin complex, including the apparently flexible central fragment involving the kringle domains of prothrombin?the goal being to understand the molecular details of the multiple cleavages;
AIM : To complete a consensus model of TF/FVIIa/FXa followed by model studies of TFalone, TF as a dimer, and TF and its putative complexes with protein disulfide isomerase (PDI) (also to be modeled), glutathione and NO?the goal being to understand more completely the issues surrounding cryptic vs procoagulant TF;
AIM III : To complete a model study with solvation of the Vitamin K cycle reactions (enzymes: vitamin K carboxylase and vitamin K epoxide reductase) using quantum mechanics.
The final aim recognizes the need to not only develop all-atom, solvated, 3D structures, but also to provide insight into the quantum mechanical bond-breaking and bond-forming mechanisms that regulate coagulation. Underlying our applied work is the continual development of new techniques?modeling the interaction of protein domains to membrane surfaces( e.g. Gla domains to phospholipid surfaces rich in phosphatidylserine), improving protein-protein docking algorithms, modeling conformational changes in proteins (e.g. the conformational change of the C2 domain of Factor Va when binding to a membrane surface, FVIIa when binding TF, the Gla domain when binding calcium ions) and improving molecular dynamics methods. The developed complex structures will be made available through the internet and these will maintain value as a base for systematic improvement even as new experimental structures are solved.
The study of molecular processes in the blood coagulation cascade (here: prothrombin, factor Vila/Tissue factor, Vitamin K cycle) have high relevance to public health. These molecular processes have impact in many blood diseases, including hemophilia, stroke and plaque in the vascular system. Our research is aimed directly at understanding the molecular processes of normal and abnormal blood coagulation.
|Bode, Michael F; Mackman, Nigel (2016) A combined deficiency of tissue factor and PAR-4 is associated with fatal pulmonary hemorrhage in mice. Thromb Res 146:46-50|
|Boulaftali, Yacine; Owens 3rd, A Phillip; Beale, Ashley et al. (2016) CalDAG-GEFI Deficiency Reduces Atherosclerotic Lesion Development in Mice. Arterioscler Thromb Vasc Biol 36:792-9|
|Owens 3rd, A Phillip; Edwards, Todd L; Antoniak, Silvio et al. (2015) Platelet Inhibitors Reduce Rupture in a Mouse Model of Established Abdominal Aortic Aneurysm. Arterioscler Thromb Vasc Biol 35:2032-41|
|Bode, Michael; Mackman, Nigel (2014) Regulation of tissue factor gene expression in monocytes and endothelial cells: Thromboxane A2 as a new player. Vascul Pharmacol 62:57-62|
|Parker, Christine H; Morgan, Christopher R; Rand, Kasper D et al. (2014) A conformational investigation of propeptide binding to the integral membrane protein Î³-glutamyl carboxylase using nanodisc hydrogen exchange mass spectrometry. Biochemistry 53:1511-20|
|Wu, Sangwook; Beard, William A; Pedersen, Lee G et al. (2014) Structural comparison of DNA polymerase architecture suggests a nucleotide gateway to the polymerase active site. Chem Rev 114:2759-74|
|Boulaftali, Yacine; Hess, Paul R; Getz, Todd M et al. (2013) Platelet ITAM signaling is critical for vascular integrity in inflammation. J Clin Invest 123:908-16|
|Feng, D; Stafford, K A; Broze, G J et al. (2013) Evidence of clinically significant extravascular stores of factorÂ IX. J Thromb Haemost 11:2176-8|
|Batra, Vinod K; Perera, Lalith; Lin, Ping et al. (2013) Amino acid substitution in the active site of DNA polymerase Î² explains the energy barrier of the nucleotidyl transfer reaction. J Am Chem Soc 135:8078-88|
|Wu, Sangwook; Liu, Shubin; Sim, Sooyeon et al. (2012) Weakly Antiferromagentic Coupling Via Superexchange Interaction Between Mn(II)-Mn(II) Atoms: A QM/MM Study of the Active Site of Human Cytosolic X-Propyl Aminopeptidase P. J Phys Chem Lett 3:2293-2297|
Showing the most recent 10 out of 49 publications