Probing Solution Dynamics of Tissue Factor Using Molecular Dynamics Simulations Guided by NMR Chemical Shifts

Structure and dynamics of proteins are key to understanding their roles in biological systems and provide a framework for rational development of novel therapeutics. Here, we combine NMR chemical shifts (CSs), X-ray crystal structures, and molecular dynamics (MD) simulations to characterize the extracellular domain of human tissue factor, i.e., soluble tissue factor (sTF), a protein that is involved in the initiation of the blood clotting process by forming a complex with the coagulation factor VIIa (fVIIa). Starting with the X-ray structures, solution NMR CSs were incorporated as restraints in CS-guided MD simulations to obtain structures in agreement with the NMR solution data of the protein. Our results reveal a dynamic ensemble of configurations in a loop that is key to sTF interaction with fVIIa. Key residues have been identified in the fVIIa-binding loop with divergent backbone and/or side-chain configurations to account for the loop dynamics. We demonstrate that the resulting structural ensemble from the incorporation of solution NMR CSs provides a better description of sTF dynamics in solution. The integrated approach used in this study can be applied to provide a better molecular guide for therapeutics that specifically target sTF.