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.
Lihan et al. (Fri,) studied this question.