Long-ranged Protein-glycan Interactions Stabilize von Willebrand Factor A2 Domain from Mechanical Unfolding

Abstract

von Willebrand Factor (vWF) is a large multimeric protein that binds to platelets and collagen in blood clotting. vWF A2 domain hosts a proteolytic site for ADAMTS13 (A Disintegrin and Metalloprotease with a ThromboSpondin type 1 motif, member 13) to regulate the size of vWF multimers. This regulation process is highly sensitive to force conditions and protein-glycan interactions as the process occurs in flowing blood. There are two sites on A2 domain (N1515 and N1574) bearing various N-linked glycan structures. In this study, we used molecular dynamics (MD) simulation to study the force-induced unfolding of A2 domain with and without a single N-linked glycan type on each site. The sequential pullout of β-strands was used to represent a characteristic unfolding sequence of A2. This unfolding sequence varied due to protein-glycan interactions. The force-extension and total energy-extension profiles also show differences in magnitude but similar characteristic shapes between the systems with and without glycans. Systems with N-linked glycans encountered higher energy barriers for full unfolding and even for unfolding up to the point of ADAMTS13 cleavage site exposure. Interestingly, there is not much difference observed for A2 domain structure itself with and without glycans from standard MD simulations, suggesting roles of N-glycans in A2 unfolding through long-ranged protein-glycan interactions.

Distribution and history of extensional stresses on vWF surrogate molecules in turbulent flow

“…The goal of the present study is not to elucidate the molecular mechanism of protein unfolding, and the approach employed in our work cannot offer molecular level information, such as molecular dynamics simulations or coarse-grained simulations can 76 , 81 , 82 . In such computations the vWF was modeled taking into account the chain-like structure of the vWF and details of the unfolding of the A1 and A2 domains and the ADAMTS-13 cleavage could be observed, but the simulations were focused on the investigation of one vWF molecule.…”

“…In such computations the vWF was modeled taking into account the chain-like structure of the vWF and details of the unfolding of the A1 and A2 domains and the ADAMTS-13 cleavage could be observed, but the simulations were focused on the investigation of one vWF molecule. The approach herein has the advantage of providing the stresses in different flow fields, so that one could potentially use results such as those in refs 76 , 81 to determine the critical stress for protein unfolding and to determine what percentage of the proteins in the flow are subject to that stress and for how long. Here, the protein was treated as a particle with a diffusivity that depends on its average radius.…”

Visualization of the HIV-1 Env glycan shield across scales

“…Computational modeling, in particular molecular dynamics (MD) simulations, has proven useful as a complementary approach for characterizing glycoprotein structure and dynamics (16)(17)(18)(19), including Env (6,(20)(21)(22). Three sets of atomistic dynamics simulations of fully glycosylated Env trimers were recently reported and these predicted that dynamics would lead to extensive shielding of the antigenic surface and the formation of extensive networks among interacting glycans (6,21,22).…”

Shear-Induced Extensional Response Behaviors of Tethered von Willebrand Factor

“…VWF made from different species could have different post-translational modifications. In particular, glycosylation has shown to affect VWF structure and function (67)(68)(69). As a result, VWF molecules in our experiments could potentially display different mechanical properties compared to VWF made from CHO cells.…”