Date

2017

Document Type

Dissertation

Degree

Doctor of Philosophy

Department

Mechanical Engineering

First Adviser

Alparslan Oztekin

Abstract

von Willebrand Factor (VWF) is a large multimeric protein which is very important for the hemostasis of bleeding blood vessels. Critical steps in the process are the accumulation and aggregation of platelets at the damaged vessel wall, forming hemostatic plugs. Near injury sites, hydrodynamic force in the bloodstream elongates VWF with a sharp increase, exposing binding sites for platelets and collagen. Flow-induced conformational change of VWF regulates its binding to clotting agents in the blood. A coarse grain molecular model is proposed for the VWF multimer that incorporates observed mechanical properties of VWF monomers. In this model, each monomer is represented by a finitely extensible nonlinear elastic (FENE) spring connecting two beads. A2 domains are represented by the FENE spring because the A2 domain, similar to FENE springs, permits extensive elongation with an applied force. The beads at each end of the spring represent relatively rigid domains adjacent to A2 in VWF monomers. Adjacent monomers are connected by a stiff harmonic spring to form VWF multimers in the model. VWF multimers represented by this model have been studied to understand the conformational change of a single VWF multimer in response to shear flow. Fluctuations in model A2 domains were shown to increase significantly at high flow, including periodic complete extension of the domain. After validating our model in normal flow scenario, we extend this study further to the binding between VWF and collagen. To investigate VWF binding to collagen that is exposed on injured arterial surfaces, Brownian dynamics simulations are performed with a coarse-grain molecular model. Accounting for hydrodynamic interactions in the presence of a stationary surface, shear flow conditions are modeled. Binding between beads in coarse-grain VWF and collagen sites on the surface is described via reversible ligand-receptor-type bond formation, governed via Bell model kinetics. For conditions where binding is energetically favored, the model predicts a high probability for binding at low shear conditions; this is counter to experimental observations but in line with what prior modeling studies have revealed. To address such discrepancies, an additional binding criterion is implemented that depends on the conformation of a sub-monomer feature in the model, local to a given VWF binding site. The modified model predicts shear-induced binding, in very good agreement with experimental observations; this is true even for conditions where binding is significantly favored energetically. Biological implications of the model modification are discussed in terms of mechanisms of VWF activity. Experimental work that investigates the properties of individual VWF molecules guided the parameters in computational study. Within this dissertation, optical tweezers are employed to study the A2-domains of VWF. Such a direct experimental method performs very precise measurement on the most fundamental properties of VWF molecules (such as force/extension behavior). This experimental method achieves great resolution and sensitivity in real time. Experimental results unveil the mechanism of VWF unfolding, contributing to the current coarse grain model development, and giving us the ability to model abnormal VWF molecules. To our knowledge, this coarse grain molecular model is the only model to render sub-monomer units of VWF and it is capable of capturing sub-monomer dynamical behavior. By introducing an additional degree of freedom, our model successfully characterizes many of the flow-induced mechanical mechanisms exhibited by VWF, such as shear-induced conformational changes and unfolding phenomena. Further, our model captures shear-induced VWF-collagen binding behavior in situations where binding is highly favorable, which had previously not been obtained in the literature.

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