Author ORCID Identifier


Defense Date


Document Type


Degree Name

Doctor of Philosophy


Pharmaceutical Sciences

First Advisor

Umesh Desai


Heparan sulfate (HS) is highly-charged, linear polysaccharide that interacts with numerous proteins in humans as consituents of proteoglycans. The action of sulfotransferase enzymes during the biosynthesis of HS can generate a combinatorially massive library of differentially sulfated sequences. Furthermore, the number and position of these sulfate groups are key to their biological activity, modulating their selectivities for certain proteins at the cell surface or ECM. The installation of a sulfate on the C3 hydroxyl of a glucosamine residue in HS represents the rarest of the sulfations, despite the HS 3-O-sulfotransferase (3OST) family being the most diverse of the other sulfotransferases. However, the diversity of the 3OST family is not surprising considering that each of the seven 3OSTs exhibit different but overlapping substrate specificities, categorized by their ability to generate a 3-O-sulfated sequence that can either bind and activate antithrombin or herpes simplex virus glycoprotein D. Until the conception of this work, the general theory to explain the diversity of the 3OST family was that they generate a strong and highly-selective ionic interaction with a particular protein, mediated exclusively by the 3-O-sulfate. This work challenges that understanding by suggesting a new mechanism of generating a selective 3OS-HS epitope, wherein a 3OS can confer unique conformations in HS in a sequence-dependent manner that recognize a particular protein binding site. Specifically, we present our findings from 1 µs molecular dynamics (MD) simulations of a library of 40 variably 3-O-sulfated HS hexasaccharides, delineating 1) sequences that are prone to the conformational effects of a 3OS and 2) the non-covalent forces responsible for these effects. Further, we introduce a novel molecular docking protocol that can effectively handle the vast conformational space of HS hexasaccharides conferred by their numerous rotatable bonds, while simultaneously biasing the docking search towards unique conformations that were unveiled from MD simulations. We show that the so-called semi-rigid docking protocol (SRD) is a powerful tool for identifying proteins that selectively recognize 3OS-induced compact topologies of HS. This work establishes a new link between the diversity of the 3OST family and the generation of selective HS motifs for proteins, and should inspire glycobiologists to have a greater appreciation for the potential conformational effects of 3-O-sulfation on sequences that they seek to characterize by experiment. Furthermore, this work demonstrates the power of computational approaches to identify HS sequences with unique conformational properties, those of which can be leveraged for the design of highly-selective GAG-based therapeutics.


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Available for download on Saturday, October 19, 2024