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dc.contributor.authorSingh, Arunima
dc.description.abstractGlycosaminoglycans (GAGs) are the most abundant hetero-polysaccharides found in mammalian tissues, and serve a variety of important biological roles in the body. They can be found predominantly in the extracellular matrix or cell surface, usually covalently attached to proteins. From providing tensile strength and tissue compressibility, to aiding in cell proliferation and recognition, to being key receptors for viral entry, they offer several avenues of therapeutic interest. GAGs are typically composed of repeating units of hexosamine and uronic acid pairs, that are often variably sulfated, leading to tremendous structural heterogeneity and a high charge density, making structural analysis and elucidation of binding modes very challenging. This presents an opportunity for computational modeling methods to provide insight into the structure and function of these molecules. The key to effective theoretical modeling of biomolecules is the use of a dependable and validated force field. This work presents a validation of the recent addition of parameters that enable modeling of sulfated GAG sequences to the GLYCAM force field, through a comparison of experimental NMR scalar coupling constants and NOE distances with theoretical data. The analysis demonstrates that the new force field parameters are capable of reproducing NMR observables for a number of GAG fragments. These parameters have been employed for designing the Glycosaminoglycan Builder, a point-and-click structure modeling utility on GLYCAM-Web, to facilitate 3D structure modeling of GAG fragments. The interface provides separate sets of monosaccharides, unique to each class of GAGs, allowing easy selection of pre-sulfated options for each monosaccharide. We also employ these parameters to study the binding of variably sulfated heparin fragments to chemokine CCL5. The study demonstrated a dependence of the ability of heparin tetrasaccharides to inhibit CCL5-CCR1 binding on the pattern and extent of sulfation. An analysis of the binding mode of a longer heparin fragment to the protein, as well as an examination of the effect of pH on CCL5-heparin binding was also performed.
dc.subjectGlycosaminoglycans, Protein-Glycosaminoglycan interactions, Force field validation, GLYCAM, Molecular dynamics simulations, Automated docking, MM-GBSA, Web-based structure building tools, Theoretical collision cross section calculation
dc.titleComputational modeling of glycosaminoglycans and their interactions with proteins
dc.description.advisorRobert Woods
dc.description.committeeRobert Woods
dc.description.committeeJames Prestegard
dc.description.committeeNatarajan Kannan
dc.description.committeeI. Jonathan Amster

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