Document Type


Date of Degree

Fall 2013

Degree Name

PhD (Doctor of Philosophy)

Degree In


First Advisor

Margulis, Claudio J.

First Committee Member

Cheatum, Christopher M.

Second Committee Member

Larsen, Sarah C.

Third Committee Member

Haes, Amanda J.

Fourth Committee Member

Fuentes, Ernesto J.


The current thesis presents work on the structure and dynamics of oligosaccharides and polysaccharides as well as the free energetics of carbohydrate-protein interactions. By applying various computational tools such as molecular dynamics simulation, our in-house fast sugar structure prediction software, replica exchange molecular dynamics, homology modeling, umbrella sampling, steered molecular dynamics as well as the thermodynamic integration formalism, we have been able to study the role of water on the surface of homopolysaccharides as well as complex oligosachharides, we have been able to produce a prediction of the bound structure of triantennary oligosaccride on the asialoglycoprotein receptor, we have been able to estimate the free energy of binding of ManΑ1→2Man to the HIV-1 inactivating protein, Cyanovirin-N as well as the relative binding free energies of mutants of Cyanovirin-N to the same ligand.


Asialoglycoprotein Receptor, Cyanovirn-N and Dimannose, Molecular Dynamics Simulations, Sugar Water Interactions, Thermodynamic Integration, Umbrella Sampling


x, 113 pages


Includes bibliographical references (pages 99-113).


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Copyright © 2013 Sai Kumar Ramadugu

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