DOI
10.17077/etd.pt1z1kw2
Document Type
Dissertation
Date of Degree
Fall 2013
Degree Name
PhD (Doctor of Philosophy)
Degree In
Chemistry
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.
Abstract
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.
Keywords
Asialoglycoprotein Receptor, Cyanovirn-N and Dimannose, Molecular Dynamics Simulations, Sugar Water Interactions, Thermodynamic Integration, Umbrella Sampling
Pages
x, 113 pages
Bibliography
Includes bibliographical references (pages 99-113).
Copyright
Copyright 2013 Sai Kumar Ramadugu
Recommended Citation
Ramadugu, Sai Kumar. "Carbohydrate-protein interactions: structure, dynamics and free energy calculations." PhD (Doctor of Philosophy) thesis, University of Iowa, 2013.
https://doi.org/10.17077/etd.pt1z1kw2
Comments
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