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dc.contributor.advisorGreen, David F.en_US
dc.contributor.authorFujimoto, Yukiji Karenen_US
dc.contributor.otherDepartment of Chemistryen_US
dc.date.accessioned2013-05-22T17:34:31Z
dc.date.available2013-05-22T17:34:31Z
dc.date.issued1-Dec-12en_US
dc.date.submitted12-Decen_US
dc.identifierFujimoto_grad.sunysb_0771E_11140en_US
dc.identifier.urihttp://hdl.handle.net/1951/59651
dc.description122 pg.en_US
dc.description.abstractHuman immunodeficiency virus (HIV) infection of T-cells begins when the viral envelope glycoprotein, gp120, binds to CD4 receptors on the target cell surface. Over the past several years, proteins isolated from various prokaryotes have been shown to inhibit HIV cell entry by binding to gp120 and thus blocking the association with CD4. Lectins that bind to high-mannose oligosaccharides on gp120 are an attractive class of antiviral agents. While several of these have been quite well characterized both structurally and biochemically, there remain many open questions regarding their mechanism of inhibition. Among the best studied is cyanovirin-N (CVN), which is currently under clinical study for use as a topical prophylactic. Large-scale molecular dynamics simulations have identified important structural features of this system that are difficult to resolve experimentally, and binding free energies of a diverse set of oligosaccharide targets computed from these structural ensembles give remarkable agreement with experiment. Detailed decompositions of the binding free energies on a residue-by-residue basis have additionally identified several key interactions that define broad affinity for &alpha -(1,2)-dimannose-containing sugars, as well as a number of determinants of specificity. These studies provide a deeper understanding of the mechanism of inhibitory activity. In addition, this work has provided a foundation for methodological improvements that allow us to more accurately capture the energetics of carbohydrate binding.en_US
dc.description.sponsorshipStony Brook University Libraries. SBU Graduate School in Department of Chemistry. Charles Taber (Dean of Graduate School).en_US
dc.formatElectronic Resourceen_US
dc.language.isoen_USen_US
dc.publisherThe Graduate School, Stony Brook University: Stony Brook, NY.en_US
dc.subject.lcshBiochemistry Ð Biophysicsen_US
dc.subject.otherbinding affinity, carbohydrate-binding protein, continuum electrostatics, molecular dynamics, protein-ligand interactions, virucidal lectinsen_US
dc.titleUnderstanding Carbohydrate Recognition by Antiviral Lectins: Applying Computational Methods to Protein-Carbohydrate Complexesen_US
dc.typeDissertationen_US
dc.description.advisorAdvisor(s): Green, David F. . Committee Member(s): Simmerling, Carlos; Carrico, Isaac Haltiwanger, Roberten_US
dc.mimetypeApplication/PDFen_US


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