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Determining Ligand-Binding Induced Conformational Changes in H-NOX Domains

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dc.contributor.advisor Boon, Elizabeth M. en_US
dc.contributor.advisor Rizzo, Robert en_US
dc.contributor.author Gorgani, Farzan Mirza en_US
dc.contributor.other Department of Chemistry en_US
dc.date.accessioned 2012-05-15T18:03:42Z
dc.date.accessioned 2015-04-24T14:44:54Z
dc.date.available 2012-05-15T18:03:42Z
dc.date.available 2015-04-24T14:44:54Z
dc.date.issued 2010-12-01
dc.identifier Gorgani_grad.sunysb_0771M_10367.pdf en_US
dc.identifier.uri http://hdl.handle.net/1951/55442 en_US
dc.identifier.uri http://hdl.handle.net/11401/70869 en_US
dc.description.abstract Nitric Oxide (NO) has diverse and important roles in prokaryote and eukaryote biology. In addition to its role as a powerful toxin used to kill pathogens and tumor cells, NO also functions as a signaling molecule that mediates mechanisms such as vasodilatation, neurotransmission and biofilm formation. Our objective is to elucidate the role of NO in bacterial biofilm formation. Due to their resistance to antibiotics, biofilms are known to plague hospitals and immune compromised patients. As a first step in this objective, we are interested in characterizing the bacterial NO sensor Heme-Nitric oxide/OXygen binding domain (H-NOX). We predict that H-NOX changes its conformation upon binding nitric oxide (NO) and this causes changes in its interactions with downstream effectors, leading ultimately to biofilm formation. Here we describe our efforts towards the use of fluorescent resonance energy transfer (FRET) and computational modeling to determine conformational changes in H-NOX that take place upon ligand binding. The unnatural fluorescent amino acid p-cyanophenylalanine was incorporated into the H-NOX of S. woodyi for use in FRET studies. Furthermore, computational simulations using AMBER force field tools were carried out in the H-NOX domain from T. tengcongensis. Root mean square deviation (RMSD) values of the amino acid backbone, certain helices, and dihedral angels of the heme were measured. Characterizing ligand-induced conformational changes in H-NOX will aid in further understanding of the role of NO in biofilm formation. Better understanding of biofilm formation will ultimately lead to strategies to eliminate them. en_US
dc.description.sponsorship This work is sponsored by the Stony Brook University Graduate School in compliance with the requirements for completion of degree. en_US
dc.format Monograph en_US
dc.format.medium Electronic Resource en_US
dc.language.iso en_US en_US
dc.publisher The Graduate School, Stony Brook University: Stony Brook, NY. en_US
dc.subject.lcsh Biochemistry. en_US
dc.title Determining Ligand-Binding Induced Conformational Changes in H-NOX Domains en_US
dc.type Thesis en_US
dc.mimetype Application/PDF en_US
dc.contributor.committeemember Joseph W. Lauher. en_US

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