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    Conformational studies of SEM1 monomer and characterization of GFP-amyloid binding

    Author
    James, Nathan Avery
    View/Open
    James_rpi_0185E_11583.pdf (6.004Mb)
    Other Contributors
    Makhatadze, George I.; Colón, Wilfredo; Barquera, Blanca L.; Royer, Catherine Ann; Hurley, Jennifer;
    Date Issued
    2019-08
    Subject
    Biochemistry and biophysics
    Degree
    PhD;
    Terms of Use
    This electronic version is a licensed copy owned by Rensselaer Polytechnic Institute (RPI), Troy, NY. Copyright of original work retained by author.;
    Metadata
    Show full item record
    URI
    https://hdl.handle.net/20.500.13015/6157
    Abstract
    Amyloid fibrils are highly ordered insoluble protein aggregates that are associated with a number of diseases, including Alzheimer’s Disease, Parkinson’s Disease, and Huntington’s Disease. These fibrils can be formed from many different protein sequences. More recently, amyloids have been found that are not associated with any disease state and may even have physiological function. Firstly, we focus on SEM1, an amyloid system found in the semen of healthy men that has been shown to increase human immunodeficiency virus (HIV) infectivity. Previous work has shown that SEM1 fibrillation is pH dependent, requiring a pH greater than 6 to occur. We completed molecular dynamics simulations to examine the monomeric structural conformations of SEM1 at pH 2 and pH 7 and compared it to NMR observables such as chemical shift perturbations and J-Coupling constants. We observed an interaction between an N-terminal α-helix and C-terminal β-hairpin that is reduced in pH 2 as compared to pH 7. We also examined 3 different SEM1 mutants and observed fibrillation at pH 5.5 but not at pH 2. Secondly, we work to characterize a novel discovery in our lab that green fluorescent protein (GFP) binds specifically to amyloid fibrils. We tracked the kinetics of fibril formation through the use of GFP and confocal microscopy and discovered that GFP was capable of detecting small particles unable to be seen by traditional dyes such as ThT or Congo Red. We also developed GFP as a novel inhibitor of fibril formation. Through the development of GFP mutants we explored the binding mechanism of GFP to fibrils and suggest a dual effect of surface aromatics and electrostatics. Moving forward, we have worked to develop GFP as a new tool in detecting endogenous plaque found in Alzheimer’s Disease.;
    Description
    August 2019; School of Science
    Department
    Biochemistry and Biophysics Program;
    Publisher
    Rensselaer Polytechnic Institute, Troy, NY
    Relationships
    Rensselaer Theses and Dissertations Online Collection;
    Access
    Restricted to current Rensselaer faculty, staff and students in accordance with the Rensselaer Standard license. Access inquiries may be directed to the Rensselaer Libraries.;
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    • RPI Theses Online (Complete)

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