Browsing by Author "Jones, Lisa M."

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    Fast photochemical oxidation of proteins coupled to mass spectrometry reveals conformational states of apurinic/apyrimidic endonuclease 1
    (2015-07-08) Hernandez Quiñones, Denisse Berenice; Jones, Lisa M.; Georgiadis, Millie M.; Hurley, Thomas D.
    Fast photochemical oxidation of proteins (FPOP) is an emerging footprinting method that utilizes hydroxyl radicals. The use of hydroxyl radicals create stable labeled products that can be analyzed with mass spectrometry. The advantage of FPOP over other methods is the fast acquisition of results and the small amount of sample required for analysis. Protein structure and protein- ligand interactions have been studied with FPOP. Here we evaluated (1) the reproducibility of FPOP, (2) the effect of hydrogen peroxide concentration on oxidation and (3) the use of FPOP to evaluate protein- nucleic acid interaction with Apurinic/Apurinic endonuclease 1 (APE1) protein. APE1 is a pleotropic protein that has been crystallized and studied widely. The 35641.5 Da protein has two major functional activities: DNA repair and redox function. An intact protein study of APE1 showed consistent global labeling by FPOP and a correlation between oxidation and hydrogen peroxide concentration. Furthermore, analysis of APE1 with DNA was done in hopes of probing the DNA binding site. Although the oxidation observed was not sufficient to define the complex pocket, a dramatic effect was seen in residue oxidation when DNA was added. Interestingly, the internal residues were labeled collectively in all APE1 experiments which indicates partial unfolding of the protein as previously suggested in the literature. Hence, these findings establish the use of FPOP to capture protein dynamics and provide evidence of the existence breathing dynamics of APE1.
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    Mechanisms and Consequences of Dopamine Depletion-Induced Attenuation of the Spinophilin/Neurofilament Medium Interaction
    (Hindawi, 2017) Hiday, Andrew C.; Edler, Michael C.; Salek, Asma B.; Morris, Cameron W.; Thang, Morrent; Rentz, Tyler J.; Rose, Kristie L.; Jones, Lisa M.; Baucum, Anthony J., II; Biology, School of Science
    Signaling changes that occur in the striatum following the loss of dopamine neurons in the Parkinson disease (PD) are poorly understood. While increases in the activity of kinases and decreases in the activity of phosphatases have been observed, the specific consequences of these changes are less well understood. Phosphatases, such as protein phosphatase 1 (PP1), are highly promiscuous and obtain substrate selectivity via targeting proteins. Spinophilin is the major PP1-targeting protein enriched in the postsynaptic density of striatal dendritic spines. Spinophilin association with PP1 is increased concurrent with decreases in PP1 activity in an animal model of PD. Using proteomic-based approaches, we observed dopamine depletion-induced decreases in spinophilin binding to multiple protein classes in the striatum. Specifically, there was a decrease in the association of spinophilin with neurofilament medium (NF-M) in dopamine-depleted striatum. Using a heterologous cell line, we determined that spinophilin binding to NF-M required overexpression of the catalytic subunit of protein kinase A and was decreased by cyclin-dependent protein kinase 5. Functionally, we demonstrate that spinophilin can decrease NF-M phosphorylation. Our data determine mechanisms that regulate, and putative consequences of, pathological changes in the association of spinophilin with NF-M that are observed in animal models of PD.
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    Probing the paramyxovirus fusion (F) protein-refolding event from pre- to postfusion by oxidative footprinting
    (PNAS, 2014-06-24) Poor, Taylor A.; Jones, Lisa M.; Sood, Amika; Leser, George P.; Plasencia, Manolo D.; Rempel, Don L.; Jardetzky, Theodore S.; Woods, Robert J.; Gross, Michael L.; Lamb, Robert A.; Department of Chemistry & Chemical Biology, School of Science
    To infect a cell, the Paramyxoviridae family of enveloped viruses relies on the coordinated action of a receptor-binding protein (variably HN, H, or G) and a more conserved metastable fusion protein (F) to effect membrane fusion and allow genomic transfer. Upon receptor binding, HN (H or G) triggers F to undergo an extensive refolding event to form a stable postfusion state. Little is known about the intermediate states of the F refolding process. Here, a soluble form of parainfluenza virus 5 F was triggered to refold using temperature and was footprinted along the refolding pathway using fast photochemical oxidation of proteins (FPOP). Localization of the oxidative label to solvent-exposed side chains was determined by high-resolution MS/MS. Globally, metastable prefusion F is oxidized more extensively than postfusion F, indicating that the prefusion state is more exposed to solvent and is more flexible. Among the first peptides to be oxidatively labeled after temperature-induced triggering is the hydrophobic fusion peptide. A comparison of peptide oxidation levels with the values of solvent-accessible surface area calculated from molecular dynamics simulations of available structural data reveals regions of the F protein that lie at the heart of its prefusion metastability. The strong correlation between the regions of F that experience greater-than-expected oxidative labeling and epitopes for neutralizing antibodies suggests that FPOP has a role in guiding the development of targeted therapeutics. Analysis of the residue levels of labeled F intermediates provides detailed insights into the mechanics of this critical refolding event.