Showing 1 - 10 of 67 Items
Determination of the Relationship Between Peptoid Catalyst Oligomeric Length and Catalytic Enantioselectivity of Trifluoromethylation of Aldehydes Access to this record is restricted to members of the Bowdoin community. Log in here to view.
- Restriction End Date: 2025-06-01
Date: 2020-01-01
Creator: Katharine Toll
Access: Access restricted to the Bowdoin Community
Targeted identification of glycosylated proteins in the gastric pathogen helicobacter pylori (Hp)
Date: 2013-09-01
Creator: Kanokwan Champasa, Scott A. Longwell, Aimee M. Eldridge, Elizabeth A. Stemmler, Danielle H., Dube
Access: Open access
- Virulence of the gastric pathogen Helicobacter pylori (Hp) is directly linked to the pathogen's ability to glycosylate proteins; for example, Hp flagellin proteins are heavily glycosylated with the unusual nine-carbon sugar pseudaminic acid, and this modification is absolutely essential for Hp to synthesize functional flagella and colonize the host's stomach. Although Hp's glycans are linked to pathogenesis, Hp's glycome remains poorly understood; only the two flagellin glycoproteins have been firmly characterized in Hp. Evidence from our laboratory suggests that Hp synthesizes a large number of as-yet unidentified glycoproteins. Here we set out to discover Hp's glycoproteins by coupling glycan metabolic labeling with mass spectrometry analysis. An assessment of the subcellular distribution of azide-labeled proteins by Western blot analysis indicated that glycoproteins are present throughout Hp and may therefore serve diverse functions. To identify these species, Hp's azide-labeled glycoproteins were tagged via Staudinger ligation, enriched by tandem affinity chromatography, and analyzed by multidimensional protein identification technology. Direct comparison of enriched azide-labeled glycoproteins with a mock-enriched control by both SDS-PAGE and mass spectrometry-based analyses confirmed the selective enrichment of azide-labeled glycoproteins. We identified 125 candidate glycoproteins with diverse biological functions, including those linked with pathogenesis. Mass spectrometry analyses of enriched azide-labeled glycoproteins before and after cleavage of O-linked glycans revealed the presence of Staudinger ligation-glycan adducts in samples only after beta-elimination, confirming the synthesis of O-linked glycoproteins in Hp. Finally, the secreted colonization factors urease alpha and urease beta were biochemically validated as glycosylated proteins via Western blot analysis as well as by mass spectrometry analysis of cleaved glycan products. These data set the stage for the development of glycosylation-based therapeutic strategies, such as new vaccines based on natively glycosylated Hp proteins, to eradicate Hp infection. Broadly, this report validates metabolic labeling as an effective and efficient approach for the identification of bacterial glycoproteins. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.
Identification of SYWKQCAFNAVSCFamide: A broadly conserved crustacean C-type allatostatin-like peptide with both neuromodulatory and cardioactive properties
Date: 2009-04-15
Creator: Patsy S. Dickinson, Teerawat Wiwatpanit, Emily R. Gabranski, Rachel J. Ackerman, Jake S., Stevens, Christopher R. Cashman, Elizabeth A. Stemmler, Andrew E. Christie
Access: Open access
- The allatostatins comprise three structurally distinct peptide families that regulate juvenile hormone production by the insect corpora allata. A-type family members contain the C-terminal motif -YXFGLamide and have been found in species from numerous arthropod taxa. Members of the B-type family exhibit a -WX6Wamide C-terminus and, like the A-type peptides, appear to be broadly conserved within the Arthropoda. By contrast, members of the C-type family, typified by the unblocked C-terminus -PISCF, a pyroglutamine blocked N-terminus, and a disulfide bridge between two internal Cys residues, have only been found in holometabolous insects, i.e. lepidopterans and dipterans. Here, using transcriptomics, we have identified SYWKQCAFNAVSCFamide (disulfide bridging predicted between the two Cys residues), a known honeybee and water flea C-typelike peptide, from the American lobster Homarus americanus (infraorder Astacidea). Using matrix assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI-FTMS), a mass corresponding to that of SYWKQCAFNAVSCFamide was detected in the H. americanus brain, supporting the existence of this peptide and its theorized structure. Furthermore, SYWKQCAFNAVSCFamide was detected by MALDI-FTMS in neural tissues from five additional astacideans as well as 19 members of four other decapod infraorders (i.e. Achelata, Anomura, Brachyura and Thalassinidea), suggesting that it is a broadly conserved decapod peptide. In H. americanus, SYWKQCAFNAVSCFamide is capable of modulating the output of both the pyloric circuit of the stomatogastric nervous system and the heart. This is the first demonstration of bioactivity for this peptide in any species.
A strategy for the selective imaging of glycans using caged metabolic precursors
Date: 2010-07-21
Creator: Pamela V. Chang, Danielle H. Dube, Ellen M. Sletten, Carolyn R. Bertozzi
Access: Open access
- Glycans can be imaged by metabolic labeling with azidosugars followed by chemical reaction with imaging probes; however, tissue-specific labeling is difficult to achieve. Here we describe a strategy for the use of a caged metabolic precursor that is activated for cellular metabolism by enzymatic cleavage. An N-azidoacetylmannosamine derivative caged with a peptide substrate for the prostate-specific antigen (PSA) protease was converted to cell-surface azido sialic acids in a PSA-dependent manner. The approach has applications in tissue-selective imaging of glycans for clinical and basic research purposes. © 2010 American Chemical Society.
CO2 induced phase transitions in diamine-appended metal-organic frameworks
Date: 2015-06-15
Creator: Bess Vlaisavljevich, Samuel O. Odoh, Sondre K. Schnell, Allison L. Dzubak, Kyuho, Lee, Nora Planas, Jeffrey B. Neaton, Laura Gagliardi, Berend Smit
Access: Open access
- Using a combination of density functional theory and lattice models, we study the effect of CO2 adsorption in an amine functionalized metal-organic framework. These materials exhibit a step in the adsorption isotherm indicative of a phase change. The pressure at which this step occurs is not only temperature dependent but is also metal center dependent. Likewise, the heats of adsorption vary depending on the metal center. Herein we demonstrate via quantum chemical calculations that the amines should not be considered firmly anchored to the framework and we explore the mechanism for CO2 adsorption. An ammonium carbamate species is formed via the insertion of CO2 into the M-Namine bonds. Furthermore, we translate the quantum chemical results into isotherms using a coarse grained Monte Carlo simulation technique and show that this adsorption mechanism can explain the characteristic step observed in the experimental isotherm while a previously proposed mechanism cannot. Furthermore, metal analogues have been explored and the CO2 binding energies show a strong metal dependence corresponding to the M-Namine bond strength. We show that this difference can be exploited to tune the pressure at which the step in the isotherm occurs. Additionally, the mmen-Ni2(dobpdc) framework shows Langmuir like behavior, and our simulations show how this can be explained by competitive adsorption between the new model and a previously proposed model.
Fast pyrolysis of lignins
Date: 2010-08-01
Creator: Sedat H. Beis, Saikrishna Mukkamala, Nathan Hill, Jincy Joseph, Cirila, Baker, Bruce Jensen, Elizabeth A. Stemmler, M. Clayton Wheeler, Brian G. Frederick
Access: Open access
- Three lignins: Indulin AT, Lignoboost™, and Acetocell lignin, were characterized and pyrolyzed in a continuous-fed fast pyrolysis process. The physical and chemical properties of the lignins included chemical composition, heat content, ash, and water content. The distributed activation energy model (DAEM) was used to describe the pyrolysis of each lignin. Activation energy distributions of each lignin were quite different and generally covered a broad range of energies, typically found in lignins. Process yields for initial continuous-fed fast pyrolysis experiments are reported. Bio-oil yield was low, ranging from 16 to 22%. Under the fast pyrolysis conditions used, the Indulin AT and Lignoboost™ lignin yielded slightly more liquid product than the Acetocell lignin. Lignin kinetic parameters and chemical composition vary considerably and fast pyrolysis processes must be specified for each type of lignin.
Deciphering the bacterial glycocode: Recent advances in bacterial glycoproteomics
Date: 2013-02-01
Creator: Scott A. Longwell, Danielle H. Dube
Access: Open access
- Bacterial glycoproteins represent an attractive target for new antibacterial treatments, as they are frequently linked to pathogenesis and contain distinctive glycans that are absent in humans. Despite their potential therapeutic importance, many bacterial glycoproteins remain uncharacterized. This review focuses on recent advances in deciphering the bacterial glycocode, including metabolic glycan labeling to discover and characterize bacterial glycoproteins, lectin-based microarrays to monitor bacterial glycoprotein dynamics, crosslinking sugars to assess the roles of bacterial glycoproteins, and harnessing bacterial glycosylation systems for the efficient production of industrially important glycoproteins. © 2012 Elsevier Ltd.
The Photodegradation of Endocrine Disrupting Compounds in Aqueous Solutions Access to this record is restricted to members of the Bowdoin community. Log in here to view.
Date: 2014-05-01
Creator: Peyton C Morss
Access: Access restricted to the Bowdoin Community
Developing methods of transient absorption spectroscopy for the study of triplet state photoacids Access to this record is restricted to members of the Bowdoin community. Log in here to view.
Date: 2023-01-01
Creator: Jack R Callahan
Access: Access restricted to the Bowdoin Community
Sorption of Cationic Heterocyclic Amines to Soils: Effects of Charge Delocalization and other Factors Access to this record is restricted to members of the Bowdoin community. Log in here to view.
Date: 2023-01-01
Creator: Mariah McKenzie
Access: Access restricted to the Bowdoin Community