Open Access. Powered by Scholars. Published by Universities.®
Other Biochemistry, Biophysics, and Structural Biology Commons™
Open Access. Powered by Scholars. Published by Universities.®
- Institution
- Keyword
-
- Mitochondria (2)
- Neurodegeneration (2)
- Oxidative stress (2)
- 13C stable isotope probing. (1)
- Absorption and Transmission (1)
-
- Allohexaploid (1)
- Alpha-Synuclein (1)
- Alzheimer disease (1)
- Amino Acids (1)
- Amyloid-beta (1)
- Anaerobic methanogenesis (1)
- Apoptotic cell death pathways (1)
- Aptamers (1)
- Archaea (1)
- Bacterial topoisomerase I (1)
- Bioenergetics (1)
- C cycle (1)
- CRISPR/Cas9 (1)
- Camelina sativa (1)
- Candida albicans (1)
- Cardiac lipotoxicity (1)
- Caspase (1)
- Cell metabolism (1)
- Cell signaling (1)
- Confocal Microscope (1)
- Conformational dynamics (1)
- Cysteine protease (1)
- Cysteine-rich proteins (1)
- Deoxyribozymes (1)
- Diabetic cardiomyopathy (1)
- Publication
- Publication Type
Articles 31 - 39 of 39
Full-Text Articles in Other Biochemistry, Biophysics, and Structural Biology
Toxoplasma Dj-1 Regulates Organelle Secretion By A Direct Interaction With Calcium-Dependent Protein Kinase 1, Matthew A. Child, Megan Garland, Ian Foe, Peter Madzelan, Moritz Treeck, Wouter A. Van Der Linden, Kristina Oresic Bender, Evanthie Weerapana, Mark A. Wilson, John C. Boothroyd, Michael L. Reese
Toxoplasma Dj-1 Regulates Organelle Secretion By A Direct Interaction With Calcium-Dependent Protein Kinase 1, Matthew A. Child, Megan Garland, Ian Foe, Peter Madzelan, Moritz Treeck, Wouter A. Van Der Linden, Kristina Oresic Bender, Evanthie Weerapana, Mark A. Wilson, John C. Boothroyd, Michael L. Reese
Department of Biochemistry: Faculty Publications
Human DJ-1 is a highly conserved and yet functionally enigmatic protein associated with a heritable form of Parkinson’s disease. It has been suggested to be a redox-dependent regulatory scaffold, binding to proteins to modulate their function. Here we present the X-ray crystal structure of the Toxoplasma orthologue Toxoplasma gondii DJ-1 (TgDJ-1) at 2.1-A resolution and show that it directly associates with calcium-dependent protein kinase 1 (CDPK1). The TgDJ-1 structure identifies an orthologously conserved arginine dyad that acts as a phospho-gatekeeper motif to control complex formation. We determined that the binding of TgDJ-1 to CDPK1 is sensitive to oxidation and calcium, …
Alpha-Synuclein: Insight Into The Hallmark Of Parkinson's Disease As A Target For Quantitative Molecular Diagnostics And Therapeutics, Baggio A. Evangelista
Alpha-Synuclein: Insight Into The Hallmark Of Parkinson's Disease As A Target For Quantitative Molecular Diagnostics And Therapeutics, Baggio A. Evangelista
Honors Undergraduate Theses
Parkinson’s disease (PD) is the second-most common neurodegenerative disease after Alzheimer’s disease. With 500,000 individuals currently living with Parkinson’s and nearly 60,000 new cases diagnosed each year, this disease causes significant financial burden on the healthcare system - amassing to annual expenditures totaling 200 billion dollars; predicted to increase through 2050. The disease phenotype is characterized by a combination of a resting tremor, bradykinesia, muscular rigidity, and depression due to dopaminergic neuronal death in the midbrain. The cause of the neurotoxicity has been largely discussed, with strong evidence suggesting that the protein, alpha-Synuclein, is a key factor. Under native conditions, …
Significant Enhancement Of Fatty Acid Composition In Seeds Of The Allohexaploid, Camelina Sativa, Using Crispr/Cas9 Gene Editing, Wen Zhi Jhang, Isabelle M. Henry, Peter G. Lynagh, Lucia Comai, Edgar B. Cahoon, Donald P. Weeks
Significant Enhancement Of Fatty Acid Composition In Seeds Of The Allohexaploid, Camelina Sativa, Using Crispr/Cas9 Gene Editing, Wen Zhi Jhang, Isabelle M. Henry, Peter G. Lynagh, Lucia Comai, Edgar B. Cahoon, Donald P. Weeks
Department of Biochemistry: Faculty Publications
The CRISPR/Cas9 nuclease system is a powerful and flexible tool for genome editing, and novel applications of this system are being developed rapidly. Here, we used CRISPR/Cas9 to target the FAD2 gene in Arabidopsis thaliana and in the closely related emerging oil seed plant, Camelina sativa, with the goal of improving seed oil composition. We successfully obtained Camelina seeds in which oleic acid content was increased from 16% to over 50% of the fatty acid composition. These increases were associated with significant decreases in the less desirable polyunsaturated fatty acids, linoleic acid (i.e. a decrease from ~16% to <4%) and linolenic acid (a decrease from ~35% to <10%). These changes result in oils that are superior on multiple levels: they are healthier, more oxidatively stable and better suited for production of certain commercial chemicals, including biofuels. As expected, A. …
Quantification Of Cell Signaling Networks Using Kinase Activity Chemosensors, Jon R. Beck, Edward N. Harris, Cliff I. Stains
Quantification Of Cell Signaling Networks Using Kinase Activity Chemosensors, Jon R. Beck, Edward N. Harris, Cliff I. Stains
Department of Biochemistry: Faculty Publications
The ability to directly determine endogenous kinase activity in tissue homogenates provides valuable insights into signaling aberrations that underlie disease phenotypes. When activity data is collected across a panel of kinases, a unique “signaling fingerprint” is generated that allows for discrimination between diseased and normal tissue. Here we describe the use of peptide-based kinase activity sensors to fingerprint the signaling changes associated with disease states. This approach leverages the phosphorylation-sensitive sulfonamido-oxine (Sox) fluorophore to provide a direct readout of kinase enzymatic activity in unfractionated tissue homogenates from animal models or clinical samples. To demonstrate the application of this technology, we …
End-To-End Molecular Communication Channels In Cell Metabolism: An Information Theoretic Study, Zahmeeth Sayed Sakkaff, Jennie L. Catlett, Mikaela Cashman, Massimiliano Pierobon, Nicole R. Buan, Myra B. Cohen, Christine A. Kelley
End-To-End Molecular Communication Channels In Cell Metabolism: An Information Theoretic Study, Zahmeeth Sayed Sakkaff, Jennie L. Catlett, Mikaela Cashman, Massimiliano Pierobon, Nicole R. Buan, Myra B. Cohen, Christine A. Kelley
Department of Biochemistry: Faculty Publications
The opportunity to control and fine-tune the behavior of biological cells is a fascinating possibility for many diverse disciplines, ranging from medicine and ecology, to chemical industry and space exploration. While synthetic biology is providing novel tools to reprogram cell behavior from their genetic code, many challenges need to be solved before it can become a true engineering discipline, such as reliability, safety assurance, reproducibility and stability. This paper aims to understand the limits in the controllability of the behavior of a natural (non-engineered) biological cell. In particular, the focus is on cell metabolism, and its natural regulation mechanisms, and …
Micro-Spectroscopy Of Bio-Assemblies At The Single Cell Level, Jeslin Kera
Micro-Spectroscopy Of Bio-Assemblies At The Single Cell Level, Jeslin Kera
Honors Undergraduate Theses
In this thesis, we investigate biological molecules on a micron scale in the ultraviolet spectral region through the non-destructive confocal absorption microscopy. The setup involves a combination of confocal microscope with a UV light excitation beam to measure the optical absorption spectra with spatial resolution of 1.4 μm in the lateral and 3.6 μm in the axial direction. Confocal absorption microscopy has the benefits of requiring no labels and only low light intensity for excitation while providing a strong signal from the contrast generated by the attenuation of propagating light due to absorption. This enables spatially resolved measurements of single …
Structural And Mechanistic Insights Into Hemoglobincatalyzed Hydrogen Sulfide Oxidation And The Fate Of Polysulfide Products, Victor Vitvitsky, Pramod K. Yadav, Sojin An, Javier Seravalli, Uhn-Soo Cho, Ruma V. Banerjee
Structural And Mechanistic Insights Into Hemoglobincatalyzed Hydrogen Sulfide Oxidation And The Fate Of Polysulfide Products, Victor Vitvitsky, Pramod K. Yadav, Sojin An, Javier Seravalli, Uhn-Soo Cho, Ruma V. Banerjee
Department of Biochemistry: Faculty Publications
Hydrogen sulfide is a cardioprotective signaling molecule but is toxic at elevated concentrations. Red blood cells can synthesize H2S but, lacking organelles, cannot dispose of H2S via the mitochondrial sulfide oxidation pathway. We have recently shown that at high sulfide concentrations, ferric hemoglobin oxidizes H2S to a mixture of thiosulfate and iron-bound polysulfides in which the latter species predominates. Here, we report the crystal structure of human hemoglobin containing low spin ferric sulfide, the first intermediate in heme-catalyzed sulfide oxidation. The structure provides molecular insights into why sulfide is susceptible to oxidation in human …
The Assembly Factor Pet117 Couples Heme A Synthase Activity To Cytochrome Oxidase Assembly, Nicholas G. Taylor, Samantha Swenson, Nicholas J. Harris, Edward M. Germany, Jennifer L. Fox, Oleh Khalimonchuk
The Assembly Factor Pet117 Couples Heme A Synthase Activity To Cytochrome Oxidase Assembly, Nicholas G. Taylor, Samantha Swenson, Nicholas J. Harris, Edward M. Germany, Jennifer L. Fox, Oleh Khalimonchuk
Department of Biochemistry: Faculty Publications
Heme a is an essential metalloporphyrin cofactor of the mitochondrial respiratory enzyme cytochrome c oxidase (CcO). Its synthesis from heme b requires several enzymes, including the evolutionarily conserved heme a synthase (Cox15). Oligomerization of Cox15 appears to be important for the process of heme a biosynthesis and transfer to maturing CcO. However, the details of this process remain elusive, and the roles of any additional CcO assembly factors that may be involved remain unclear. Here we report the systematic analysis of one such uncharacterized assembly factor, Pet117, and demonstrate in Saccharomyces cerevisiae that this evolutionarily conserved protein is necessary for …
Short Carboxylic Acid-Carboxylate Hydrogen Bonds Can Have Fully Localized Protons, Jiusheng Lin, Edwin Pozharski, Mark A. Wilson
Short Carboxylic Acid-Carboxylate Hydrogen Bonds Can Have Fully Localized Protons, Jiusheng Lin, Edwin Pozharski, Mark A. Wilson
Department of Biochemistry: Faculty Publications
Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low barrier hydrogen bonds (LBHBs). Experimentally determining proton location in H-bonds is challenging. Here, bond length analysis of atomic (1.15–0.98 Å) resolution X-ray crystal structures of the human protein DJ-1 and its bacterial homolog YajL was used to determine the protonation states of H-bonded carboxylic acids. DJ-1 contains a buried, dimer-spanning 2.49 Å H-bond between Glu15 and Asp23 that satisfies standard donor-acceptor distance criteria for …