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- DNA methylation (3)
- Alternative splicing (2)
- Inorganic arsenic (2)
- 3D structure (1)
- Anaerobic respiration (1)
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- AniA (1)
- BAM complex (1)
- BamD (1)
- BamE (1)
- Bidentation (1)
- Biolayer interferometry (1)
- CTCF binding (1)
- Carbohydrate biosynthesis (1)
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- Chromatin (1)
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- Conformational change (1)
- Crystal structure (1)
- DNMT expression (1)
- Docking studies (1)
- Environmental impact (1)
- Epigenetics (1)
- Epithelial-to-mesenchymal transition (1)
- Epithelial-to-mesynchymal transition (1)
- Fusion protein (1)
- Glycosyltranferase (1)
- Histones (1)
- Infinium Methylation EPIC Bead-Chip (1)
Articles 1 - 9 of 9
Full-Text Articles in Chemicals and Drugs
Structural And Functional Insights Into The Role Of Bamd And Bame Within The Β-Barrel Assembly Machinery In Neisseria Gonorrhoeae, Aleksandra E. Sikora, Igor H. Wierzbicki, Ryszard A. Zielke, Rachael F. Ryner, Konstantin V. Korotkov, Susan K. Buchanan, Nicholas Noinaj
Structural And Functional Insights Into The Role Of Bamd And Bame Within The Β-Barrel Assembly Machinery In Neisseria Gonorrhoeae, Aleksandra E. Sikora, Igor H. Wierzbicki, Ryszard A. Zielke, Rachael F. Ryner, Konstantin V. Korotkov, Susan K. Buchanan, Nicholas Noinaj
Molecular and Cellular Biochemistry Faculty Publications
The β-barrel assembly machinery (BAM) is a conserved multicomponent protein complex responsible for the biogenesis of β-barrel outer membrane proteins (OMPs) in Gram-negative bacteria. Given its role in the production of OMPs for survival and pathogenesis, BAM represents an attractive target for the development of therapeutic interventions, including drugs and vaccines against multidrug-resistant bacteria such as Neisseria gonorrhoeae. The first structure of BamA, the central component of BAM, was from N. gonorrhoeae, the etiological agent of the sexually transmitted disease gonorrhea. To aid in pharmaceutical targeting of BAM, we expanded our studies to BamD and BamE within …
Transcriptome-Wide Identification Of The Rna-Binding Landscape Of The Chromatin-Associated Protein Parp1 Reveals Functions In Rna Biogenesis, Manana Melikishvili, Julia H. Chariker, Eric C. Rouchka, Yvonne N. Fondufe-Mittendorf
Transcriptome-Wide Identification Of The Rna-Binding Landscape Of The Chromatin-Associated Protein Parp1 Reveals Functions In Rna Biogenesis, Manana Melikishvili, Julia H. Chariker, Eric C. Rouchka, Yvonne N. Fondufe-Mittendorf
Molecular and Cellular Biochemistry Faculty Publications
Recent studies implicate Poly (ADP-ribose) polymerase 1 (PARP1) in alternative splicing regulation, and PARP1 may be an RNA-binding protein. However, detailed knowledge of RNA targets and the RNA-binding region for PARP1 are unknown. Here we report the first global study of PARP1–RNA interactions using PAR–CLIP in HeLa cells. We identified a largely overlapping set of 22 142 PARP1–RNA-binding peaks mapping to mRNAs, with 20 484 sites located in intronic regions. PARP1 preferentially bound RNA containing GC-rich sequences. Using a Bayesian model, we determined positional effects of PARP1 on regulated exon-skipping events: PARP1 binding upstream and downstream of the skipped exons …
The Molecular Mechanism Of N-Acetylglucosamine Side-Chain Attachment To The Lancefield Group A Carbohydrate In Streptococcus Pyogenes, Jeffrey Rush, Rebecca J. Edgar, Pan Deng, Jing Chen, Haining Zhu, Nina M. Van Sorge, Andrew J. Morris, Konstantin V. Korotkov, Natalia Korotkova
The Molecular Mechanism Of N-Acetylglucosamine Side-Chain Attachment To The Lancefield Group A Carbohydrate In Streptococcus Pyogenes, Jeffrey Rush, Rebecca J. Edgar, Pan Deng, Jing Chen, Haining Zhu, Nina M. Van Sorge, Andrew J. Morris, Konstantin V. Korotkov, Natalia Korotkova
Molecular and Cellular Biochemistry Faculty Publications
In many Lactobacillales species (i.e. lactic acid bacteria), peptidoglycan is decorated by polyrhamnose polysaccharides that are critical for cell envelope integrity and cell shape and also represent key antigenic determinants. Despite the biological importance of these polysaccharides, their biosynthetic pathways have received limited attention. The important human pathogen, Streptococcus pyogenes, synthesizes a key antigenic surface polymer, the Lancefield group A carbohydrate (GAC). GAC is covalently attached to peptidoglycan and consists of a polyrhamnose polymer, with N-acetylglucosamine (GlcNAc) side chains, which is an essential virulence determinant. The molecular details of the mechanism of polyrhamnose modification with GlcNAc are …
Peptide Inhibitors Targeting The Neisseria Gonorrhoeae Pivotal Anaerobic Respiration Factor Ania, Aleksandra E. Sikora, Robert H. Mills, Jacob V. Weber, Adel Hamza, Bryan W. Passow, Andrew Romaine, Zachary A. Williamson, Robert W. Reed, Ryszard A. Zielke, Konstantin V. Korotkov
Peptide Inhibitors Targeting The Neisseria Gonorrhoeae Pivotal Anaerobic Respiration Factor Ania, Aleksandra E. Sikora, Robert H. Mills, Jacob V. Weber, Adel Hamza, Bryan W. Passow, Andrew Romaine, Zachary A. Williamson, Robert W. Reed, Ryszard A. Zielke, Konstantin V. Korotkov
Molecular and Cellular Biochemistry Faculty Publications
Neisseria gonorrhoeae causes the sexually transmitted infection gonorrhea, which is highly prevalent worldwide and has a major impact on reproductive and neonatal health. The superbug status of N. gonorrhoeae necessitates the development of drugs with different mechanisms of action. Here, we focused on targeting the nitrite reductase AniA, which is a pivotal component of N. gonorrhoeae anaerobic respiration and biofilm formation. Our studies showed that gonococci expressing AniA containing the altered catalytic residues D137A and H280A failed to grow under anaerobic conditions, demonstrating that the nitrite reductase function is essential. To facilitate the pharmacological targeting of AniA, new crystal structures …
Microarray Dataset Of Transient And Permanent Dna Methylation Changes In Hela Cells Undergoing Inorganic Arsenic-Mediated Epithelial-To-Mesenchymal Transition, Meredith Eckstein, Matthew Rea, Yvonne N. Fondufe-Mittendorf
Microarray Dataset Of Transient And Permanent Dna Methylation Changes In Hela Cells Undergoing Inorganic Arsenic-Mediated Epithelial-To-Mesenchymal Transition, Meredith Eckstein, Matthew Rea, Yvonne N. Fondufe-Mittendorf
Molecular and Cellular Biochemistry Faculty Publications
The novel dataset presented here represents the results of the changing pattern of DNA methylation profiles in HeLa cells exposed to chronic low dose (0.5 µM) sodium arsenite, resulting in epithelial-to-mesenchymal transition, as well as DNA methylation patterns in cells where inorganic arsenic has been removed. Inorganic arsenic is a known carcinogen, though not mutagenic. Several mechanisms have been proposed as to how inorganic arsenic drives carcinogenesis such as regulation of the cell׳s redox potential and/or epigenetics. In fact, there are gene specific studies and limited genome-wide studies that have implicated epigenetic factors such as DNA methylation in inorganic arsenic-mediated …
Aberrant Coordination Geometries Discovered In The Most Abundant Metalloproteins, Sen Yao, Robert M. Flight, Eric C. Rouchka, Hunter N. B. Moseley
Aberrant Coordination Geometries Discovered In The Most Abundant Metalloproteins, Sen Yao, Robert M. Flight, Eric C. Rouchka, Hunter N. B. Moseley
Molecular and Cellular Biochemistry Faculty Publications
Metalloproteins bind and utilize metal ions for a variety of biological purposes. Due to the ubiquity of metalloprotein involvement throughout these processes across all domains of life, how proteins coordinate metal ions for different biochemical functions is of great relevance to understanding the implementation of these biological processes. Toward these ends, we have improved our methodology for structurally and functionally characterizing metal binding sites in metalloproteins. Our new ligand detection method is statistically much more robust, producing estimated false positive and false negative rates of ∼0.11% and ∼1.2%, respectively. Additional improvements expand both the range of metal ions and their …
Epigenomic Reprogramming In Inorganic Arsenic-Mediated Gene Expression Patterns During Carcinogenesis, Meredith Eckstein, Rebekah Eleazer, Matthew Rea, Yvonne N. Fondufe-Mittendorf
Epigenomic Reprogramming In Inorganic Arsenic-Mediated Gene Expression Patterns During Carcinogenesis, Meredith Eckstein, Rebekah Eleazer, Matthew Rea, Yvonne N. Fondufe-Mittendorf
Molecular and Cellular Biochemistry Faculty Publications
Arsenic is a ubiquitous metalloid that is not mutagenic but is carcinogenic. The mechanism(s) by which arsenic causes cancer remain unknown. To date, several mechanisms have been proposed, including the arsenic-induced generation of reactive oxygen species (ROS). However, it is also becoming evident that inorganic arsenic (iAs) may exert its carcinogenic effects by changing the epigenome, and thereby modifying chromatin structure and dynamics. These epigenetic changes alter the accessibility of gene regulatory factors to DNA, resulting in specific changes in gene expression both at the levels of transcription initiation and gene splicing. In this review, we discuss recent literature reports …
Hendra Virus Fusion Protein Transmembrane Domain Contributes To Pre-Fusion Protein Stability, Stacy Webb, Tamas Nagy, Hunter Moseley, Michael G. Fried, Rebecca Ellis Dutch
Hendra Virus Fusion Protein Transmembrane Domain Contributes To Pre-Fusion Protein Stability, Stacy Webb, Tamas Nagy, Hunter Moseley, Michael G. Fried, Rebecca Ellis Dutch
Molecular and Cellular Biochemistry Faculty Publications
Enveloped viruses utilize fusion (F) proteins studding the surface of the virus to facilitate membrane fusion with a target cell membrane. Fusion of the viral envelope with a cellular membrane is required for release of viral genomic material, so the virus can ultimately reproduce and spread. To drive fusion, the F protein undergoes an irreversible conformational change, transitioning from a metastable pre-fusion conformation to a more thermodynamically stable post-fusion structure. Understanding the elements that control stability of the pre-fusion state and triggering to the post-fusion conformation is important for understanding F protein function. Mutations in F protein transmembrane (TM) domains …
Genome-Wide Dna Methylation Reprogramming In Response To Inorganic Arsenic Links Inhibition Of Ctcf Binding, Dnmt Expression And Cellular Transformation, Matthew Rea, Meredith Eckstein, Rebekah Eleazer, Caroline Smith, Yvonne N. Fondufe-Mittendorf
Genome-Wide Dna Methylation Reprogramming In Response To Inorganic Arsenic Links Inhibition Of Ctcf Binding, Dnmt Expression And Cellular Transformation, Matthew Rea, Meredith Eckstein, Rebekah Eleazer, Caroline Smith, Yvonne N. Fondufe-Mittendorf
Molecular and Cellular Biochemistry Faculty Publications
Chronic low dose inorganic arsenic (iAs) exposure leads to changes in gene expression and epithelial-to-mesenchymal transformation. During this transformation, cells adopt a fibroblast-like phenotype accompanied by profound gene expression changes. While many mechanisms have been implicated in this transformation, studies that focus on the role of epigenetic alterations in this process are just emerging. DNA methylation controls gene expression in physiologic and pathologic states. Several studies show alterations in DNA methylation patterns in iAs-mediated pathogenesis, but these studies focused on single genes. We present a comprehensive genome-wide DNA methylation analysis using methyl-sequencing to measure changes between normal and iAs-transformed cells. …