A5019267575- Ubiquitin and proteasome pathways
- RNA modifications and cancer
- Ferroptosis and cancer prognosis
- Erythrocyte Function and Pathophysiology
- Genomics and Chromatin Dynamics
- DNA Repair Mechanisms
- Fungal and yeast genetics research
- Pancreatic function and diabetes
- RNA and protein synthesis mechanisms
- Cancer, Lipids, and Metabolism
- RNA Research and Splicing
- Mitochondrial Function and Pathology
- Bacteriophages and microbial interactions
- Protein Degradation and Inhibitors
- Calcium signaling and nucleotide metabolism
- Microtubule and mitosis dynamics
- Endoplasmic Reticulum Stress and Disease
- HIV/AIDS drug development and treatment
- Hereditary Neurological Disorders
- Cellular transport and secretion
- Monoclonal and Polyclonal Antibodies Research
- Advanced biosensing and bioanalysis techniques
- Cellular Mechanics and Interactions
- Glycosylation and Glycoproteins Research
- Computational Drug Discovery Methods
University of Pittsburgh
2015-2024
University of Utah
2002-2007
Howard Hughes Medical Institute
2005
Johns Hopkins University
2000
We report the crystal structure of catalytic domain human ADAR2, an RNA editing enzyme, at 1.7 angstrom resolution. The reveals a zinc ion in active site and suggests how substrate adenosine is recognized. Unexpectedly, inositol hexakisphosphate (IP 6 ) buried within enzyme core, contributing to protein fold. Although there are no reports that deaminases act on (ADARs) require cofactor, we show IP required for activity. Amino acids coordinate conserved some transfer (tRNA) (ADATs), related...
Metabolic networks are interconnected and influence diverse cellular processes. The protein-metabolite interactions that mediate these frequently low affinity challenging to systematically discover. We developed mass spectrometry integrated with equilibrium dialysis for the discovery of allostery (MIDAS) identify such interactions. Analysis 33 enzymes from human carbohydrate metabolism identified 830 interactions, including known regulators, substrates, products as well previously unreported...
Abstract The vast majority of membrane phospholipids (PLs) include two asymmetrically positioned fatty acyls: oxidizable polyunsaturated acids (PUFA) attached predominantly at the sn2 position, and non‐oxidizable saturated/monounsaturated (SFA/MUFA) localized sn1 position. peroxidation PUFA‐PLs, particularly sn2‐arachidonoyl(AA)‐ sn2‐adrenoyl(AdA)‐containing phosphatidylethanolamines (PE), has been associated with execution ferroptosis, a program regulated cell death. There is minor...
During HIV-1 entry, the highly conserved gp41 N-trimer pocket region becomes transiently exposed and vulnerable to inhibition. Using mirror-image phage display structure-assisted design, we have discovered protease-resistant D-amino acid peptides (D-peptides) that bind with high affinity potently inhibit viral entry. We also report high-resolution crystal structures of two these D-peptides in complex a mimic suggest sources their potency. A trimeric version one is most potent pocket-specific...
Hydroperoxy-eicosatetraenoyl-phosphatidylethanolamine (HpETE-PE) is a ferroptotic cell death signal. HpETE-PE produced by the 15-Lipoxygenase (15LOX)/Phosphatidylethanolamine Binding Protein-1 (PEBP1) complex or via an Fe-catalyzed non-enzymatic radical reaction. Ferrostatin-1 (Fer-1), common ferroptosis inhibitor, lipophilic scavenger but poor 15LOX inhibitor arguing against having role in ferroptosis. In current work, we demonstrate that Fer-1 does not affect alone, however, it effectively...
Significance Our work identifies regulatory mechanisms between ferroptosis and autophagy. We discovered that PE-binding protein-1 (PEBP1) is pivotal for dynamic interactions the ferroptotic cell death program prosurvival autophagy in asthmatic/Type 2 stimulated airway epithelial cells concurrent activation of protects from mitochondrial DNA release. Similar findings are observed Type Hi asthmatic where high 15-lipoxygenase-1 (15LO1)–PEBP1 light chain-3 II (LC3-II) levels associate with low...
Significance The polymerase associated factor 1 complex (Paf1C) is an RNA (pol) II accessory that broadly influences gene expression by regulating chromatin structure and the recruitment of RNA-processing factors during transcription. This study shows how phosphorylation a repeated motif within additional factor, Spt5, recognized used Plus3 domain Paf1C subunit Rtf1 (restores TBP function 1) to promote transcription machinery. Deletions both C Cdc73 (Cell Division Cycle 73) are required...
Abstract The conserved budding yeast Rad51 paralogues, including Rad55, Rad57, Csm2 and Psy3 are indispensable for homologous recombination (HR)-mediated chromosome damage repair. Rad55 Rad57 associated in a heterodimer, while form the Shu complex with Shu1 Shu2. Here we show that bridges an interaction between Rad52 and, using fully reconstituted system, demonstrate synergizes Rad55–Rad57 to promote nucleation of on single-stranded DNA pre-occupied by replication protein A (RPA). csm2–F46A...
sn2-15-Hydroperoxy-eicasotetraenoyl-phosphatidylethanolamines (sn2-15-HpETE-PE) generated by mammalian 15-lipoxygenase/phosphatidylethanolamine binding protein-1 (15-LO/PEBP1) complex is a death signal in recently identified type of programmed cell demise, ferroptosis. How the enzymatic selects sn2-ETE-PE as substrate among 1 ∼100 total oxidizable membrane PUFA phospholipids central, yet unresolved question. To unearth highly selective and specific mechanisms catalytic competence, we used...
Ferroptosis and necroptosis are two pro-inflammatory cell death programs contributing to major pathologies their inhibition has gained attention treat a wide range of disease states. Necroptosis relies on activation RIP1 RIP3 kinases. is triggered by oxidation polyunsaturated phosphatidylethanolamines (PUFA-PE) complexes 15-Lipoxygenase (15LOX) with phosphatidylethanolamine-binding protein 1 (PEBP1). The latter, also known as RAF kinase inhibitory protein, displays promiscuity towards...
The Saccharomyces cerevisiae Shu complex, consisting of Shu1, Shu2, Csm2 and Psy3, promotes error-free homologous recombination (HR) by an unknown mechanism. Recent structural analysis two proteins, has revealed that these proteins are Rad51 paralogues mediate DNA binding this complex. We show in vitro the Csm2–Psy3 heterodimer preferentially binds synthetic forked or 3′-DNA overhang substrates resembling structures used during HR vivo . find interacts with paralogues, Rad55–Rad57 complex...
Accurate modeling of structural dynamics proteins and their differentiation across different species can help us understand generic mechanisms function shared by family members the molecular basis specificity individual members. We focused here on lipoxygenases, enzymes that catalyze lipid oxidation, mammalian bacterial structures which have been elucidated. present a systematic method approach for characterizing sequence, structure, dynamics, allosteric signaling properties these using...
Programmed ferroptotic death eliminates cells in all major organs and tissues with imbalanced redox metabolism due to overwhelming iron-catalyzed lipid peroxidation under insufficient control by thiols (Glutathione (GSH)). Ferroptosis has been associated the pathogenesis of chronic degenerative diseases acute injuries brain, cardiovascular system, liver, kidneys, other organs, its manipulation offers a promising new strategy for anticancer therapy. This explains high interest designing...
Reactive oxygen species (ROS) play essential roles in cell signaling, survival, and homeostasis. Aberrant ROS lead to disease contribute the aging process. Numerous enzymes vigilant antioxidant pathways are required regulate for normal cellular health. Mitochondria a major source of ROS, mechanisms prevent elevated during oxidative phosphorylation require super oxide dismutase (SOD) activity. SOD2, also known as MnSOD, is targeted mitochondria instrumental regulating by conversion...
Shroom3 is an actin-associated regulator of cell morphology that required for neural tube closure, formation the lens placode, and gut morphogenesis in mice has been linked to chronic kidney disease directional heart looping humans. Numerous studies have shown likely regulates these developmental processes by directly binding Rho-kinase facilitating assembly apically positioned contractile actomyosin networks. We characterized molecular basis defects caused ENU-induced mutation results...
Abstract Accurate DNA replication is essential for genomic stability and cancer prevention. Homologous recombination important high-fidelity damage tolerance during replication. How the homologous machinery recruited to intermediates unknown. Here, we provide evidence that a Rad51 paralog-containing complex, budding yeast Shu directly recognizes enables of predominantly lagging strand abasic sites. We show complex becomes chromatin associated when cells accumulate sites S phase. also...