A5082853865- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- RNA and protein synthesis mechanisms
- Redox biology and oxidative stress
- RNA Research and Splicing
- Analytical Chemistry and Chromatography
- Alzheimer's disease research and treatments
- Genetics, Aging, and Longevity in Model Organisms
- Parkinson's Disease Mechanisms and Treatments
- Genomics and Chromatin Dynamics
- Metabolomics and Mass Spectrometry Studies
- Glycosylation and Glycoproteins Research
- Galectins and Cancer Biology
- Biochemical effects in animals
- Vibrio bacteria research studies
- RNA modifications and cancer
- Escherichia coli research studies
- Aortic aneurysm repair treatments
- Advanced Biosensing Techniques and Applications
- Epigenetics and DNA Methylation
- Sirtuins and Resveratrol in Medicine
- Connective tissue disorders research
- Molecular Biology Techniques and Applications
- Advanced Glycation End Products research
- Prion Diseases and Protein Misfolding
Southwestern Medical Center
2012-2024
The University of Texas Southwestern Medical Center
2012-2024
University of California, Irvine
2014
Institute for Systems Biology
2007-2013
Purdue University West Lafayette
2003-2011
Seattle University
2010
Harvard University
2007
University of Alberta
2007
InSysBio (Russia)
2007
Lomonosov Moscow State University
2006
The P7C3 class of aminopropyl carbazole chemicals fosters the survival neurons in a variety rodent models neurodegeneration or nerve cell injury. To uncover its mechanism action, an active derivative was modified to contain both benzophenone for photocrosslinking and alkyne CLICK chemistry. This found bind nicotinamide phosphoribosyltransferase (NAMPT), rate-limiting enzyme involved conversion into adenine dinucleotide (NAD). Administration cells treated with doxorubicin, which induces NAD...
Tauopathies feature progressive accumulation of tau amyloids. Pathology may begin when these amplify from a protein template, or seed, whose structure is unknown. We have purified and characterized distinct forms monomer—inert (Mi) seed-competent (Ms). Recombinant Ms triggered intracellular aggregation, induced fibrillization in vitro, self-assembled. Alzheimer’s disease also seeded aggregation self-assembled vitro to form multimers. used crosslinking with mass spectrometry probe structural...
Significance The recently discovered type VI secretion system (T6SS) is used by Gram-negative bacteria to deliver effector proteins into both eukaryotic and prokaryotic neighboring cells mediate virulence competition, respectively. Even though several T6SS families have been described, many T6SSs are not associated with known effectors. In this work, we report the discovery of a conserved motif named MIX (marker for six effectors) that often located near genome neighborhood found in numerous...
The polyketide natural product Leptomycin B inhibits nuclear export mediated by the karyopherin protein chromosomal region maintenance 1 (CRM1). Here, we present 1.8- to 2.0-Å-resolution crystal structures of CRM1 bound and related inhibitors Anguinomycin A Ratjadone A. Structural complementary chemical analyses reveal an unexpected mechanism inhibition involving covalent conjugation CRM1-mediated hydrolysis products’ lactone rings. Furthermore, mutagenesis reveals CRM1. signal (NES)-binding...
Vibrio spp. are associated with infections caused by contaminated food and water. A type III secretion system (T3SS2) is a shared feature of all clinical isolates V. parahaemolyticus some cholerae strains. Despite its being responsible for enterotoxicity, no molecular mechanism has been determined the T3SS2-dependent pathogenicity. Here, we show that although typically thought as extracellular pathogens, T3SS2 mediates host cell invasion, vacuole formation, replication intracellular...
Bottom-up proteomics largely relies on tryptic peptides for protein identification and quantification. Tryptic digestion often provides limited coverage of sequence because issues such as peptide length, ionization efficiency, post-translational modification colocalization. Unfortunately, a region interest in protein, example, proximity to an active site or the presence important modifications, may not be covered by peptides. Detection limits, quantification accuracy, isoform differentiation...
It has been shown that oxidatively modified forms of proteins accumulate during oxidative stress, aging, and in some age-related diseases. One the unique features a wide variety routes by which are oxidized is generation carbonyl groups. This paper reports method for isolation proteins, involves (1) biotinylation with biotin hydrazide (2) affinity enrichment using monomeric avidin chromatography columns. The selectivity was validated adding vitro biotinylated BSA to yeast lysate showing...
A new strategy for amino acid analysis is reported involving derivatization with an N-hydroxysuccinimide ester of N-alkylnicotinic (Cn-NA-NHS) followed by reversed-phase chromatography and electrospray ionization mass spectrometry (RPC−MS). Detection sensitivity increased as the N-alkyl chain length nicotinic derivatizing agent was from 1 to 4. N-Acylation acids Cn-NA-NHS reagents in water produced a stable product roughly min using 4-fold molar excess 0.1 M sodium borate buffer at pH values...
Cholera toxin (CT) enters and intoxicates host cells after binding cell surface receptors using its B subunit (CTB). The ganglioside (glycolipid) GM1 is thought to be the sole CT receptor; however, mechanism by which CTB mediates internalization of remains enigmatic. Here we report that binds glycoproteins. Relative contributions gangliosides glycoproteins depend on type, primarily in colonic epithelial lines. Using a metabolically incorporated photocrosslinking sugar, identified one...
The type VI secretion system (T6SS) is a widespread protein apparatus used by Gram-negative bacteria to deliver toxic effector proteins into adjacent bacterial or host cells. Here, we uncovered role in interbacterial competition for the two T6SSs encoded marine pathogen Vibrio alginolyticus. Using comparative proteomics and genetics, identified their repertoires. In addition previously described V12G01_02265, three new effectors secreted T6SS1, indicating that T6SS1 secretes at least four...
Abstract Nuclear factor (erythroid-derived 2)-like 2 and its Caenorhabditis elegans ortholog, SKN-1, are transcription factors that have a pivotal role in the oxidative stress response, cellular homeostasis, organismal lifespan. Similar to other defense systems, NRF2-mediated response is compromised aging neurodegenerative diseases. Here, we report FDA approved drug hydralazine bona fide activator of NRF2/SKN-1 signaling pathway. We demonstrate extends healthy lifespan (~25%) wild type...
With the advent of electrospray ionization mass spectrometry, world was given a new way to look at complex peptide mixtures. Identification proteins via their signature peptides requires representative portion derived from by proteolysis. Unfortunately, matrix effects prohibited many peptides. This paper describes development labeling reagent that simultaneously adds permanent positive charge and increases hydrophobicity enhance efficiency. The agent is preactivated with N-hydroxysuccinimide...
Two methods have been developed for protein identification from tandem mass spectra: database searching and de novo sequencing. De sequencing identifies peptide directly spectra. Among many proposed algorithms, we evaluated the performance of five AUDENS, Lutefisk, NovoHMM, PepNovo, PEAKS. Our evaluation are based on calculation relative sequence distance (RSD), algorithm sensitivity, spectrum quality. We found that algorithms different in analyzing QSTAR LCQ spectrometer data, but general,...
Absolute quantification of peptides by mass spectrometry requires a reference, frequently using heavy isotope-coded as internal standards. These have traditionally been generated chemical stepwise synthesis. Recently new way to supply such was described in which nucleotide sequences coding for the respective are concatenated into synthetic gene (QconCAT). QconCATs then expressed produce polypeptide consisting peptides, purified, quantified various methods, and digested yield final standard...
J. Neurochem. (2011) 118 , 902–914. Abstract Cyclin dependent kinase‐5 (Cdk5) activity is deregulated in Alzheimer’s disease (AD) and contributes to all three hallmarks: neurotoxic β‐amyloid formation, neurofibrillary tangles, neuronal death. However, the mechanism leading Cdk5 deregulation remains controversial. AD usually linked formation of p25, a proteolysis product activator p35, which leads mislocalization hyperactivation. A few studies have indeed shown increased p25 levels brains;...
Multiple reaction monitoring (MRM) is a highly sensitive method of targeted mass spectrometry (MS) that can be used to selectively detect and quantify peptides based on the screening specified precursor peptide-to-fragment ion transitions. MRM-MS sensitivity depends critically tuning instrument parameters, such as collision energy cone voltage, for generation maximal product signal. Although generalized equations values exist there no clear indication optimal signal reliably produced all...