A5100684042- Seismic Waves and Analysis
- Methane Hydrates and Related Phenomena
- Earthquake Detection and Analysis
- Ionosphere and magnetosphere dynamics
- Geophysics and Gravity Measurements
- Seismology and Earthquake Studies
- Solar and Space Plasma Dynamics
- Astrophysics and Cosmic Phenomena
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Superconducting Materials and Applications
- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Analytical Chemistry and Chromatography
- Cancer-related gene regulation
- Single-cell and spatial transcriptomics
- Physiological and biochemical adaptations
- Protein Structure and Dynamics
- Ubiquitin and proteasome pathways
- Genomics and Chromatin Dynamics
- Cell Image Analysis Techniques
- Epigenetics and DNA Methylation
- Metabolomics and Mass Spectrometry Studies
- RNA regulation and disease
Environmental Molecular Sciences Laboratory
2001-2024
University of Colorado Anschutz Medical Campus
2008-2024
Pacific Northwest National Laboratory
1999-2024
University of Colorado Denver
2010-2023
Soochow University
2023
Battelle
2018-2022
Chongqing University
2022
Institute of Soil Science
2022
Chinese Academy of Sciences
2022
Nanjing University of Information Science and Technology
2022
Understanding biological systems and the roles of their constituents is facilitated by ability to make quantitative, sensitive, comprehensive measurements how proteome changes, e.g., in response environmental perturbations. To this end, we have developed a high-throughput methodology characterize an organism's dynamic based on combination global enzymatic digestion, high-resolution liquid chromatographic separations, analysis Fourier transform ion cyclotron resonance mass spectrometry. The...
Mass spectrometry (MS)-based proteomics has great potential for overcoming the limitations of antibody-based immunoassays antibody-independent, comprehensive, and quantitative proteomic analysis single cells. Indeed, recent advances in nanoscale sample preparation have enabled effective processing In particular, concept using boosting/carrier channels isobaric labeling to increase sensitivity MS detection also been increasingly used small-sized samples including However, full such approaches...
The spliceosome undergoes dramatic changes in a splicing cycle. Structures of B, B
Abstract Effective phosphoproteome of nanoscale sample analysis remains a daunting task, primarily due to significant loss associated with non-specific surface adsorption during enrichment low stoichiometric phosphopeptide. We develop tandem tip phosphoproteomics preparation method that is capable cleanup and without additional transfer, its integration our recently developed SOP (Surfactant-assisted One-Pot preparation) iBASIL (improved Boosting Amplify Signal Isobaric Labeling) approaches...
In this study, high-efficiency packed capillary reversed-phase liquid chromatography (RPLC) coupled on-line with high-performance Fourier transform ion cyclotron resonance (FTICR) mass spectrometry has been investigated for the characterization of complex cellular proteolytic digests. Long columns (80-cm) small (3-μm) C18 bonded particles provided a total peak capacity ∼1000 polypeptides when interfaced an ESI-FTICR spectrometer under composition gradient conditions at pressure 10 000 psi....
Ultrasensitive nanoscale proteomics approaches for characterizing proteins from complex proteomic samples of <50 ng total mass are described. Protein identifications 0.5 pg whole proteome extracts were enabled by ultrahigh sensitivity (<75 zmol individual proteins) achieved using high-efficiency (peak capacities ∼103) 15-μm-i.d. capillary liquid chromatography separations (i.e., nanoLC, ∼20 nL/min mobile-phase flow rate at the optimal linear velocity ∼0.2 cm/s) coupled on-line with a...
JMJD6 is a Jumonji C domain-containing hydroxylase. binds α-ketoglutarate and iron has been characterized as either histone arginine demethylase or U2AF65 lysyl Here, we describe the structures of with without α-ketoglutarate, which revealed novel substrate binding groove two positively charged surfaces. The also contain stack aromatic residues located near active center. side chain one residue within this assumed different conformations in structures. Interestingly, bound efficiently to...
The essential splicing factor human UAP56 (hUAP56) is a DExD/H-box protein known to promote prespliceosome assembly. Here, using series of hUAP56 mutants that are defective for ATP-binding, ATP hydrolysis, or dsRNA unwindase/helicase activity, we assess the relative contributions these biochemical functions pre-mRNA splicing. We show assembly requires hUAP56’s ATP-binding and ATPase activities, which, unexpectedly, required interact with U2AF 65 be recruited into complexes. Surprisingly,...
Eya genes encode a unique family of multifunctional proteins that serve as transcriptional co-activators and haloacid dehalogenase-family Tyr phosphatases. Intriguingly, the N-terminal domain Eyas, which does not share sequence similarity to any known phosphatases, contains separable Ser/Thr phosphatase activity. Here, we demonstrate activity is intrinsic, but arises from its direct interaction with protein 2A (PP2A)-B55α holoenzyme. Importantly, Eya3 alters regulation c-Myc by PP2A,...
U1 snRNP plays a critical role in 5'-splice site recognition and is frequent target of alternative splicing factors. These factors transiently associate with human are not amenable for structural studies, while their Saccharomyces cerevisiae (yeast) homologs stable components snRNP. Here, we report the cryoEM structure yeast at 3.6 Å resolution atomic models ten core proteins, nearly all essential domains its RNA, five stably associated auxiliary proteins. The foot-shaped contains...
Abstract The leaf-cutter ant fungal garden ecosystem is a naturally evolved model system for efficient plant biomass degradation. Degradation processes mediated by the symbiotic fungus Leucoagaricus gongylophorus are difficult to characterize due dynamic metabolisms and spatial complexity of system. Herein, we performed microscale imaging across 12-µm-thick adjacent sections Atta cephalotes gardens applied metabolome-informed proteome approach map lignin This combines two multiomics mass...
DEXD/H-box protein UAP56 is an essential pre-mRNA splicing factor required for the first ATP-dependent spliceosome assembly step. also export of majority mRNAs from nucleus to cytoplasm. We performed biochemical characterization UAP56's ATPase and helicase activity, which important further understanding role these activities in function. showed that RNA-stimulated can only hydrolyze ATP. demonstrated RNA unwind substrates with 5' or 3' overhangs blunt ends vitro. U2AF(65) Aly, two proteins...
Prp8 stands out among hundreds of splicing factors as a key regulator spliceosome activation and potential cofactor the reaction. We present here crystal structure 274-residue domain (residues 1,822–2,095) near C terminus Saccharomyces cerevisiae Prp8. The most striking feature this is β-hairpin finger protruding protein (hence, will be referred to β-finger domain), resembling many globular ribosomal proteins with extensions. Mutations throughout change conformational equilibrium between...
Interleukin-37 (IL-37), a member of the IL-1 family cytokines, is fundamental suppressor innate and acquired immunities. Here, we used an integrative approach that combines biophysical, biochemical, biological studies to elucidate unique characteristics IL-37. Our reveal single amino acid mutations at IL-37 dimer interface result in stable formation monomers also remain monomeric high micromolar concentrations these forms comprise higher antiinflammatory activities than native on multiple...
The ability to manipulate and effectively utilize small proteomic samples is important for analyses using liquid chromatography (LC) in combination with mass spectrometry (MS) becomes more challenging very low flow rates due extra column volume effects on separation quality. Here we report the use of commercial switching valves (150-microm channels) implementing on-line coupling capillary LC columns operated at 10,000 psi relatively large solid-phase extraction (SPE) columns. With optimized...
An improved spatial proteomics platform to quantify >1500 proteins at a high resolution based on hanging-drop arrangement during protein extraction and digestion.