A5059297673- Glycosylation and Glycoproteins Research
- Ubiquitin and proteasome pathways
- Protein Degradation and Inhibitors
- Carbohydrate Chemistry and Synthesis
- Galectins and Cancer Biology
- Click Chemistry and Applications
- Peptidase Inhibition and Analysis
- Multiple Myeloma Research and Treatments
- Chemical Synthesis and Analysis
- Microbial Natural Products and Biosynthesis
- Monoclonal and Polyclonal Antibodies Research
- Receptor Mechanisms and Signaling
- Cancer therapeutics and mechanisms
- Signaling Pathways in Disease
- Synthesis and Biological Evaluation
- Advanced Proteomics Techniques and Applications
- Bioactive Compounds and Antitumor Agents
- Crystallization and Solubility Studies
- Biotin and Related Studies
- Histone Deacetylase Inhibitors Research
- Synthesis and Catalytic Reactions
- Toxin Mechanisms and Immunotoxins
- X-ray Diffraction in Crystallography
- Cyclopropane Reaction Mechanisms
- Synthetic Organic Chemistry Methods
Broad Institute
2023-2025
Harvard University
2017-2025
Harvard University Press
2020-2025
Stanford Medicine
2018
Stanford University
2016-2017
University of California, Berkeley
2015-2017
Howard Hughes Medical Institute
2017
University of Utah
2017
University of Georgia
2017
Yale University
2009-2016
Diazirines are widely used in photoaffinity labeling (PAL) to trap noncovalent interactions with biomolecules. However, design and interpretation of PAL experiments is challenging without a molecular understanding the reactivity diazirines protein Herein, we report systematic evaluation preferences alkyl aryl individual amino acids, single proteins, whole cell proteome. We find that exhibit preferential acidic acids pH-dependent manner characteristic reactive diazo intermediate, while...
Abstract Glycoproteomics is a powerful yet analytically challenging research tool. Software packages aiding the interpretation of complex glycopeptide tandem mass spectra have appeared, but their relative performance remains untested. Conducted through HUPO Human Initiative, this community study, comprising both developers and users glycoproteomics software, evaluates solutions for system-wide analysis. The same spectrometry based datasets from human serum were shared with participants team...
The University of California, Irvine ADD Center recently conducted a synthesis the literature on use stimulants with children attention deficit disorder (ADD), using unique “review reviews” methodology. In this article, we compare three reviews from each review types (traditional, meta-analytic, general audience) and illustrate how coding variables can highlight sources divergence. general, divergent conclusions stemmed variations in goal rather than selected to review. Across quantitative...
Post-translational modifications (PTMs) on proteins often function to regulate signaling cascades, with the activation of T cells during an adaptive immune response being a classic example. Mounting evidence indicates that modification by O-linked N-acetylglucosamine (O-Glcnac), only mammalian glycan found nuclear and cytoplasmic proteins, helps cell activation. Yet, mechanistic understanding how O-Glcnac functions in remains elusive, partly because difficulties mapping quantifying sites....
O-Linked β-N-acetylglucosamine (O-GlcNAc) is a monosaccharide that plays an essential role in cellular signaling throughout the nucleocytoplasmic proteome of eukaryotic cells. Strategies for selectively increasing O-GlcNAc levels on target protein cells would accelerate studies this modification. Here, we report generalizable strategy introducing into selected proteins using nanobody as proximity-directing agent fused to transferase (OGT). Fusion recognizes GFP (nGFP) or four-amino acid...
Many therapeutics elicit cell-type specific polypharmacology that is executed by a network of molecular recognition events between small molecule and the whole proteome. However, measurement structures underpin associations proteome even common therapeutics, such as nonsteroidal anti-inflammatory drugs (NSAIDs), limited inability to map interactome. To address this gap, we developed platform termed interactome mapping photoaffinity labeling (SIM-PAL) applied it in cellulo direct...
Protein glycosylation can have an enormous variety of biological consequences, reflecting the molecular diversity encoded in glycan structures. This same structural has imposed major challenges on development methods to study intact glycoproteome. We recently introduced a method termed isotope-targeted glycoproteomics (IsoTaG), which utilizes isotope recoding characterize azidosugar-labeled glycopeptides bearing fully glycans. Here, we describe broad application analyze glycoproteomes from...
O-GlcNAc is an abundant post-translational modification found on nuclear and cytoplasmic proteins in all metazoans. This regulates a wide variety of cellular processes, elevated levels have been implicated cancer progression. A single essential enzyme, transferase (OGT), responsible for nucleocytoplasmic O-GlcNAcylation. Understanding how this enzyme chooses its substrates critical understanding, potentially manipulating, functions. Here we use protein microarray technology proteome-wide...
The thalidomide analogue lenalidomide (Len) is a clinical therapeutic that alters the substrate engagement of cereblon (CRBN), receptor for CRL4 E3 ubiquitin ligase. Here, we report development photolenalidomide (pLen), Len probe with photoaffinity label and enrichment handle, designed target identification by chemical proteomics. pLen preserves degradation profile, phenotypic antiproliferative immunomodulatory properties Len, enhances interactions thalidomide-binding domain CRBN, as...
We describe the isolation of (–)-lomaiviticins C–E (6–8), elucidation complete absolute and relative stereochemistry (–)-lomaiviticin A (1), synthetic conversion C (6) to first evidence that dimeric diazofluorene (1) plays a defining critical role in antiproliferative activity.
Lomaiviticins A and B are complex antitumor antibiotics that were isolated from a strain of Micromonospora. confluence several unusual structural features renders the lomaiviticins exceedingly challenging targets for chemical synthesis. We report an 11-step, enantioselective synthetic route to lomaiviticin aglycon. Our proceeds by late-stage, stereoselective dimerization two equivalent monomeric intermediates, transformation may share parallels with natural products' biosyntheses. The we...
Structural characterization of small molecule binding site hotspots within the global proteome is uniquely enabled by photoaffinity labeling (PAL) coupled with chemical enrichment and unbiased analysis mass spectrometry (MS). MS-based maps provide structural resolution interaction sites in conjunction identification target proteins. However, hotspot mapping has been confined to relatively simple molecules date; extension more complex compounds would enable definition new modes proteome....
Metabolic chemical reporters of glycosylation in combination with bioorthogonal reactions have been known for two decades and used by many different research laboratories the identification visualization glycoconjugates. More recently, however, they begun to see utility investigation cellular metabolism tolerance biosynthetic enzymes glycosyltransferases sugars. Here, we take this concept one step further using metabolic reporter 6-azido-6-deoxy-glucose (6AzGlc). We show that treatment...
Abstract Photoaffinity labeling (PAL) is one of the few biochemical techniques that can give direct evidence biomolecular interactions in cells. Several photoactivatable functional groups have been adapted for use PAL since its first implementation. The diversity these chemistries has expanded scope and fidelity experiments, but also increased considerations during probe design. In this review, we describe major used experiments their relative benefits disadvantages. We additionally discuss...
Alkyl diazirines are frequently used in photoaffinity labeling to map small molecule–protein interactions target identification studies. However, the alkyl can preferentially label acidic amino acids and protein surfaces a pH-dependent manner, presumably via reactive diazo intermediate. Here, we explore use of ring strain alter these reactivity preferences report development cyclobutane diazirine tag with reduced reactivity, termed PALBOX. We show that PALBOX possesses differential profiles...