Science in the Aye Lab
Welcome to the Laboratory of Electrophile And Genome Operation (LEAGO). Our business is understanding cellular communication processes. We are most well-known for our studies into electrophile signalling, but we also study nucleotide signalling pathways. Our work is slowly bringing both eclectic forms of cellular communication into focus. Critically, we have proven that electrophile signalling impinges on all aspects of cellular processes, and we have uncovered hidden aspects of nucleotide signalling pathways that serve to guard the genome. We pioneered the use of photocaged electrophiles (REX technologies) to bypass many of the limitations associated with the use of reactive electrophiles in cells/whole organisms. These technologies that can trigger protein specific electrophile-mediated signalling or can profile the best electrophile sensors are proving to be uniquely useful. We have also used biochemistry/cell biology/genetics to uncover novel roles of one of the most ancient enzymes, ribonucleotide reductase. Unsurprisingly, we are a multidisciplinary lab that uses chemistry, biochemistry, cell biology, genetics and a number of model organisms to solve complex problems. Our work is of significant relevance to human health. Through our united team effort, we strive to develop novel interventions, and to better understanding of current drugs through active collaborations with industrial scientists.
Our Research Arena
- Synthetic Methodology
- Chemical Biology
- Molecular and Cell Biology
- Beyond in vitro and cell-based mechanistic studies, we use more complex and biologically-relevant systems, namely, C. elegans and zebrafish, as our in vivo models:
Interrogating precision electrophile signaling events with single-protein-target specificity and spatiotemporal resolution directly in live larval fish
Simultaneous profiling and validation of privileged electrophile sensors in precise time, space, and biological context, directly in vivo
1) T-REX™ Electrophile Delivery & G-REX™ Profiling of Privileged Sensors Responsive to Native Signaling Electrophiles & Covalent Drugs
We are exploiting T-REX target-specific electrophile delivery and G-REX direct profiling platforms that our lab has recently developed, to deconstruct individual electrophilic signaling events in living systems, specifically, cultured animal cells, larval zebrafish, and C. elegans.
J Am Chem Soc (2013) 135 14496
J Am Chem Soc (2015) 137 10
J Am Chem Soc (2015) 137 6232
J Am Chem Soc (2016) 138 3610 – Selected by the JACS Editors as a JACS SpotsLight Article
Nature Protocols (2016) 11 2328
ACS CRT (2016) 29 1575 (in honor of ACS CRT Young Investigator Award) – Selected as an ACS Editors’ Choice Article; Selected for Journal Cover Art
ACS Chemical Biology (2017) 12 586
Cell Chemical Biology (2017) (perspective) Early view on line
Cell Chemical Biology (2017) (original research) Early view on line
ACS Biochemistry (2017) (original research)- DOI: 10.1021/acs.biochem.7b00642 Selected as an ACS Editors’ Choice Article
ACS Central Science (2018) (original research) Just Accepted (Feb 2018)
ACS Chemical Biology (2018) (original research) Just Accepted (Feb 2018)
Current Protocols in Chemical Biology (2018)– Wiley (protocols) Accepted (Feb 2018)
BioEssays (2018) – Wiley (problems & paradigms) Accepted (Feb 2018)
Chemical Reviews (2018) – ACS (review article) Accepted (Aug 2018)
Trends in Biochemical Sciences (2018) (review article) Accepted (Oct 2018)
Methods in Enzymology (2019) (techniques review) – Accepted
Trends in Biochemical Sciences (2019) (technological corner) – Accepted
Frontiers Chemistry: contribution to rising stars in chemistry special issue (2019) (chemical biology primer) – Accepted
J Am Chem Soc (2019) (original research in collaboration with the Nagorny lab) – Accepted
Liu et al. (2019) Submitted (original research)
Zhao et al. (2019) In peer review (original research)
Poganik et al. (2019) Submitted (original research)
Long, Van Hall-Beauvais & Parvez et al. (2019) In in-depth peer review (original research)
2) Novel Functions of Protein Multimers in Nucleotide Signaling, DNA Biogenesis, and Genome Maintenance
We are seeking to advance mechanistic understanding of nucleotide drugs-driven protein oligomeric regulation and functional consequences in DNA replication and genome integrity through approaches that combine in vitro studies, cell culture, and through collaboration, electron microscopy and studies in mice models.
Biochemistry (2013) 52 7050
ChemBioChem (2014) 15 2598
Oncogene (2015) 34 2011
ACS Chem Bio (2016) 11 2021
Nature Chemical Biology (2018) (original research) Accepted (August 2018)
ChemBioChem (2018) – ChemBioTalents special issue (review article) Just Accepted (Dec 2018)
Long and Zhao et al. (2019) In Revision (original research)
3) Biophysics and Biochemical Regulation of Redox-Dependent Metalloenzymes
We are investigating the mechanism and regulation of redox-dependent metalloenzymes in isolated systems and in intact mammalian cells. This program interfaces Program (1) and (2) above.
Specific Opportunities for Training & Experience in-House
synthetic methodology and new reaction discovery, protein expression/purification, mammalian tissue culture, cloning and gene delivery, lentiviral vector-mediated transduction of short-hairpin RNAs, live-cell imaging (confocal fluorescence & multiphoton excitation microscopy), flow cytometry, immunoprecipitation, quantitative real-time PCR, proteomics analyses, RNA biology, and protein-RNA interactions, and chemical biology/biochemical techniques in zebrafish and C. elegans including microinjection techniques.
chemical and chemoenzymatic synthesis, protein expression/purification, enzyme inhibition kinetics, oligomeric state analyses, fluorescence assays (using both synthetic dyes & fluorescent proteins): fluorescence resonance energy transfer (FRET) and fluorescence anisotropy, stopped-flow kinetics, mammalian tissue culture, cloning and gene delivery, fluorescence-activated cell sorting (FACS) analysis, live-cell imaging (confocal fluorescence microscopy), cell-based DNA damage assays, single DNA fiber staining method, RNA-seq analysis, and high-throughput drug discovery.
anaerobic techniques in metalloenzymology, in vitro and whole-cell electron paramagnetic resonance spectroscopy, mammalian tissue culture, cloning, generation and maintenance of stable cell lines, microscopy.
Additional Training Opportunities through Research Collaborations
- Single particle electron microscopy
- Macromolecular X-ray crystallography
- Animal model studies in mice
- Computational modeling of cell signaling networks