Science in the Aye Lab

Laboratory of Electrophiles and Genome Operation (LEGO)

We innovate original chemical biology technologies and apply them to understand biochemistry and cell biology of electrophile signaling pathways and molecular regulation of electrophile-responsive proteins of importance in human pathophysiology. In a parallel program distinct from electrophile signaling, we study proteins and pathways involved in mammalian genome maintenance, including the mechanisms of anticancer agents in clinical use that tap into DNA biogenesis.


Our Research Arena

  • Synthetic Methodology
  • Chemical Biology
  • Biochemistry
  • Biophysics
  • 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:

Research Programs

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.

Fang & Fu et al., J Am Chem Soc (2013) 135 14496

Parvez & Fu et al., J Am Chem Soc (2015) 137 10

Lin et al., J Am Chem Soc (2015) 137 6232

Long et al., J Am Chem Soc (2016) 138 3610 – Selected by the JACS Editors as a JACS SpotsLight Article

Parvez & Long et al., Nature Protocols (201611 2328

Long et al. ACS CRT (201629 1575 (in honor of ACS CRT Young Investigator Award) – Selected as an ACS Editors’ Choice Article; Selected for Journal Cover Art

Long & Parvez et al. Nature Chemical Biology (2017) 13 333
[Selected for News & Views in the same journal (2017) Nature Chemical Biology 13 244]

Long et al. ACS Chemical Biology (2017) 12 586

Long et al. Cell Chemical Biology (2017) (Perspective) Early view on line

Lin & Long et al. Cell Chemical Biology (2017) (original research) Early view on line

Long, Urul, & Chawla et al. ACS Biochemistry (2017) (original research)- DOI: 10.1021/acs.biochem.7b00642 Selected as an ACS Editors’ Choice Article

Zhao et al. (2018) ACS Central Science (original research) Just Accepted (Feb 2018)

Surya & Long et al. (2018ACS Chemical Biology (original research) Just Accepted (Feb 2018)

Van Hall-Beauvais et al. (2018) Current Protocols in Chemical Biology  – Wiley (Protocols) Just Accepted (Feb 2018)

Poganik & Long et al. (2018BioEssays  – Wiley (Problems & Paradigms) Just Accepted (Feb 2018)

Long et al. (2018) In Revision (original research)

Poganik et al. (2018) Submitted (original research)

Parvez & Long et al. (2018) In Revision (Review)

Parvez & Long et al. (2018) In Revision (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.

Fu et al., Biochemistry (201352 7050

Fu et al., ChemBioChem (2014) 15  2598

Aye and Weiss labs, Oncogene (2015) 34 2011

Wisitpitthaya et al., ACS Chem Bio (2016) 11 2021

Fu & Long et al. (2018) Revised & resubmitted (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

Program 1:
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.

Program 2:
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.

Program 3:
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