The objective of this proposal is to develop new probe targeting methodology based on the enzyme lipoic acid ligase (LplA). LplA catalyzes the site-specific covalent conjugation of the cofactor lipoic acid onto the lysine sidechain of one of three bacterial protein substrates. We propose to re-engineer LplA for probe targeting inside living mammalian cells. We previously engineered a transposable 12-amino acid peptide substrate for LplA, and mutagenized the lipoate binding pocket to accommodate a coumarin fluorophore. Here, we propose to (1) use a combination of rational design and directed evolution to engineer LplA-derived ligases for the red fluorophore resorufin and the photocrosslinker benzophenone. For directed evolution, we will explore FACS, cell laser ablation, and antibiotic selection strategies in parallel;(2) develop two-step probe targeting schemes based on LplA-catalyzed ligation of functional group handles such as alkyl azides;and (3) apply our new probe ligases to the study of neurexin and neuroligin biology in living neurons. Our work should benefit cell biologists interested in minimally- invasive analysis of protein function in single living cells, and neuroscientists interested in understanding the molecular bases of synapse development.

Public Health Relevance

We are proposing new chemical technology that has the potential to transform biological microscopy. As an alternative to Green Fluorescent Protein, which received this year's Nobel Prize in Chemistry, our """"""""probe ligase"""""""" technology is far less invasive to proteins under study, and can introduce a much wider variety of fluorophore, photocrosslinker, and other probe structures with superior properties to the GFP chromophore. In this proposal, we also plan in-depth studies of neurexin and neuroligin biology, using probe ligase technology;these studies will shed light on the molecular mechanisms of synapse development and could accelerate the discovery of drugs to treat diseases such as autism.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Synthetic and Biological Chemistry A Study Section (SBCA)
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Fabian, Miles
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Massachusetts Institute of Technology
Schools of Arts and Sciences
United States
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Liu, Daniel S; Nivón, Lucas G; Richter, Florian et al. (2014) Computational design of a red fluorophore ligase for site-specific protein labeling in living cells. Proc Natl Acad Sci U S A 111:E4551-9
Uttamapinant, Chayasith; Sanchez, Mateo I; Liu, Daniel S et al. (2013) Site-specific protein labeling using PRIME and chelation-assisted click chemistry. Nat Protoc 8:1620-34
Liu, Daniel S; Tangpeerachaikul, Anupong; Selvaraj, Ramajeyam et al. (2012) Diels-Alder cycloaddition for fluorophore targeting to specific proteins inside living cells. J Am Chem Soc 134:792-5
Uttamapinant, Chayasith; Tangpeerachaikul, Anupong; Grecian, Scott et al. (2012) Fast, cell-compatible click chemistry with copper-chelating azides for biomolecular labeling. Angew Chem Int Ed Engl 51:5852-6
Liu, Daniel S; Phipps, William S; Loh, Ken H et al. (2012) Quantum dot targeting with lipoic acid ligase and HaloTag for single-molecule imaging on living cells. ACS Nano 6:11080-7
Slavoff, Sarah A; Liu, Daniel S; Cohen, Justin D et al. (2011) Imaging protein-protein interactions inside living cells via interaction-dependent fluorophore ligation. J Am Chem Soc 133:19769-76
Zou, Peng; Ting, Alice Y (2011) Imaging LDL receptor oligomerization during endocytosis using a co-internalization assay. ACS Chem Biol 6:308-13
Jin, Xin; Uttamapinant, Chayasith; Ting, Alice Y (2011) Synthesis of 7-aminocoumarin by Buchwald-Hartwig cross coupling for specific protein labeling in living cells. Chembiochem 12:65-70
Cohen, Justin D; Thompson, Samuel; Ting, Alice Y (2011) Structure-guided engineering of a Pacific Blue fluorophore ligase for specific protein imaging in living cells. Biochemistry 50:8221-5
Uttamapinant, Chayasith; White, Katharine A; Baruah, Hemanta et al. (2010) A fluorophore ligase for site-specific protein labeling inside living cells. Proc Natl Acad Sci U S A 107:10914-9

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