1
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Minoshima M, Reja SI, Hashimoto R, Iijima K, Kikuchi K. Hybrid Small-Molecule/Protein Fluorescent Probes. Chem Rev 2024; 124:6198-6270. [PMID: 38717865 DOI: 10.1021/acs.chemrev.3c00549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.
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Affiliation(s)
- Masafumi Minoshima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Shahi Imam Reja
- Immunology Frontier Research Center, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Ryu Hashimoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kohei Iijima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kazuya Kikuchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
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2
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Jiang Y, Neti SS, Sitarik I, Pradhan P, To P, Xia Y, Fried SD, Booker SJ, O'Brien EP. How synonymous mutations alter enzyme structure and function over long timescales. Nat Chem 2023; 15:308-318. [PMID: 36471044 DOI: 10.1038/s41557-022-01091-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/17/2022] [Indexed: 12/12/2022]
Abstract
The specific activity of enzymes can be altered over long timescales in cells by synonymous mutations that alter a messenger RNA molecule's sequence but not the encoded protein's primary structure. How this happens at the molecular level is unknown. Here, we use multiscale modelling of three Escherichia coli enzymes (type III chloramphenicol acetyltransferase, D-alanine-D-alanine ligase B and dihydrofolate reductase) to understand experimentally measured changes in specific activity due to synonymous mutations. The modelling involves coarse-grained simulations of protein synthesis and post-translational behaviour, all-atom simulations to test robustness and quantum mechanics/molecular mechanics calculations to characterize enzymatic function. We show that changes in codon translation rates induced by synonymous mutations cause shifts in co-translational and post-translational folding pathways that kinetically partition molecules into subpopulations that very slowly interconvert to the native, functional state. Structurally, these states resemble the native state, with localized misfolding near the active sites of the enzymes. These long-lived states exhibit reduced catalytic activity, as shown by their increased activation energies for the reactions they catalyse.
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Affiliation(s)
- Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Syam Sundar Neti
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Ian Sitarik
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Priya Pradhan
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Philip To
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Yingzi Xia
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Squire J Booker
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Howard Hughes Medical Institute, Pennsylvania State University, University Park, PA, USA
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA.
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, USA.
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3
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Shen D, Bai Y, Liu Y. Chemical Biology Toolbox to Visualize Protein Aggregation in Live Cells. Chembiochem 2021; 23:e202100443. [PMID: 34613660 DOI: 10.1002/cbic.202100443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/05/2021] [Indexed: 11/09/2022]
Abstract
Protein misfolding and aggregation is a complex biochemical process and has been associated with numerous human degenerative diseases. Developing novel chemical and biological tools and approaches to visualize aggregated proteins in live cells is in high demand for mechanistic studies, diagnostics, and therapeutics. In this review, we summarize the recent developments in the chemical biology toolbox applied to protein aggregation studies in live cells. These methods exploited fluorescent protein tags, fluorescent chemical tags, and small-molecule probes to visualize the protein-aggregation process, detect proteome stresses, and quantify the protein homeostasis network capacity. Inspired by these seminal works, we have generalized design principles for the development of new detection methods and probes in the future that will illuminate this important biological process.
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Affiliation(s)
- Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
| | - Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
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4
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Abstract
Protein folding in the cell is mediated by an extensive network of >1,000 chaperones, quality control factors, and trafficking mechanisms collectively termed the proteostasis network. While the components and organization of this network are generally well established, our understanding of how protein-folding problems are identified, how the network components integrate to successfully address challenges, and what types of biophysical issues each proteostasis network component is capable of addressing remains immature. We describe a chemical biology-informed framework for studying cellular proteostasis that relies on selection of interesting protein-folding problems and precise researcher control of proteostasis network composition and activities. By combining these methods with multifaceted strategies to monitor protein folding, degradation, trafficking, and aggregation in cells, researchers continue to rapidly generate new insights into cellular proteostasis.
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Affiliation(s)
- Rebecca M Sebastian
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
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5
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Trigo D, Nadais A, da Cruz e Silva OA. Unravelling protein aggregation as an ageing related process or a neuropathological response. Ageing Res Rev 2019; 51:67-77. [PMID: 30763619 DOI: 10.1016/j.arr.2019.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 01/07/2019] [Accepted: 02/07/2019] [Indexed: 12/18/2022]
Abstract
Protein aggregation is normally associated with amyloidosis, namely motor neurone, Alzheimer's, Parkinson's or prion diseases. However, recent results have unveiled a concept of gradual increase of protein aggregation associated with the ageing process, apparently not necessarily associated with pathological conditions. Given that protein aggregation is sufficient to activate stress-response and inflammation, impairing protein synthesis and quality control mechanisms, the former is assumed to negatively affect cellular metabolism and behaviour. In this review the state of the art in protein aggregation research is discussed, namely the relationship between pathology and proteostasis. The role of pathology and ageing in overriding protein quality-control mechanisms, and consequently, the effect of these faulty cellular processes on pathological and healthy ageing, are also addressed.
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6
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Zhang S, Liu M, Tan LYF, Hong Q, Pow ZL, Owyong TC, Ding S, Wong WWH, Hong Y. A Maleimide‐functionalized Tetraphenylethene for Measuring and Imaging Unfolded Proteins in Cells. Chem Asian J 2019; 14:904-909. [DOI: 10.1002/asia.201900150] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/14/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Shouxiang Zhang
- Department of Chemistry and Physics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
| | - Mengjie Liu
- Department of Chemistry and Physics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
| | - Lewis Yi Fong Tan
- Department of Chemistry and Physics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
| | - Quentin Hong
- ARC Centre of Excellence in Exciton Science, School of Chemistry Bio21 Institute The University of Melbourne Parkville VIC 3010 Australia
| | - Ze Liang Pow
- ARC Centre of Excellence in Exciton Science, School of Chemistry Bio21 Institute The University of Melbourne Parkville VIC 3010 Australia
| | - Tze Cin Owyong
- Department of Chemistry and Physics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
- ARC Centre of Excellence in Exciton Science, School of Chemistry Bio21 Institute The University of Melbourne Parkville VIC 3010 Australia
| | - Siyang Ding
- Department of Chemistry and Physics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
| | - Wallace W. H. Wong
- ARC Centre of Excellence in Exciton Science, School of Chemistry Bio21 Institute The University of Melbourne Parkville VIC 3010 Australia
| | - Yuning Hong
- Department of Chemistry and Physics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
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7
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Fares M, Li Y, Liu Y, Miao K, Gao Z, Zhai Y, Zhang X. A Molecular Rotor-Based Halo-Tag Ligand Enables a Fluorogenic Proteome Stress Sensor to Detect Protein Misfolding in Mildly Stressed Proteome. Bioconjug Chem 2018; 29:215-224. [DOI: 10.1021/acs.bioconjchem.7b00763] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Matthew Fares
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §The Huck Institutes
of Life Sciences, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Yinghao Li
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §The Huck Institutes
of Life Sciences, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Yu Liu
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §The Huck Institutes
of Life Sciences, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Kun Miao
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §The Huck Institutes
of Life Sciences, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Zi Gao
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §The Huck Institutes
of Life Sciences, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Yufeng Zhai
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §The Huck Institutes
of Life Sciences, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Xin Zhang
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §The Huck Institutes
of Life Sciences, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
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8
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Otte KB, Maurer E, Kirtz M, Grabs D, Althoff E, Bartsch S, Vogel A, Nestl BM, Hauer B. Synthesis of Sebacic Acid Using a De Novo Designed Retro-Aldolase as a Key Catalyst. ChemCatChem 2017. [DOI: 10.1002/cctc.201601551] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Konrad B. Otte
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Elena Maurer
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Marko Kirtz
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | | | | | | | - Andreas Vogel
- c-LEcta GmbH; Perlickstrasse 5 04103 Leipzig Germany
| | - Bettina M. Nestl
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
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9
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Radwan M, Wood RJ, Sui X, Hatters DM. When proteostasis goes bad: Protein aggregation in the cell. IUBMB Life 2017; 69:49-54. [PMID: 28066979 DOI: 10.1002/iub.1597] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/09/2016] [Indexed: 12/12/2022]
Abstract
Protein aggregation is a hallmark of the major neurodegenerative diseases including Alzheimer's, Parkinson's, Huntington's and motor neuron and is a symptom of a breakdown in the management of proteome foldedness. Indeed, it is remarkable that under normal conditions cells can keep their proteome in a highly crowded and confined space without uncontrollable aggregation. Proteins pose a particular challenge relative to other classes of biomolecules because upon synthesis they must typically follow a complex folding pathway to reach their functional conformation (native state). Non-native conformations, including the unfolded nascent chain, are highly prone to aberrant interactions, leading to aggregation. Here we review recent advances in knowledge of proteostasis, approaches to monitor proteostasis and the impact that protein aggregation has on biology. We also include discussion of the outstanding challenges. © 2017 IUBMB Life, 69(2):49-54, 2017.
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Affiliation(s)
- Mona Radwan
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Melbourne, Victoria, Australia
| | - Rebecca J Wood
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Melbourne, Victoria, Australia
| | - Xiaojing Sui
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Melbourne, Victoria, Australia
| | - Danny M Hatters
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Melbourne, Victoria, Australia
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10
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Tripathi A, Gupta K, Khare S, Jain PC, Patel S, Kumar P, Pulianmackal AJ, Aghera N, Varadarajan R. Molecular Determinants of Mutant Phenotypes, Inferred from Saturation Mutagenesis Data. Mol Biol Evol 2016; 33:2960-2975. [PMID: 27563054 PMCID: PMC5062330 DOI: 10.1093/molbev/msw182] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Understanding how mutations affect protein activity and organismal fitness is a major challenge. We used saturation mutagenesis combined with deep sequencing to determine mutational sensitivity scores for 1,664 single-site mutants of the 101 residue Escherichia coli cytotoxin, CcdB at seven different expression levels. Active-site residues could be distinguished from buried ones, based on their differential tolerance to aliphatic and charged amino acid substitutions. At nonactive-site positions, the average mutational tolerance correlated better with depth from the protein surface than with accessibility. Remarkably, similar results were observed for two other small proteins, PDZ domain (PSD95pdz3) and IgG-binding domain of protein G (GB1). Mutational sensitivity data obtained with CcdB were used to derive a procedure for predicting functional effects of mutations. Results compared favorably with those of two widely used computational predictors. In vitro characterization of 80 single, nonactive-site mutants of CcdB showed that activity in vivo correlates moderately with thermal stability and solubility. The inability to refold reversibly, as well as a decreased folding rate in vitro, is associated with decreased activity in vivo. Upon probing the effect of modulating expression of various proteases and chaperones on mutant phenotypes, most deleterious mutants showed an increased in vivo activity and solubility only upon over-expression of either Trigger factor or SecB ATP-independent chaperones. Collectively, these data suggest that folding kinetics rather than protein stability is the primary determinant of activity in vivo. This study enhances our understanding of how mutations affect phenotype, as well as the ability to predict fitness effects of point mutations.
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Affiliation(s)
- Arti Tripathi
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Kritika Gupta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Shruti Khare
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Pankaj C Jain
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Siddharth Patel
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Prasanth Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | - Nilesh Aghera
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore, India
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11
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Campos RI, Wu X, Elgland M, Konradsson P, Hammarström P. Novel trans-Stilbene-based Fluorophores as Probes for Spectral Discrimination of Native and Protofibrillar Transthyretin. ACS Chem Neurosci 2016; 7:924-40. [PMID: 27144293 DOI: 10.1021/acschemneuro.6b00062] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Accumulation of misfolded transthyretin (TTR) as amyloid fibrils causes various human disorders. Native transthyretin is a neurotrophic protein and is a putative extracellular molecular chaperone. Several fluorophores have been shown in vitro to bind selectively to native TTR. Other compounds, such as thioflavin T, bind TTR amyloid fibrils. The probe 1-anilinonaphthalene-8-sulfonate (ANS) binds to both native and fibrillar TTR, becoming highly fluorescent, but with indistinguishable emission spectra for native and fibrillar TTR. Herein we report our efforts to develop a fluorescent small molecule capable of binding both native and misfolded protofibrillar TTR, providing distinguishable emission spectra. We used microwave synthesis for efficient production of a small library of trans-stilbenes and fluorescence spectral screening of their binding properties. We synthesized and tested 22 trans-stilbenes displaying a variety of functional groups. We successfully developed two naphthyl-based trans-stilbenes probes that detect both TTR states at physiological concentrations. The compounds bound with nanomolar to micromolar affinities and displayed distinct emission maxima upon binding native or misfolded protofibrillar TTR (>100 nm difference). The probes were mainly responsive to environment polarity providing evidence for the divergent hydrophobic structure of the binding sites of these protein conformational states. Furthermore, we were able to successfully use one of these probes to quantify the relative amounts of native and protofibrillar TTR in a dynamic equilibrium. In conclusion, we identified two trans-stilbene-based fluorescent probes, (E)-4-(2-(naphthalen-1-yl)vinyl)benzene-1,2-diol (11) and (E)-4-(2-(naphthalen-2-yl)vinyl)benzene-1,2-diol (14), that bind native and protofibrillar TTR, providing a wide difference in emission maxima allowing conformational discrimination by fluorescence spectroscopy. We expect these novel molecules to serve as important chemical biology research tools in studies of TTR folding and misfolding.
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Affiliation(s)
- Raúl I Campos
- IFM−Department of Chemistry, Linköping University, Linköping 581 83, Sweden
| | - Xiongyu Wu
- IFM−Department of Chemistry, Linköping University, Linköping 581 83, Sweden
| | - Mathias Elgland
- IFM−Department of Chemistry, Linköping University, Linköping 581 83, Sweden
| | - Peter Konradsson
- IFM−Department of Chemistry, Linköping University, Linköping 581 83, Sweden
| | - Per Hammarström
- IFM−Department of Chemistry, Linköping University, Linköping 581 83, Sweden
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12
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Chen W, Dong J, Plate L, Mortenson DE, Brighty GJ, Li S, Liu Y, Galmozzi A, Lee PS, Hulce JJ, Cravatt BF, Saez E, Powers ET, Wilson IA, Sharpless KB, Kelly JW. Arylfluorosulfates Inactivate Intracellular Lipid Binding Protein(s) through Chemoselective SuFEx Reaction with a Binding Site Tyr Residue. J Am Chem Soc 2016; 138:7353-64. [PMID: 27191344 PMCID: PMC4909538 DOI: 10.1021/jacs.6b02960] [Citation(s) in RCA: 197] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Arylfluorosulfates have appeared only rarely in the literature and have not been explored as probes for covalent conjugation to proteins, possibly because they were assumed to possess high reactivity, as with other sulfur(VI) halides. However, we find that arylfluorosulfates become reactive only under certain circumstances, e.g., when fluoride displacement by a nucleophile is facilitated. Herein, we explore the reactivity of structurally simple arylfluorosulfates toward the proteome of human cells. We demonstrate that the protein reactivity of arylfluorosulfates is lower than that of the corresponding aryl sulfonyl fluorides, which are better characterized with regard to proteome reactivity. We discovered that simple hydrophobic arylfluorosulfates selectively react with a few members of the intracellular lipid binding protein (iLBP) family. A central function of iLBPs is to deliver small-molecule ligands to nuclear hormone receptors. Arylfluorosulfate probe 1 reacts with a conserved tyrosine residue in the ligand-binding site of a subset of iLBPs. Arylfluorosulfate probes 3 and 4, featuring a biphenyl core, very selectively and efficiently modify cellular retinoic acid binding protein 2 (CRABP2), both in vitro and in living cells. The X-ray crystal structure of the CRABP2-4 conjugate, when considered together with binding site mutagenesis experiments, provides insight into how CRABP2 might activate arylfluorosulfates toward site-specific reaction. Treatment of breast cancer cells with probe 4 attenuates nuclear hormone receptor activity mediated by retinoic acid, an endogenous client lipid of CRABP2. Our findings demonstrate that arylfluorosulfates can selectively target single iLBPs, making them useful for understanding iLBP function.
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Affiliation(s)
- Wentao Chen
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jiajia Dong
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Lars Plate
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David E. Mortenson
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabriel J. Brighty
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Suhua Li
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yu Liu
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrea Galmozzi
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Peter S. Lee
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan J. Hulce
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Benjamin F. Cravatt
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Enrique Saez
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Evan T. Powers
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A. Wilson
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - K. Barry Sharpless
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeffery W. Kelly
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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13
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Liu Y, Zhang X, Chen W, Tan YL, Kelly JW. Fluorescence Turn-On Folding Sensor To Monitor Proteome Stress in Live Cells. J Am Chem Soc 2015; 137:11303-11. [PMID: 26305239 PMCID: PMC4755273 DOI: 10.1021/jacs.5b04366] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Proteome misfolding and/or aggregation, caused by a thermal perturbation or a related stress, transiently challenges the cellular protein homeostasis (proteostasis) network capacity of cells by consuming chaperone/chaperonin pathway and degradation pathway capacity. Developing protein client-based probes to quantify the cellular proteostasis network capacity in real time is highly desirable. Herein we introduce a small-molecule-regulated fluorescent protein folding sensor based on a thermo-labile mutant of the de novo designed retroaldolase (RA) enzyme. Since RA enzyme activity is not present in any cell, the protein folding sensor is bioorthogonal. The fluorogenic small molecule was designed to become fluorescent when it binds to and covalently reacts with folded and functional RA. Thus, in the first experimental paradigm, cellular proteostasis network capacity and its dynamics are reflected by RA-small molecule conjugate fluorescence, which correlates with the amount of folded and functional RA present, provided that pharmacologic chaperoning is minimized. In the second experimental scenario, the RA-fluorogenic probe conjugate is pre-formed in a cell by simply adding the fluorogenic probe to the cell culture media. Unreacted probe is then washed away before a proteome misfolding stress is applied in a pulse-chase-type experiment. Insufficient proteostasis network capacity is reflected by aggregate formation of the fluorescent RA-fluorogenic probe conjugate. Removal of the stress results in apparent RA-fluorogenic probe conjugate re-folding, mediated in part by the heat-shock response transcriptional program augmenting cytosolic proteostasis network capacity, and in part by time-dependent RA-fluorogenic probe conjugate degradation by cellular proteolysis.
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Affiliation(s)
- Yu Liu
- Department of Chemistry, ‡Department of Molecular and Experimental Medicine, and §The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Xin Zhang
- Department of Chemistry, ‡Department of Molecular and Experimental Medicine, and §The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Wentao Chen
- Department of Chemistry, ‡Department of Molecular and Experimental Medicine, and §The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Yun Lei Tan
- Department of Chemistry, ‡Department of Molecular and Experimental Medicine, and §The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Jeffery W Kelly
- Department of Chemistry, ‡Department of Molecular and Experimental Medicine, and §The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
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14
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Baranczak A, Liu Y, Connelly S, Du WGH, Greiner ER, Genereux JC, Wiseman RL, Eisele YS, Bradbury NC, Dong J, Noodleman L, Sharpless KB, Wilson IA, Encalada SE, Kelly JW. A fluorogenic aryl fluorosulfate for intraorganellar transthyretin imaging in living cells and in Caenorhabditis elegans. J Am Chem Soc 2015; 137:7404-14. [PMID: 26051248 PMCID: PMC4472559 DOI: 10.1021/jacs.5b03042] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Fluorogenic probes, due to their often greater spatial and temporal sensitivity in comparison to permanently fluorescent small molecules, represent powerful tools to study protein localization and function in the context of living systems. Herein, we report fluorogenic probe 4, a 1,3,4-oxadiazole designed to bind selectively to transthyretin (TTR). Probe 4 comprises a fluorosulfate group not previously used in an environment-sensitive fluorophore. The fluorosulfate functional group does not react covalently with TTR on the time scale required for cellular imaging, but does red shift the emission maximum of probe 4 in comparison to its nonfluorosulfated analogue. We demonstrate that probe 4 is dark in aqueous buffers, whereas the TTR·4 complex exhibits a fluorescence emission maximum at 481 nm. The addition of probe 4 to living HEK293T cells allows efficient binding to and imaging of exogenous TTR within intracellular organelles, including the mitochondria and the endoplasmic reticulum. Furthermore, live Caenorhabditis elegans expressing human TTR transgenically and treated with probe 4 display TTR·4 fluorescence in macrophage-like coelomocytes. An analogue of fluorosulfate probe 4 does react selectively with TTR without labeling the remainder of the cellular proteome. Studies on this analogue suggest that certain aryl fluorosulfates, due to their cell and organelle permeability and activatable reactivity, could be considered for the development of protein-selective covalent probes.
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Affiliation(s)
- Aleksandra Baranczak
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Yu Liu
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Stephen Connelly
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Erin R. Greiner
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Joseph C. Genereux
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - R. Luke Wiseman
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Yvonne S. Eisele
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Nadine C. Bradbury
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Jiajia Dong
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Louis Noodleman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - K. Barry Sharpless
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Sandra E. Encalada
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- Dorris Neuroscience Center, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Jeffery W. Kelly
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
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15
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Individual and collective contributions of chaperoning and degradation to protein homeostasis in E. coli. Cell Rep 2015; 11:321-33. [PMID: 25843722 DOI: 10.1016/j.celrep.2015.03.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/29/2015] [Accepted: 03/07/2015] [Indexed: 11/24/2022] Open
Abstract
The folding fate of a protein in vivo is determined by the interplay between a protein's folding energy landscape and the actions of the proteostasis network, including molecular chaperones and degradation enzymes. The mechanisms of individual components of the E. coli proteostasis network have been studied extensively, but much less is known about how they function as a system. We used an integrated experimental and computational approach to quantitatively analyze the folding outcomes (native folding versus aggregation versus degradation) of three test proteins biosynthesized in E. coli under a variety of conditions. Overexpression of the entire proteostasis network benefited all three test proteins, but the effect of upregulating individual chaperones or the major degradation enzyme, Lon, varied for proteins with different biophysical properties. In sum, the impact of the E. coli proteostasis network is a consequence of concerted action by the Hsp70 system (DnaK/DnaJ/GrpE), the Hsp60 system (GroEL/GroES), and Lon.
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16
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Roth DM, Hutt DM, Tong J, Bouchecareilh M, Wang N, Seeley T, Dekkers JF, Beekman JM, Garza D, Drew L, Masliah E, Morimoto RI, Balch WE. Modulation of the maladaptive stress response to manage diseases of protein folding. PLoS Biol 2014; 12:e1001998. [PMID: 25406061 PMCID: PMC4236052 DOI: 10.1371/journal.pbio.1001998] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 10/07/2014] [Indexed: 12/31/2022] Open
Abstract
Diseases of protein folding arise because of the inability of an altered peptide sequence to properly engage protein homeostasis components that direct protein folding and function. To identify global principles of misfolding disease pathology we examined the impact of the local folding environment in alpha-1-antitrypsin deficiency (AATD), Niemann-Pick type C1 disease (NPC1), Alzheimer's disease (AD), and cystic fibrosis (CF). Using distinct models, including patient-derived cell lines and primary epithelium, mouse brain tissue, and Caenorhabditis elegans, we found that chronic expression of misfolded proteins not only triggers the sustained activation of the heat shock response (HSR) pathway, but that this sustained activation is maladaptive. In diseased cells, maladaptation alters protein structure-function relationships, impacts protein folding in the cytosol, and further exacerbates the disease state. We show that down-regulation of this maladaptive stress response (MSR), through silencing of HSF1, the master regulator of the HSR, restores cellular protein folding and improves the disease phenotype. We propose that restoration of a more physiological proteostatic environment will strongly impact the management and progression of loss-of-function and gain-of-toxic-function phenotypes common in human disease.
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Affiliation(s)
- Daniela Martino Roth
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Darren M. Hutt
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jiansong Tong
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Marion Bouchecareilh
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ning Wang
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois, United States of America
| | - Theo Seeley
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Johanna F. Dekkers
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
- Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Jeffrey M. Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
- Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Dan Garza
- Proteostasis Therapeutics Inc., Cambridge, Massachusetts, United States of America
| | - Lawrence Drew
- Proteostasis Therapeutics Inc., Cambridge, Massachusetts, United States of America
| | - Eliezer Masliah
- Department of Neurosciences, University of California, San Diego, La Jolla, California, United States of America
| | - Richard I. Morimoto
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois, United States of America
| | - William E. Balch
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
- The Institute for Childhood and Neglected Diseases, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
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17
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Correia AR, Naik S, Fisher MT, Gomes CM. Probing the kinetic stabilities of Friedreich's ataxia clinical variants using a solid phase GroEL chaperonin capture platform. Biomolecules 2014; 4:956-79. [PMID: 25333765 PMCID: PMC4279165 DOI: 10.3390/biom4040956] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 08/29/2014] [Accepted: 09/19/2014] [Indexed: 11/17/2022] Open
Abstract
Numerous human diseases are caused by protein folding defects where the protein may become more susceptible to degradation or aggregation. Aberrant protein folding can affect the kinetic stability of the proteins even if these proteins appear to be soluble in vivo. Experimental discrimination between functional properly folded and misfolded nonfunctional conformers is not always straightforward at near physiological conditions. The differences in the kinetic behavior of two initially folded frataxin clinical variants were examined using a high affinity chaperonin kinetic trap approach at 25 °C. The kinetically stable wild type frataxin (FXN) shows no visible partitioning onto the chaperonin. In contrast, the clinical variants FXN-p.Asp122Tyr and FXN-p.Ile154Phe kinetically populate partial folded forms that tightly bind the GroEL chaperonin platform. The initially soluble FXN-p.Ile154Phe variant partitions onto GroEL more rapidly and is more kinetically liable. These differences in kinetic stability were confirmed using differential scanning fluorimetry. The kinetic and aggregation stability differences of these variants may lead to the distinct functional impairments described in Friedreich's ataxia, the neurodegenerative disease associated to frataxin functional deficiency. This chaperonin platform approach may be useful for identifying small molecule stabilizers since stabilizing ligands to frataxin variants should lead to a concomitant decrease in chaperonin binding.
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Affiliation(s)
- Ana R Correia
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, Oeiras 2784-505, Portugal.
| | - Subhashchandra Naik
- Department of Biochemistry and Molecular Biology, Hemenway Life Sciences Innovation Center (HLSIC), University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA.
| | - Mark T Fisher
- Department of Biochemistry and Molecular Biology, Hemenway Life Sciences Innovation Center (HLSIC), University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA.
| | - Cláudio M Gomes
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, Oeiras 2784-505, Portugal.
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18
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Zhang X, Liu Y, Genereux JC, Nolan C, Singh M, Kelly JW. Heat-shock response transcriptional program enables high-yield and high-quality recombinant protein production in Escherichia coli. ACS Chem Biol 2014; 9:1945-9. [PMID: 25051296 PMCID: PMC4168666 DOI: 10.1021/cb5004477] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The biosynthesis of soluble, properly
folded recombinant proteins
in large quantities from Escherichia coli is desirable
for academic research and industrial protein production. The basal E. coli protein homeostasis (proteostasis) network capacity
is often insufficient to efficiently fold overexpressed proteins.
Herein we demonstrate that a transcriptionally reprogrammed E. coli proteostasis network is generally superior for producing
soluble, folded, and functional recombinant proteins. Reprogramming
is accomplished by overexpressing a negative feedback deficient heat-shock
response
transcription factor before and during overexpression of the protein-of-interest.
The advantage of transcriptional reprogramming versus simply overexpressing
select proteostasis network components (e.g., chaperones and co-chaperones,
which has been explored previously) is that a large number of proteostasis
network components are upregulated at their evolved stoichiometry,
thus maintaining the system capabilities of the proteostasis network
that are currently incompletely understood. Transcriptional proteostasis
network reprogramming mediated by stress-responsive signaling in the
absence of stress should also be useful for protein production in
other cells.
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Affiliation(s)
- Xin Zhang
- Department of Chemistry, ‡Department of Molecular and Experimental
Medicine, and §Department of
Chemical Physiology, ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yu Liu
- Department of Chemistry, ‡Department of Molecular and Experimental
Medicine, and §Department of
Chemical Physiology, ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Joseph C. Genereux
- Department of Chemistry, ‡Department of Molecular and Experimental
Medicine, and §Department of
Chemical Physiology, ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Chandler Nolan
- Department of Chemistry, ‡Department of Molecular and Experimental
Medicine, and §Department of
Chemical Physiology, ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Meha Singh
- Department of Chemistry, ‡Department of Molecular and Experimental
Medicine, and §Department of
Chemical Physiology, ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jeffery W. Kelly
- Department of Chemistry, ‡Department of Molecular and Experimental
Medicine, and §Department of
Chemical Physiology, ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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19
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Liu Y, Zhang X, Tan YL, Bhabha G, Ekiert DC, Kipnis Y, Bjelic S, Baker D, Kelly JW. De novo-designed enzymes as small-molecule-regulated fluorescence imaging tags and fluorescent reporters. J Am Chem Soc 2014; 136:13102-5. [PMID: 25209927 PMCID: PMC4183642 DOI: 10.1021/ja5056356] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Enzyme-based tags attached to a protein-of-interest (POI) that react with a small molecule, rendering the conjugate fluorescent, are very useful for studying the POI in living cells. These tags are typically based on endogenous enzymes, so protein engineering is required to ensure that the small-molecule probe does not react with the endogenous enzyme in the cell of interest. Here we demonstrate that de novo-designed enzymes can be used as tags to attach to POIs. The inherent bioorthogonality of the de novo-designed enzyme-small-molecule probe reaction circumvents the need for protein engineering, since these enzyme activities are not present in living organisms. Herein, we transform a family of de novo-designed retroaldolases into variable-molecular-weight tags exhibiting fluorescence imaging, reporter, and electrophoresis applications that are regulated by tailored, reactive small-molecule fluorophores.
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Affiliation(s)
- Yu Liu
- Department of Chemistry, Department of Molecular and Experimental Medicine, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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20
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Misfolded protein? we have a chemical for that. Biotechniques 2014; 56:212-5. [DOI: 10.2144/000114163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Can small molecule studies decipher protein folding landscapes and perhaps identify the next wonder drug? Nathan Blow looks at how chemical biology is changing our view of protein folding.
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