1
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Saini G, Parasa MK, Clayton KN, Fraseur JG, Bolton SC, Lin KP, Wereley ST, Kinzer-Ursem TL. Immobilization of azide-functionalized proteins to micro- and nanoparticles directly from cell lysate. Mikrochim Acta 2023; 191:46. [PMID: 38129631 PMCID: PMC10739308 DOI: 10.1007/s00604-023-06068-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/23/2023] [Indexed: 12/23/2023]
Abstract
Immobilization of proteins and enzymes on solid supports has been utilized in a variety of applications, from improved protein stability on supported catalysts in industrial processes to fabrication of biosensors, biochips, and microdevices. A critical requirement for these applications is facile yet stable covalent conjugation between the immobilized and fully active protein and the solid support to produce stable, highly bio-active conjugates. Here, we report functionalization of solid surfaces (gold nanoparticles and magnetic beads) with bio-active proteins using site-specific and biorthogonal labeling and azide-alkyne cycloaddition, a click chemistry. Specifically, we recombinantly express and selectively label calcium-dependent proteins, calmodulin and calcineurin, and cAMP-dependent protein kinase A (PKA) with N-terminal azide-tags for efficient conjugation to nanoparticles and magnetic beads. We successfully immobilized the proteins on to the solid supports directly from the cell lysate with click chemistry, forgoing the step of purification. This approach is optimized to yield low particle aggregation and high levels of protein activity post-conjugation. The entire process enables streamlined workflows for bioconjugation and highly active conjugated proteins.
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Affiliation(s)
- Gunjan Saini
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Mrugesh Krishna Parasa
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Katherine N Clayton
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Julia G Fraseur
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Scott C Bolton
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Kevin P Lin
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47906, USA
| | - Steven T Wereley
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Tamara L Kinzer-Ursem
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47906, USA.
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2
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Diestelkoetter-Bachert P, Beck R, Reckmann I, Hellwig A, Garcia-Saez A, Zelman-Hopf M, Hanke A, Nunes Alves A, Wade RC, Mayer MP, Wieland F. Structural characterization of an Arf dimer interface: molecular mechanism of Arf-dependent membrane scission. FEBS Lett 2020; 594:2240-2253. [PMID: 32394429 DOI: 10.1002/1873-3468.13808] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/20/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022]
Abstract
Dimerization of the small GTPase Arf is prerequisite for the scission of COPI-coated transport vesicles. Here, we quantify the monomer/dimer equilibrium of Arf within the membrane and show that after membrane scission, Arf dimers are restricted to donor membranes. By hydrogen exchange mass spectrometry, we define the interface of activated dimeric Arf within its switch II region. Single amino acid exchanges in this region reduce the propensity of Arf to dimerize. We suggest a mechanism of membrane scission by which the dimeric form of Arf is segregated to the donor membrane. Our data are consistent with the previously reported absence of dimerized Arf in COPI vesicles and could explain the presence of one single scar-like noncoated region in each COPI vesicle.
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Affiliation(s)
| | - Rainer Beck
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Germany
| | - Inge Reckmann
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Germany
| | - Andrea Hellwig
- Interdisciplinary Center for Neurosciences (IZN), University of Heidelberg, Germany
| | - Ana Garcia-Saez
- Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Germany.,CECAD Research Center, CECAD Cologne, Germany
| | | | - Anton Hanke
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Germany
| | - Ariane Nunes Alves
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Germany
| | - Matthias P Mayer
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Germany
| | - Felix Wieland
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Germany
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3
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Ho S, Tirrell DA. Enzymatic Labeling of Bacterial Proteins for Super-resolution Imaging in Live Cells. ACS CENTRAL SCIENCE 2019; 5:1911-1919. [PMID: 31893220 PMCID: PMC6935894 DOI: 10.1021/acscentsci.9b00617] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Indexed: 06/10/2023]
Abstract
Methods that enable the super-resolution imaging of intracellular proteins in live bacterial cells provide powerful tools for the study of prokaryotic cell biology. Photoswitchable organic dyes exhibit many of the photophysical properties needed for super-resolution imaging, including high brightness, photostability, and photon output, but most such dyes require organisms to be fixed and permeabilized if intracellular targets are to be labeled. We recently reported a general strategy for the chemoenzymatic labeling of bacterial proteins with azide-bearing fatty acids in live cells using the eukaryotic enzyme N-myristoyltransferase. Here we demonstrate the labeling of proteins in live Escherichia coli using cell-permeant bicyclononyne-functionalized photoswitchable rhodamine spirolactams. Single-molecule fluorescence measurements on model rhodamine spirolactam salts show that these dyes emit hundreds of photons per switching event. Super-resolution imaging was performed on bacterial chemotaxis proteins Tar and CheA and cell division proteins FtsZ and FtsA. High-resolution imaging of Tar revealed a helical pattern; imaging of FtsZ yielded banded patterns dispersed throughout the cell. The precision of radial and axial localization in reconstructed images approaches 15 and 30 nm, respectively. The simplicity of the method, which does not require redox imaging buffers, should make this approach broadly useful for imaging intracellular bacterial proteins in live cells with nanometer resolution.
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4
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Shadish JA, Strange AC, DeForest CA. Genetically Encoded Photocleavable Linkers for Patterned Protein Release from Biomaterials. J Am Chem Soc 2019; 141:15619-15625. [PMID: 31525979 DOI: 10.1021/jacs.9b07239] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Given the critical role that proteins play in almost all biological processes, there is great interest in controlling their presentation within and release from biomaterials. Despite such outstanding enthusiasm, previously developed strategies in this regard result in ill-defined and heterogeneous populations with substantially decreased activity, precluding their successful application to fragile species including growth factors. Here, we introduce a modular and scalable method for creating monodisperse, genetically encoded chimeras that enable bioactive proteins to be immobilized within and subsequently photoreleased from polymeric hydrogels. Building upon recent developments in chemoenzymatic reactions, bioorthogonal chemistry, and optogenetics, we tether fluorescent proteins, model enzymes, and growth factors site-specifically to gel biomaterials through a photocleavable protein (PhoCl) that undergoes irreversible backbone photoscission upon exposure to cytocompatible visible light (λ ≈ 400 nm) in a dose-dependent manner. Mask-based and laser-scanning lithographic strategies using commonly available light sources are employed to spatiotemporally pattern protein release from hydrogels while retaining their full activity. The photopatterned epidermal growth factor presentation is exploited to promote anisotropic cellular proliferation in 3D. We expect these methods to be broadly useful for applications in diagnostics, drug delivery, and regenerative medicine.
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Affiliation(s)
| | | | - Cole A DeForest
- Department of Bioengineering , University of Washington , Seattle , Washington 98105 , United States.,Institute for Stem Cell & Regenerative Medicine , University of Washington , Seattle , Washington 98109 , United States
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5
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Ejendal KFK, Fraseur JG, Kinzer-Ursem TL. Protein Labeling and Bioconjugation Using N-Myristoyltransferase. Methods Mol Biol 2019; 2033:149-165. [PMID: 31332753 DOI: 10.1007/978-1-4939-9654-4_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Methods that allow for labeling of proteins cotranslationally within protein expression systems have had wide-ranging applications in health, engineering, and medicine. Bioorthogonal chemistries that allow for conjugation of proteins or biomolecules of interest to substrates (fluorophores, gold nanoparticles, polymers, etc.) in living cells without prior enrichment or purification have likewise enabled advances in technology to study and engineer cellular and biomolecular systems. At the intersection of these, chemoenzymatic labeling of proteins at specific sites of interest and their subsequent selective bioconjugation to substrates without prior purification has dramatically streamlined workflows that allow proteins to reside in the native expression volumes as long as possible prior to conjugation, be readily isolated upon conjugation, and remain functionally active after conjugation. Here we present methods and protocols to express and label proteins of interest at the N-terminus with azide derivatives of myristic acid, a small, soluble, 14-carbon fatty acid, and conjugate the labeled protein to fluorophores and gold nanoparticle substrates. These methods can be extended to label proteins with other myristoyl derivatives and to conjugation to other solid or polymeric substrates of interest.
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Affiliation(s)
- Karin F K Ejendal
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Julia G Fraseur
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Tamara L Kinzer-Ursem
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
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6
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Ho SH, Tirrell DA. N-Myristoyl Transferase (NMT)-Catalyzed Labeling of Bacterial Proteins for Imaging in Fixed and Live Cells. Methods Mol Biol 2019; 2012:315-326. [PMID: 31161515 DOI: 10.1007/978-1-4939-9546-2_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Methods for selective protein imaging are critical for elucidating how cells orchestrate fundamental biological processes. We recently developed a chemoenzymatic method to modify bacterial proteins in situ for fluorescence imaging using N-myristoyl transferase (NMT). Target proteins outfitted with an N-terminal NMT recognition sequence are covalently modified with an azido fatty acid. Subsequent strain-promoted azide-alkyne cycloaddition allows for conjugation to cell-permeant fluorophores and imaging by fluorescence microscopy. Here we describe sample preparation and labeling protocols for imaging bacterial proteins in fixed and live cells.
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Affiliation(s)
- Samuel H Ho
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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7
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Adolf F, Rhiel M, Hessling B, Gao Q, Hellwig A, Béthune J, Wieland FT. Proteomic Profiling of Mammalian COPII and COPI Vesicles. Cell Rep 2019; 26:250-265.e5. [DOI: 10.1016/j.celrep.2018.12.041] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 09/08/2018] [Accepted: 12/10/2018] [Indexed: 12/26/2022] Open
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8
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Liu L, Shadish JA, Arakawa CK, Shi K, Davis J, DeForest CA. Cyclic Stiffness Modulation of Cell-Laden Protein-Polymer Hydrogels in Response to User-Specified Stimuli including Light. ADVANCED BIOSYSTEMS 2018; 2:1800240. [PMID: 34316509 PMCID: PMC8312699 DOI: 10.1002/adbi.201800240] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Indexed: 11/10/2022]
Abstract
Although mechanical signals presented by the extracellular matrix are known to regulate many essential cell functions, the specific effects of these interactions, particularly in response to dynamic and heterogeneous cues, remain largely unknown. Here, we introduce a modular semisynthetic approach to create protein-polymer hydrogel biomaterials that undergo reversible stiffening in response to user-specified inputs. Employing a novel dual-chemoenzymatic modification strategy, we create fusion protein-based gel crosslinkers that exhibit stimuli-dependent intramolecular association. Linkers based on calmodulin yield calcium-sensitive materials, while those containing the photosensitive LOV2 (light, oxygen, and voltage sensing domain 2) protein give phototunable constructs whose moduli can be cycled on demand with spatiotemporal control about living cells. We exploit these unique materials to demonstrate the significant role that cyclic mechanical loading plays on fibroblast-to-myofibroblast transdifferentiation in three-dimensional (3D) space. Our moduli-switchable materials should prove useful for studies in mechanobiology, providing new avenues to probe and direct matrix-driven changes in 4D cell physiology.
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Affiliation(s)
- Luman Liu
- Department of Chemical Engineering, University of Washington, 3781 Okanogan Lane NE, Seattle, WA, 98195, USA
| | - Jared A Shadish
- Department of Chemical Engineering, University of Washington, 3781 Okanogan Lane NE, Seattle, WA, 98195, USA
| | - Christopher K Arakawa
- Department of Bioengineering, University of Washington, 3720 15th Ave NE, Seattle, WA, 98105, USA
| | - Kevin Shi
- Department of Bioengineering, University of Washington, 3720 15th Ave NE, Seattle, WA, 98105, USA
| | - Jennifer Davis
- Department of Bioengineering, University of Washington, 3720 15th Ave NE, Seattle, WA, 98105, USA; Department of Pathology, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA; Institute of Stem Cell & Regenerative Medicine, University of Washington, 850 Republican St., Seattle, WA, 98109, USA
| | - Cole A DeForest
- Department of Chemical Engineering, University of Washington, 3781 Okanogan Lane NE, Seattle, WA, 98195, USA; Department of Bioengineering, University of Washington, 3720 15th Ave NE, Seattle, WA, 98105, USA; Institute of Stem Cell & Regenerative Medicine, University of Washington, 850 Republican St., Seattle, WA, 98109, USA; Molecular Engineering & Sciences Institute, University of Washington, 3946 W Stevens Way NE, Seattle, WA, 98195, USA
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9
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Abstract
Protein synthesis is initiated by methionine in eukaryotes and by formylmethionine in prokaryotes. N-terminal methionine can be co-translationally cleaved by the enzyme methionine aminopeptidase (MAP). When recombinant proteins are expressed in bacterial and mammalian expression systems, there is a simple universal rule that predicts whether the initiating methionine will be processed by MAP based on the size of the residue adjacent (penultimate) to the N-methionine. In general, if the side chains of the penultimate residues have a radius of gyration of 1.29 Å or less, methionine is cleaved. © 2017 by John Wiley & Sons, Inc.
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10
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Ho SH, Tirrell DA. Chemoenzymatic Labeling of Proteins for Imaging in Bacterial Cells. J Am Chem Soc 2016; 138:15098-15101. [PMID: 27933886 DOI: 10.1021/jacs.6b07067] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Reliable methods to determine the subcellular localization of bacterial proteins are needed for the study of prokaryotic cell biology. We describe here a simple and general technique for imaging of bacterial proteins in situ by fluorescence microscopy. The method uses the eukaryotic enzyme N-myristoyltransferase to modify the N-terminus of the protein of interest with an azido fatty acid. Subsequent strain-promoted azide-alkyne cycloaddition allows conjugation of dyes and imaging of tagged proteins by confocal fluorescence microscopy. We demonstrate the method by labeling the chemotaxis proteins Tar and CheA and the cell division proteins FtsZ and FtsA in Escherichia coli. We observe distinct spatial patterns for each of these proteins in both fixed and live cells. The method should prove broadly useful for protein imaging in bacteria.
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Affiliation(s)
- Samuel H Ho
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States
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11
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Kerr SC, Kahn RA. Tool box: Plasmids for the expression or knockdown of human ARF Family GTPases (ARF/ARL/SAR) and their co-expression in bacteria with N-myristoyltransferases. CELLULAR LOGISTICS 2016; 5:e1090523. [PMID: 27057421 PMCID: PMC4820815 DOI: 10.1080/21592799.2015.1090523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 08/26/2015] [Accepted: 08/28/2015] [Indexed: 10/30/2022]
Affiliation(s)
- Shana C Kerr
- School of Biology; Georgia Institute of Technology ; Atlanta, GA USA
| | - Richard A Kahn
- Department of Biochemistry; Emory University School of Medicine ; Atlanta, GA USA
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12
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The TRPM1 channel in ON-bipolar cells is gated by both the α and the βγ subunits of the G-protein Go. Sci Rep 2016; 6:20940. [PMID: 26883481 PMCID: PMC4756708 DOI: 10.1038/srep20940] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/16/2015] [Indexed: 12/25/2022] Open
Abstract
Transmission from photoreceptors to ON bipolar cells in mammalian retina is mediated by a sign-inverting cascade. Upon binding glutamate, the metabotropic glutamate receptor mGluR6 activates the heterotrimeric G-protein Gαoβ3γ13, and this leads to closure of the TRPM1 channel (melastatin). TRPM1 is thought to be constitutively open, but the mechanism that leads to its closure is unclear. We investigated this question in mouse rod bipolar cells by dialyzing reagents that modify the activity of either Gαo or Gβγ and then observing their effects on the basal holding current. After opening the TRPM1 channels with light, a constitutively active mutant of Gαo closed the channel, but wild-type Gαo did not. After closing the channels by dark adaptation, phosducin or inactive Gαo (both sequester Gβγ) opened the channel while the active mutant of Gαo did not. Co-immunoprecipitation showed that TRPM1 interacts with Gβ3 and with the active and inactive forms of Gαo. Furthermore, bioluminescent energy transfer assays indicated that while Gαo interacts with both the N- and the C- termini of TRPM1, Gβγ interacts only with the N-terminus. Our physiological and biochemical results suggest that both Gαo and Gβγ bind TRPM1 channels and cooperate to close them.
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13
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Kulkarni C, Lo M, Fraseur JG, Tirrell DA, Kinzer-Ursem TL. Bioorthogonal Chemoenzymatic Functionalization of Calmodulin for Bioconjugation Applications. Bioconjug Chem 2015; 26:2153-60. [PMID: 26431265 DOI: 10.1021/acs.bioconjchem.5b00449] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Calmodulin (CaM) is a widely studied Ca(2+)-binding protein that is highly conserved across species and involved in many biological processes, including vesicle release, cell proliferation, and apoptosis. To facilitate biophysical studies of CaM, researchers have tagged and mutated CaM at various sites, enabling its conjugation to fluorophores, microarrays, and other reactive partners. However, previous attempts to add a reactive label to CaM for downstream studies have generally employed nonselective labeling methods or resulted in diminished CaM function. Here we report the first engineered CaM protein that undergoes site-specific and bioorthogonal labeling while retaining wild-type activity levels. By employing a chemoenzymatic labeling approach, we achieved selective and quantitative labeling of the engineered CaM protein with an N-terminal 12-azidododecanoic acid tag; notably, addition of the tag did not interfere with the ability of CaM to bind Ca(2+) or a partner protein. The specificity of our chemoenzymatic labeling approach also allowed for selective conjugation of CaM to reactive partners in bacterial cell lysates, without intermediate purification of the engineered protein. Additionally, we prepared CaM-affinity resins that were highly effective in purifying a representative CaM-binding protein, demonstrating that the engineered CaM remains active even after surface capture. Beyond studies of CaM and CaM-binding proteins, the protein engineering and surface capture methods described here should be translatable to other proteins and other bioconjugation applications.
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Affiliation(s)
- Chethana Kulkarni
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Blvd., Pasadena, California 91125, United States
| | - Megan Lo
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Blvd., Pasadena, California 91125, United States
| | - Julia G Fraseur
- Weldon School of Biomedical Engineering, Purdue University , 206 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Blvd., Pasadena, California 91125, United States
| | - Tamara L Kinzer-Ursem
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Blvd., Pasadena, California 91125, United States.,Weldon School of Biomedical Engineering, Purdue University , 206 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
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14
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Co-expression for intracellular processing in microbial protein production. Biotechnol Lett 2013; 36:427-41. [DOI: 10.1007/s10529-013-1379-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 10/04/2013] [Indexed: 12/19/2022]
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15
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Kulkarni C, Kinzer-Ursem TL, Tirrell DA. Selective functionalization of the protein N terminus with N-myristoyl transferase for bioconjugation in cell lysate. Chembiochem 2013; 14:1958-62. [PMID: 24030852 DOI: 10.1002/cbic.201300453] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Indexed: 12/16/2022]
Abstract
A site to behold: Robust site-specific functionalization of engineered proteins is achieved with N-myristoyl transferase (NMT) in bacterial cells. NMT tolerates non-natural substrate proteins as well as reactive fatty acid tags, rendering it a powerful tool for protein conjugation applications, including the construction of protein microarrays from lysate.
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Affiliation(s)
- Chethana Kulkarni
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125 (USA) http://tirrell-lab.caltech.edu
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16
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Expression and purification of active mouse and human NEIL3 proteins. Protein Expr Purif 2012; 84:130-9. [PMID: 22569481 DOI: 10.1016/j.pep.2012.04.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 04/24/2012] [Accepted: 04/27/2012] [Indexed: 11/23/2022]
Abstract
Endonuclease VIII-like 3 (Neil3) is one of the five DNA glycosylases found in mammals that recognize and remove oxidized bases, and initiate the base excision repair (BER) pathway. Previous attempts to express and purify the mouse and human orthologs of Neil3 in their active form have not been successful. Here we report the construction of bicistronic expression vectors for expressing in Escherichia coli the full-length mouse Neil3 (MmuNeil3), its glycosylase domain (MmuNeil3Δ324), as well as the glycosylase domain of human Neil3 (NEIL3Δ324). The purified Neil3 proteins are all active, and NEIL3Δ324 exhibits similar glycosylase/lyase activity as MmuNeil3Δ324 on both single-stranded and double-stranded substrates containing thymine glycol (Tg), spiroiminodihydantoin (Sp) or an abasic site (AP). We show that N-terminal initiator methionine processing is critical for the activity of both mouse and human Neil3 proteins. Co-expressing an E. coli methionine aminopeptidase (EcoMap) Y168A variant with MmuNeil3, MmuNeil3Δ324 and NEIL3Δ324 improves the N-terminal methionine processing and increases the percentage of active Neil3 proteins in the preparation. The purified Neil3 proteins are suitable for biochemical, structural and functional studies.
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17
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Heal WP, Wickramasinghe SR, Leatherbarrow RJ, Tate EW. N-Myristoyl transferase-mediated protein labelling in vivo. Org Biomol Chem 2008; 6:2308-15. [PMID: 18563263 DOI: 10.1039/b803258k] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
N-Myristoyl transferase-mediated labelling using a substrate modified with an azide or alkyne tag is described as an efficient and site-selective method for the introduction of a bioorthogonal tag at the N-terminus of a recombinant protein. The procedure may be performed in vitro, or in a single over-expression/tagging step in vivo in bacteria; tagged proteins may then be captured using Staudinger-Bertozzi or 'click' chemistry protocols to introduce a secondary label for downstream analysis. The straightforward synthesis of the chemical and molecular biological tools described should enable their use in a wide range of N-terminal labelling applications.
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Affiliation(s)
- William P Heal
- Department of Chemistry, South Kensington Campus, Imperial College, London, UK SW7 2AZ
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18
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Expressed Protein Ligation of 5-Enolpyruvylshikimate-3-phosphate (EPSP) Synthase: An Application to a Protein Expressed as an Inclusion Body. B KOREAN CHEM SOC 2007. [DOI: 10.5012/bkcs.2007.28.12.2303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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Heal WP, Wickramasinghe SR, Bowyer PW, Holder AA, Smith DF, Leatherbarrow RJ, Tate EW. Site-specific N-terminal labelling of proteins in vitro and in vivo using N-myristoyl transferase and bioorthogonal ligation chemistry. Chem Commun (Camb) 2007:480-2. [PMID: 18188474 DOI: 10.1039/b716115h] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
N-Myristoyl transferase-mediated modification with azide-bearing substrates is introduced as a highly selective and practical method for in vitro and in vivo N-terminal labelling of a recombinant protein using bioorthogonal ligation chemistry.
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Affiliation(s)
- William P Heal
- Department of Chemistry, South Kensington Campus, Imperial College, London, UK
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20
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Király O, Guan L, Szepessy E, Tóth M, Kukor Z, Sahin-Tóth M. Expression of human cationic trypsinogen with an authentic N terminus using intein-mediated splicing in aminopeptidase P deficient Escherichia coli. Protein Expr Purif 2006; 48:104-11. [PMID: 16542853 PMCID: PMC1604731 DOI: 10.1016/j.pep.2006.01.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2005] [Revised: 01/24/2006] [Accepted: 01/27/2006] [Indexed: 01/29/2023]
Abstract
High-level expression of human trypsinogens as inclusion bodies in Escherichia coli requires deletion of the secretory signal sequence and placement of an initiator methionine at the N terminus. Trypsinogen preparations obtained this way contain a mixture of abnormal N termini, as a result of processing by cytoplasmic aminopeptidases. Here, we describe an expression system that produces recombinant human cationic trypsinogen with a native, intact N terminus, using intein-mediated protein splicing and an aminopeptidase P (pepP) deficient E. coli strain. As a first application of this system, the effect of the pancreatitis-associated mutation A16V on the autoactivation of human cationic trypsinogen was characterized. The use of the novel pepP knock-out E. coli strain should be generally applicable to the expression of recombinant proteins, which undergo unwanted N-terminal trimming by aminopeptidase P.
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Affiliation(s)
- Orsolya Király
- Department of Molecular and Cell Biology, Goldman School of Dental Medicine, Boston University, Boston, MA, 02118
| | - Lan Guan
- Department of Physiology, University of California Los Angeles, Los Angeles, CA 90095
| | - Edit Szepessy
- Department of Molecular and Cell Biology, Goldman School of Dental Medicine, Boston University, Boston, MA, 02118
| | - Miklós Tóth
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Zoltán Kukor
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Miklós Sahin-Tóth
- Department of Molecular and Cell Biology, Goldman School of Dental Medicine, Boston University, Boston, MA, 02118
- Mailing address: 715 Albany Street, Evans-433; Boston, MA 02118, Tel: (617) 414-1070; Fax: (617) 414-1041; E-mail:
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21
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Desmeules P, Penney SE, Salesse C. Single-step purification of myristoylated and nonmyristoylated recoverin and substrate dependence of myristoylation level. Anal Biochem 2005; 349:25-32. [PMID: 16376289 DOI: 10.1016/j.ab.2005.11.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2005] [Revised: 11/13/2005] [Accepted: 11/14/2005] [Indexed: 10/25/2022]
Abstract
Recoverin is cotranslationally modified by the covalent linkage of a myristoyl group to its N terminus. It is a member of a family of Ca(2+)-myristoyl switch proteins. Recombinant myristoylated revoverin is currently produced by the cotransformation of bacteria with recoverin and an enzyme that allows N-myristoylation and by supplementing the culture medium with myristic acid. A large variation in the myristoylation level of recoverin and in the amount of myristic acid supplied to the culture medium can be found in the literature. Moreover, although it is known to strongly affect bacterial growth, the amount of ethanol used to solubilize myristic acid is only scarcely mentioned. To improve our understanding of the parameters responsible for recombinant recoverin myristoylation, the effects of myristic acid and ethanol on recoverin myristoylation and expression levels have been systematically studied. In addition, a single-step purification procedure to produce purified myristoylated and nonmyristoylated recombinant recoverin has also been devised. Finally, sodium myristate has been used as an efficient alternative substrate to achieve high myristoylation and expression levels of recoverin. Given that a large number of proteins are myristoylated, these procedures could be applied to several other proteins in addition to recoverin.
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Affiliation(s)
- Philippe Desmeules
- Unité de Recherche en Ophtalmologie, Centre de Recherche du CHUL, Faculté de Médecine, Université Laval, 2705 Blvd. Laurier, Ste-Foy, Que., Canada G1V 4G2
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22
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Shern JF, Sharer JD, Pallas DC, Bartolini F, Cowan NJ, Reed MS, Pohl J, Kahn RA. Cytosolic Arl2 is complexed with cofactor D and protein phosphatase 2A. J Biol Chem 2003; 278:40829-36. [PMID: 12912990 DOI: 10.1074/jbc.m308678200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Arl2 is a member of the ADP-ribosylation factor family of 20-kDa GTPases that is highly conserved in eukaryotes. Recent results revealed that a portion of cellular Arl2 and its binding partner, BART, localize to mitochondria. Because approximately 90% of cellular Arl2 is cytosolic, we investigated properties of the soluble protein and found that it is stably bound in a complex that migrates in gel filtration medium with a predicted molecular mass of approximately 300 kDa. This complex was purified approximately 500-fold from the soluble fraction of bovine brain. Protein components were identified by mass spectroscopy and revealed the presence of four other proteins that include the tubulin folding cochaperone cofactor D and all three subunits of at least two protein phosphatase 2A (PP2A) protein phosphatase trimers. The presence of more than one PP2A B-type subunit and the low stoichiometry of Arl2 indicate that the purified preparation still contains a mixture of complexes that cannot currently be completely resolved. Thus, although all the soluble Arl2 in bovine brain is in high molecular mass complexes, only a portion of the total cellular cofactor D and PP2A are associated with the Arl2. We further show that the Arl2 in the complex cannot bind GTP and that complexed cofactor D does not efficiently participate in tubulin refolding reactions in a manner comparable with free cofactor D. Our data suggest functional roles for the cytosolic Arl2 complex in modulating tubulin and microtubule behavior as well as a possible role in apoptosis.
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Affiliation(s)
- Jack F Shern
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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23
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Sharer JD, Shern JF, Van Valkenburgh H, Wallace DC, Kahn RA. ARL2 and BART enter mitochondria and bind the adenine nucleotide transporter. Mol Biol Cell 2002; 13:71-83. [PMID: 11809823 PMCID: PMC65073 DOI: 10.1091/mbc.01-05-0245] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The ADP-ribosylation factor-like 2 (ARL2) GTPase and its binding partner binder of ARL2 (BART) are ubiquitously expressed in rodent and human tissues and are most abundant in brain. Both ARL2 and BART are predominantly cytosolic, but a pool of each was found associated with mitochondria in a protease-resistant form. ARL2 was found to lack covalent N-myristoylation, present on all other members of the ARF family, thereby preserving the N-terminal amphipathic alpha-helix as a potential mitochondrial import sequence. An overlay assay was developed to identify binding partners for the BART.ARL2.GTP complex and revealed a specific interaction with a protein in bovine brain mitochondria. Purification and partial microsequencing identified the protein as an adenine nucleotide transporter (ANT). The overlay assay was performed on mitochondria isolated from five different tissues from either wild-type or transgenic mice deleted for ANT1. Results confirmed that ANT1 is the predominant binding partner for the BART.ARL2.GTP complex and that the structurally homologous ANT2 protein does not bind the complex. Cardiac and skeletal muscle mitochondria from ant1(-)/ant1(-) mice had increased levels of ARL2, relative to that seen in mitochondria from wild-type animals. We conclude that the amount of ARL2 in mitochondria is subject to regulation via an ANT1-sensitive pathway in muscle tissues.
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Affiliation(s)
- J Daniel Sharer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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