1
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Jing R, Walczak MA. Peptide and Protein Desulfurization with Diboron Reagents. Org Lett 2024; 26:2590-2595. [PMID: 38517348 PMCID: PMC10999128 DOI: 10.1021/acs.orglett.4c00609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
In this Letter, we report a direct and robust desulfurization method employing water-soluble phosphine, specifically tris(2-carboxyethyl)phosphine hydrochloride (TCEP), and tetrahydroxydiboron (B2(OH)4), which serves as a radical initiator. This innovative reaction exhibits compatibility with a diverse array of substrates, including cysteine residues in chemically synthesized oligopeptides and cyclic peptides, alkyl thiols in bioactive molecules, disulfides in commercial proteins, and selenocysteine. We optimized the reaction conditions to minimize the formation of undesired oxidized and borylated byproducts. Furthermore, the refined desulfurization process is executed after native chemical ligation (NCL) in a single pot, streamlining the existing synthetic approaches. This demonstrates its potential applications in the synthesis of complex peptides and proteins, showcasing a significant advancement in the field.
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Affiliation(s)
- Ruiheng Jing
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Maciej A Walczak
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
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2
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Galesic A, Pan B, Ramirez J, Rhoades E, Pratt MR, Petersson EJ. Combining non-canonical amino acid mutagenesis and native chemical ligation for multiply modifying proteins: A case study of α-synuclein post-translational modifications. Methods 2023; 218:101-109. [PMID: 37549799 PMCID: PMC10657485 DOI: 10.1016/j.ymeth.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023] Open
Abstract
The Parkinson's disease associated protein α-synuclein (αS) has been found to contain numerous post-translational modifications (PTMs), in both physiological and pathological states. One PTM site of particular interest is serine 87, which is subject to both O-linked β-N-acetylglucosamine (gS) modification and phosphorylation (pS), with αS-pS87 enriched in Parkinson's disease. An often-overlooked aspect of these PTMs is their effect on the membrane-binding properties of αS, which are important to its role in regulating neurotransmitter release. Here, we show how one can study these effects by synthesizing αS constructs containing authentic PTMs and labels for single molecule fluorescence correlation spectroscopy measurements. We synthesize αS-gS87 and αS-pS87 by combining native chemical ligation with genetic code expansion approaches. We introduce the fluorophore by a click reaction with a non-canonical amino acid. Beyond the specific problem of PTM effects on αS, our studies highlight the value of this combination of methods for multiply modifying proteins.
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Affiliation(s)
- Ana Galesic
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Buyan Pan
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
| | - Jennifer Ramirez
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Elizabeth Rhoades
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Matthew R. Pratt
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - E. James Petersson
- Department of Chemistry; University of Pennsylvania; 231 South 34th Street; Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
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3
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Cory MB, Jones CM, Shaffer KD, Venkatesh Y, Giannakoulias S, Perez RM, Lougee MG, Hummingbird E, Pagar VV, Hurley CM, Li A, Mach RH, Kohli RM, Petersson EJ. FRETing about the details: Case studies in the use of a genetically encoded fluorescent amino acid for distance-dependent energy transfer. Protein Sci 2023; 32:e4633. [PMID: 36974585 PMCID: PMC10108435 DOI: 10.1002/pro.4633] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023]
Abstract
Förster resonance energy transfer (FRET) is a valuable method for monitoring protein conformation and biomolecular interactions. Intrinsically fluorescent amino acids that can be genetically encoded, such as acridonylalanine (Acd), are particularly useful for FRET studies. However, quantitative interpretation of FRET data to derive distance information requires careful use of controls and consideration of photophysical effects. Here we present two case studies illustrating how Acd can be used in FRET experiments to study small molecule induced conformational changes and multicomponent biomolecular complexes.
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Affiliation(s)
- Michael B. Cory
- Graduate Group in Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Chloe M. Jones
- Graduate Group in Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Kyle D. Shaffer
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Yarra Venkatesh
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Sam Giannakoulias
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Ryann M. Perez
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Marshall G. Lougee
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Eshe Hummingbird
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Vinayak V. Pagar
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Christina M. Hurley
- Graduate Group in Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Allen Li
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Robert H. Mach
- Department of RadiologyPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Rahul M. Kohli
- Department of Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
- Department of MedicinePerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - E. James Petersson
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
- Department of Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
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4
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Wagner AM, Warner JB, Garrett HE, Walters CR, Petersson EJ. Transferase-Mediated Labeling of Protein N-Termini with Click Chemistry Handles. Methods Mol Biol 2023; 2620:157-175. [PMID: 37010762 DOI: 10.1007/978-1-0716-2942-0_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
The E. coli aminoacyl transferase (AaT) can be used to transfer a variety of unnatural amino acids, including those with azide or alkyne groups, to the α-amine of a protein with an N-terminal Lys or Arg. Subsequent functionalization through either copper-catalyzed or strain-promoted click reactions can be used to label the protein with fluorophores or biotin. This can be used to directly detect AaT substrates or in a two-step protocol to detect substrates of the mammalian ATE1 transferase.
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Affiliation(s)
- Anne M Wagner
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - John B Warner
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Haviva E Garrett
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | | | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA.
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5
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Kashina AS. Development of New Tools for the Studies of Protein Arginylation. Methods Mol Biol 2023; 2620:287-293. [PMID: 37010771 DOI: 10.1007/978-1-0716-2942-0_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
Studies of posttranslational modifications present many unique challenges, stemming from their role as the major drivers of biological complexity. Perhaps the most immediate challenge to researchers working on virtually any posttranslational modification is the shortage of reliable easy-to-use tools that can enable massive identification and characterization of posttranslationally modified proteins, as well as their functional modulation in vitro and in vivo. In the case of protein arginylation, which utilizes charged Arg-tRNA that is also used by the ribosomes, detection and labeling of arginylated proteins is especially difficult, because of the necessity of distinguishing these proteins from the products of conventional translation. As of now, this difficulty remains the major obstacle to new researchers entering the field. This chapter discusses some of the strategies for developing antibodies for arginylation detection, as well as some general considerations for development of other tools for studies of arginylation.
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Affiliation(s)
- Anna S Kashina
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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6
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Pan B, Kamo N, Shimogawa M, Huang Y, Kashina A, Rhoades E, Petersson EJ. Effects of Glutamate Arginylation on α-Synuclein: Studying an Unusual Post-Translational Modification through Semisynthesis. J Am Chem Soc 2020; 142:21786-21798. [PMID: 33337869 DOI: 10.1021/jacs.0c10054] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A variety of post-translational modifications (PTMs) are believed to regulate the behavior and function of α-synuclein (αS), an intrinsically disordered protein that mediates synaptic vesicle trafficking. Fibrils of αS are implicated in neurodegenerative disorders such as Parkinson's disease. In this study, we used chemical synthesis and biophysical techniques to characterize the neuroprotective effects of glutamate arginylation, a hitherto little characterized PTM in αS. We developed semisynthetic routes combining peptide synthesis, unnatural amino acid mutagenesis, and native chemical ligation (NCL) to site-specifically introduce the PTM of interest along with fluorescent probes into αS. We synthesized the arginylated glutamate as a protected amino acid, as well as a novel ligation handle for NCL, in order to generate full-length αS modified at various individual sites or a combination of sites. We assayed the lipid-vesicle binding affinities of arginylated αS using fluorescence correlation spectroscopy (FCS) and found that arginylated αS has the same vesicle affinity compared to control protein, suggesting that this PTM does not alter the native function of αS. On the other hand, we studied the aggregation kinetics of modified αS and found that arginylation at E83, but not E46, slows aggregation and decreases the percentage incorporation of monomer into fibrils in a dose-dependent manner. Arginylation at both sites also resulted in deceleration of fibril formation. Our study represents the first synthetic strategy for incorporating glutamate arginylation into proteins and provides insight into the neuroprotective effect of this unusual PTM.
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Affiliation(s)
- Buyan Pan
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Naoki Kamo
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States.,Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Marie Shimogawa
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Yun Huang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Anna Kashina
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, Pennsylvania 19104, United States
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
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7
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Abstract
Site-specific protein labeling can be used to monitor protein motions and interactions in real time using Förster resonance energy transfer (FRET). While there are many fluorophores available for protein labeling, few FRET pairs are suitable for monitoring intramolecular protein motions without being disruptive to protein folding and function. Here, we describe the synthesis and use of a minimally perturbing FRET pair comprised of methoxycoumarin maleimide (Mcm-Mal) and acridonylalanine (Acd). Acd can be incorporated into a protein through unnatural amino acid mutagenesis. Mcm-Mal is fluorogenic when reacted with cysteine and can label cysteine/Acd double mutant proteins. This labeling strategy provides an easy to install FRET pair with a working range or 15-40Å, making it ideal for monitoring most intramolecular motions. Additionally, Mcm/Acd FRET can be combined with tryptophan fluorescence for monitoring multiple protein motions via three color FRET.
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Affiliation(s)
- Chloe M Jones
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States; Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, United States
| | - Yarra Venkatesh
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States.
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8
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Abstract
Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.
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Affiliation(s)
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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9
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Pan B, Rhoades E, Petersson EJ. Chemoenzymatic Semisynthesis of Phosphorylated α-Synuclein Enables Identification of a Bidirectional Effect on Fibril Formation. ACS Chem Biol 2020; 15:640-645. [PMID: 32065743 DOI: 10.1021/acschembio.9b01038] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Post-translational modifications (PTMs) impact the pathological aggregation of α-synuclein (αS), a hallmark of Parkinson's disease (PD). Here, we synthesize αS phosphorylated at tyrosine 39 (pY39) through a novel route using in vitro enzymatic phosphorylation of a fragment followed by ligation to form the full-length protein. We can execute this synthesis in combination with unnatural amino acid mutagenesis to include two fluorescent labels for Förster resonance energy transfer (FRET) studies. We determine the effect of pY39 on the aggregation of αS and compare our authentically phosphorylated material to the corresponding glutamate 39 "phosphomimetic." Intriguingly, we find that αS-pY39 can either accelerate or decelerate aggregation, depending on the fraction of phosphorylated protein. The αS-E39 mutant can qualitatively reproduce some, but not all, of these effects. FRET measurements and analysis of existing structures of αS help to provide an explanation for this phenomenon. Our results have important implications for the treatment of PD patients with tyrosine kinase inhibitors and highlight the importance of validating phosphomimetics through studies of authentic PTMs.
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Affiliation(s)
- Buyan Pan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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10
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Wang S, Thopate YA, Zhou Q, Wang P. Chemical Protein Synthesis by Native Chemical Ligation and Variations Thereof. CHINESE J CHEM 2019. [DOI: 10.1002/cjoc.201900246] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Siyao Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical EngineeringShanghai Jiao Tong University 800 Dongchuan Road, Shanghai 200240 China
| | - Yogesh Abaso Thopate
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical EngineeringShanghai Jiao Tong University 800 Dongchuan Road, Shanghai 200240 China
| | - Qingqing Zhou
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical EngineeringShanghai Jiao Tong University 800 Dongchuan Road, Shanghai 200240 China
| | - Ping Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical EngineeringShanghai Jiao Tong University 800 Dongchuan Road, Shanghai 200240 China
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11
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Abstract
Protein arginylation-enzymatic addition of the amino acid arginine (Arg) to proteins, mediated by arginyltransferase ATE1, has been discovered in 1963, but is still relatively poorly understood. Studies of arginylation present many technical challenges, which arise from the fact that Arg is a regular amino acid that also incorporates into proteins during translation. Thus, in vitro arginylation needs to be conducted in a strictly ribosome-free system, in highly controlled conditions. Identification of arginylated proteins is currently only possible by high precision mass spectrometry, which relies on very high mass accuracy of the instruments, specific ionization patterns during mass fragmentation, as well as multiple stringent steps of automated and manual validation. Below we describe the methods of in vitro arginylation and mass spectrometry analysis of arginylated proteins, developed by our groups during the last 15 years.
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Affiliation(s)
- Junling Wang
- University of Pennsylvania, Philadelphia, PA, United States
| | - John R Yates
- The Scripps Research Institute, LaJolla, CA, United States
| | - Anna Kashina
- University of Pennsylvania, Philadelphia, PA, United States.
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12
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Chandrashekar C, Okamoto R, Izumi M, Kajihara Y. Chemical Modification of the N Termini of Unprotected Peptides for Semisynthesis of Modified Proteins by Utilizing a Hydrophilic Protecting Group. Chemistry 2019; 25:10197-10203. [DOI: 10.1002/chem.201901778] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/15/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Chaitra Chandrashekar
- Department of Chemistry and Project Research Center for, Fundamental SciencesGraduate School of ScienceOsaka University1-1 Toyonaka Osaka 5600043 Japan
| | - Ryo Okamoto
- Department of Chemistry and Project Research Center for, Fundamental SciencesGraduate School of ScienceOsaka University1-1 Toyonaka Osaka 5600043 Japan
| | - Masayuki Izumi
- Department of Chemistry and Project Research Center for, Fundamental SciencesGraduate School of ScienceOsaka University1-1 Toyonaka Osaka 5600043 Japan
| | - Yasuhiro Kajihara
- Department of Chemistry and Project Research Center for, Fundamental SciencesGraduate School of ScienceOsaka University1-1 Toyonaka Osaka 5600043 Japan
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13
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Agouridas V, El Mahdi O, Diemer V, Cargoët M, Monbaliu JCM, Melnyk O. Native Chemical Ligation and Extended Methods: Mechanisms, Catalysis, Scope, and Limitations. Chem Rev 2019; 119:7328-7443. [DOI: 10.1021/acs.chemrev.8b00712] [Citation(s) in RCA: 243] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Vangelis Agouridas
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Ouafâa El Mahdi
- Faculté Polydisciplinaire de Taza, University Sidi Mohamed Ben Abdellah, BP 1223 Taza Gare, Morocco
| | - Vincent Diemer
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Marine Cargoët
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Jean-Christophe M. Monbaliu
- Center for Integrated Technology and Organic Synthesis, Department of Chemistry, University of Liège, Building B6a, Room 3/16a, Sart-Tilman, B-4000 Liège, Belgium
| | - Oleg Melnyk
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
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14
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Dardashti RN, Metanis N. Revisiting ligation at selenomethionine: Insights into native chemical ligation at selenocysteine and homoselenocysteine. Bioorg Med Chem 2017; 25:4983-4989. [DOI: 10.1016/j.bmc.2017.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 04/30/2017] [Accepted: 05/04/2017] [Indexed: 10/19/2022]
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15
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Gosavi PM, Korendovych IV. Minimalist IR and fluorescence probes of protein function. Curr Opin Chem Biol 2016; 34:103-109. [PMID: 27599185 DOI: 10.1016/j.cbpa.2016.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/16/2016] [Accepted: 08/18/2016] [Indexed: 11/19/2022]
Abstract
Spectroscopic studies of small proteins and peptides, especially those requiring fine spatial and/or temporal resolution, demand synthetic probes that confer the minimal possible steric and functional change on the native properties. Here we review the recent progress in development of minimally disruptive probes for fluorescence and infrared spectroscopies, as well as the methods to efficiently incorporate them into proteins. Advances in spectroscopy on the one hand result in high specialization of synthetic probes for a particular purpose, but on the other hand allow for the same probes be used for different techniques to gather complementary biochemical information.
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Affiliation(s)
- Pallavi M Gosavi
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, United States
| | - Ivan V Korendovych
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, United States.
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16
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Ta DT, Guedens W, Vranken T, Vanschoenbeek K, Steen Redeker E, Michiels L, Adriaensens P. Enhanced Biosensor Platforms for Detecting the Atherosclerotic Biomarker VCAM1 Based on Bioconjugation with Uniformly Oriented VCAM1-Targeting Nanobodies. BIOSENSORS-BASEL 2016; 6:bios6030034. [PMID: 27399790 PMCID: PMC5039653 DOI: 10.3390/bios6030034] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 06/27/2016] [Accepted: 06/29/2016] [Indexed: 01/05/2023]
Abstract
Surface bioconjugation of biomolecules has gained enormous attention for developing advanced biomaterials including biosensors. While conventional immobilization (by physisorption or covalent couplings using the functional groups of the endogenous amino acids) usually results in surfaces with low activity, reproducibility and reusability, the application of methods that allow for a covalent and uniformly oriented coupling can circumvent these limitations. In this study, the nanobody targeting Vascular Cell Adhesion Molecule-1 (NbVCAM1), an atherosclerotic biomarker, is engineered with a C-terminal alkyne function via Expressed Protein Ligation (EPL). Conjugation of this nanobody to azidified silicon wafers and Biacore™ C1 sensor chips is achieved via Copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) “click” chemistry to detect VCAM1 binding via ellipsometry and surface plasmon resonance (SPR), respectively. The resulting surfaces, covered with uniformly oriented nanobodies, clearly show an increased antigen binding affinity, sensitivity, detection limit, quantitation limit and reusability as compared to surfaces prepared by random conjugation. These findings demonstrate the added value of a combined EPL and CuAAC approach as it results in strong control over the surface orientation of the nanobodies and an improved detecting power of their targets—a must for the development of advanced miniaturized, multi-biomarker biosensor platforms.
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Affiliation(s)
- Duy Tien Ta
- Biomolecule Design Group, Institute for Materials Research (IMO), Hasselt University, Diepenbeek BE-3590, Belgium.
- Faculty of Food Technology and Biotechnology, Can Tho University of Technology, Can Tho 900000, Vietnam.
| | - Wanda Guedens
- Biomolecule Design Group, Institute for Materials Research (IMO), Hasselt University, Diepenbeek BE-3590, Belgium.
| | - Tom Vranken
- Biomolecule Design Group, Institute for Materials Research (IMO), Hasselt University, Diepenbeek BE-3590, Belgium.
| | - Katrijn Vanschoenbeek
- Immunology and Biochemistry, Biomedical Research Institute (Biomed) and School of Life Sciences, Transnationale Universiteit Limburg, Hasselt University, Diepenbeek BE-3590, Belgium.
| | - Erik Steen Redeker
- Maastricht Science Programme, Maastricht University, Maastricht 6200 MD, The Netherlands.
| | - Luc Michiels
- Immunology and Biochemistry, Biomedical Research Institute (Biomed) and School of Life Sciences, Transnationale Universiteit Limburg, Hasselt University, Diepenbeek BE-3590, Belgium.
| | - Peter Adriaensens
- Biomolecule Design Group, Institute for Materials Research (IMO), Hasselt University, Diepenbeek BE-3590, Belgium.
- Applied and Analytical Chemistry, Institute for Materials Research (IMO), Hasselt University, Diepenbeek BE-3590, Belgium.
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17
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Wang YJ, Szantai-Kis DM, Petersson EJ. Chemoselective modifications for the traceless ligation of thioamide-containing peptides and proteins. Org Biomol Chem 2016; 14:6262-9. [PMID: 27264841 DOI: 10.1039/c6ob01020b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Thioamides are single-atom substitutions of canonical amide bonds, and have been proven to be versatile and minimally perturbing probes in protein folding studies. Previously, our group showed that thioamides can be incorporated into proteins by native chemical ligation (NCL) with Cys as a ligation handle. In this study, we report the expansion of this strategy into non-Cys ligation sites, utilizing radical initiated desulfurization to "erase" the side chain thiol after ligation. The reaction exhibited high chemoselectivity against thioamides, which can be further enhanced with thioacetamide as a sacrificial scavenger. As a proof-of-concept example, we demonstrated the incorporation of a thioamide probe into a 56 amino acid protein, the B1 domain of Protein G (GB1). Finally, we showed that the method can be extended to β-thiol amino acid analogs and selenocysteine.
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Affiliation(s)
- Yanxin J Wang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA.
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18
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Wagner AM, Warner JB, Garrett HE, Walters CR, Petersson EJ. Transferase-Mediated Labeling of Protein N-Termini with Click Chemistry Handles. Methods Mol Biol 2016; 1337:109-27. [PMID: 26285888 DOI: 10.1007/978-1-4939-2935-1_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The E. coli aminoacyl transferase (AaT) can be used to transfer a variety of unnatural amino acids, including those with azide or alkyne groups, to the α-amine of a protein with an N-terminal Lys or Arg. Subsequent functionalization through either copper-catalyzed or strain-promoted click reactions can be used to label the protein with fluorophores or biotin. This method can be used to directly detect AaT substrates or in a two-step protocol to detect substrates of the mammalian ATE1 transferase.
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Affiliation(s)
- Anne M Wagner
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA, 19104-6323, USA
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Abstract
Studies of posttranslational modifications present many unique challenges, stemming from their role as the major drivers of biological complexity. Perhaps the most immediate challenge to researchers working on virtually any posttranslational modification is the shortage of reliable easy-to-use tools that can enable massive identification and characterization of posttranslationally modified proteins, as well as their functional modulation in vitro and in vivo. In the case of protein arginylation, which utilizes charged Arg-tRNA that is also used by the ribosomes, detection and labeling of arginylated proteins are especially difficult, because of the necessity of distinguishing these proteins from the products of conventional translation. As of now, this difficulty remains the major obstacle to new researchers entering the field. This chapter discusses some of the strategies for developing antibodies for arginylation detection, as well as some general considerations for development of other tools for the studies of arginylation.
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Wright TH, Vallée MRJ, Davis BG. Von der chemischen Mutagenese zur Postexpressions‐Mutagenese: eine 50 Jahre währende Odyssee. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Tom H. Wright
- Department of Chemistry University of Oxford Chemistry Research Laboratory Mansfield Road OX1 3TA Vereinigtes Königreich
| | - M. Robert J. Vallée
- Department of Chemistry University of Oxford Chemistry Research Laboratory Mansfield Road OX1 3TA Vereinigtes Königreich
| | - Benjamin G. Davis
- Department of Chemistry University of Oxford Chemistry Research Laboratory Mansfield Road OX1 3TA Vereinigtes Königreich
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Wright TH, Vallée MRJ, Davis BG. From Chemical Mutagenesis to Post-Expression Mutagenesis: A 50 Year Odyssey. Angew Chem Int Ed Engl 2016; 55:5896-903. [PMID: 27119221 PMCID: PMC5074284 DOI: 10.1002/anie.201509310] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 01/02/2016] [Indexed: 01/06/2023]
Abstract
Site‐directed (gene) mutagenesis has been the most useful method available for the conversion of one amino acid residue of a given protein into another. Until relatively recently, this strategy was limited to the twenty standard amino acids. The ongoing maturation of stop codon suppression and related technologies for unnatural amino acid incorporation has greatly expanded access to nonstandard amino acids by expanding the scope of the translational apparatus. However, the necessity for translation of genetic changes restricts the diversity of residues that may be incorporated. Herein we highlight an alternative approach, termed post‐expression mutagenesis, which operates at the level of the very functional biomolecules themselves. Using the lens of retrosynthesis, we highlight prospects for new strategies in protein modification, alteration, and construction which will enable protein science to move beyond the constraints of the “translational filter” and lead to a true synthetic biology.
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Affiliation(s)
- Tom H Wright
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, OX1 3TA, UK
| | - M Robert J Vallée
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, OX1 3TA, UK
| | - Benjamin G Davis
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, OX1 3TA, UK.
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22
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Haney CM, Wissner RF, Warner JB, Wang YJ, Ferrie JJ, J Covell D, Karpowicz RJ, Lee VMY, Petersson EJ. Comparison of strategies for non-perturbing labeling of α-synuclein to study amyloidogenesis. Org Biomol Chem 2016; 14:1584-92. [PMID: 26695131 PMCID: PMC4733880 DOI: 10.1039/c5ob02329g] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Characterization of the amyloidogenic Parkinson's disease protein α-synuclein (αS) has proven difficult due to its structural plasticity. Here, we present a number of complementary methods to site-specifically introduce fluorescent probes to examine αS fibril formation and cellular uptake. By using various combinations of conventional Cys modification, amber codon suppression, transferase mediated N-terminal modification, and native chemical ligation, several variants of singly- and doubly-labeled αS were produced. We validated the nonperturbative nature of the label by a combination of in vitro aggregation kinetics measurements and imaging of the resulting fibrils. The labeled αS can then be used to monitor conformational changes during fibril formation or cellular uptake of αS fibrils in models of disease propagation.
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Affiliation(s)
- Conor M Haney
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA.
| | - Rebecca F Wissner
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA.
| | - John B Warner
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA.
| | - Yanxin J Wang
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA.
| | - John J Ferrie
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA.
| | - Dustin J Covell
- Center for Neurodegenerative Disease Research, University of Pennsylvania, 3600 Spruce Street, Philadelphia, PA 19104, USA
| | - Richard J Karpowicz
- Center for Neurodegenerative Disease Research, University of Pennsylvania, 3600 Spruce Street, Philadelphia, PA 19104, USA
| | - Virginia M-Y Lee
- Center for Neurodegenerative Disease Research, University of Pennsylvania, 3600 Spruce Street, Philadelphia, PA 19104, USA
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA.
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Wang YJ, Szantai-Kis DM, Petersson EJ. Semi-synthesis of thioamide containing proteins. Org Biomol Chem 2016; 13:5074-81. [PMID: 25811732 DOI: 10.1039/c5ob00224a] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Our laboratory has shown that the thioamide, a single atom O-to-S substitution, can be a versatile fluorescence quenching probe that is minimally-perturbing when placed at many locations in a protein sequence. In order to make these and other thioamide experiments applicable to full-sized proteins, we have developed methods for incorporating thioamides by generating thiopeptide fragments through solid phase synthesis and ligating them to protein fragments expressed in E. coli. To install donor fluorophores, we have adapted unnatural amino acid mutagenesis methods, including the generation of new tRNA synthetases for the incorporation of small, intrinsically fluorescent amino acids. We have used a combination of these two methods, as well as chemoenzymatic protein modification, to efficiently install sidechain and backbone modifications to generate proteins labeled with fluorophore/thioamide pairs.
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Affiliation(s)
- Yanxin J Wang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA.
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Bajaj K, Sakhuja R, Pillai GG. Traceless reductive ligation at a tryptophan site: a facile access to β-hydroxytryptophan appended peptides. Org Biomol Chem 2016; 14:9578-9587. [DOI: 10.1039/c6ob01542e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
One-pot methodology (reduction & O to N migration); synthesis of β-hydroxytryptophan appended native peptides; computational support for the mechanism.
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Affiliation(s)
- Kiran Bajaj
- Department of Chemistry
- Birla Institute of Technology and Science
- Pilani 333031
- India
| | - Rajeev Sakhuja
- Department of Chemistry
- Birla Institute of Technology and Science
- Pilani 333031
- India
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25
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Chen M, Heimer P, Imhof D. Synthetic strategies for polypeptides and proteins by chemical ligation. Amino Acids 2015; 47:1283-99. [DOI: 10.1007/s00726-015-1982-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/02/2015] [Indexed: 11/30/2022]
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Petersson EJ, Goldberg JM, Wissner RF. On the use of thioamides as fluorescence quenching probes for tracking protein folding and stability. Phys Chem Chem Phys 2014; 16:6827-37. [PMID: 24598971 DOI: 10.1039/c3cp55525a] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Our laboratory has developed thioamide analogs of the natural amino acids as minimally-perturbing fluorescence quenching probes that can be placed at many locations in a protein sequence. We have shown that the mechanism of quenching can be either Förster resonance energy transfer (FRET) or photoinduced electron transfer (PET), depending on the identity of the donor fluorophore. Furthermore, we have shown that one can use a combination of semi-synthetic methods to label full-sized proteins with fluorophore-thioamide pairs. These probes can be used to study protein-protein interactions, protein folding or misfolding, and proteolysis.
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Affiliation(s)
- E James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA.
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27
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Wissner RF, Wagner AM, Warner JB, Petersson EJ. Efficient, Traceless Semi-Synthesis of α-Synuclein Labeled with a Fluorophore/Thioamide FRET Pair. Synlett 2013; 24:2454-2458. [PMID: 26893537 PMCID: PMC4755331 DOI: 10.1055/s-0033-1339853] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We have shown that thioamides can be incorporated into proteins through semi-synthesis and used as probes to monitor structural changes. To date, our methods have required the presence of a cysteine at the peptide ligation site, which may not be present in the native peptide sequence. Here, we present a strategy for the semi-synthesis of thioproteins using homocysteine as a ligation point with subsequent masking as methionine, making the ligation "traceless."
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Affiliation(s)
- Rebecca F. Wissner
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Anne M. Wagner
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - John B. Warner
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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