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Title: Affinity Bioorthogonal Chemistry (ABC) Tags for Site‐Selective Conjugation, On‐Resin Protein‐Protein Coupling, and Purification of Protein Conjugates
Abstract

The site‐selective functionalization of proteins has broad application in chemical biology, but can be limited when mixtures result from incomplete conversion or the formation of protein containing side products. It is shown here that when proteins are covalently tagged with pyridyl‐tetrazines, the nickel‐iminodiacetate (Ni‐IDA) resins commonly used for His‐tags can be directly used for protein affinity purification. These Affinity Bioorthogonal Chemistry (ABC) tags serve a dual role by enabling affinity‐based protein purification while maintaining rapid kinetics in bioorthogonal reactions. ABC‐tagging works with a range of site‐selective bioconjugation methods with proteins tagged at the C‐terminus, N‐terminus or at internal positions. ABC‐tagged proteins can also be purified from complex mixtures including cell lysate. The combination of site‐selective conjugation and clean‐up with ABC‐tagged proteins also allows for facile on‐resin reactions to provide protein‐protein conjugates.

 
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NSF-PAR ID:
10378121
Author(s) / Creator(s):
 ;  ;  
Publisher / Repository:
Wiley Blackwell (John Wiley & Sons)
Date Published:
Journal Name:
Angewandte Chemie International Edition
Volume:
61
Issue:
45
ISSN:
1433-7851
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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    The site‐selective functionalization of proteins has broad application in chemical biology, but can be limited when mixtures result from incomplete conversion or the formation of protein containing side products. It is shown here that when proteins are covalently tagged with pyridyl‐tetrazines, the nickel‐iminodiacetate (Ni‐IDA) resins commonly used for His‐tags can be directly used for protein affinity purification. These Affinity Bioorthogonal Chemistry (ABC) tags serve a dual role by enabling affinity‐based protein purification while maintaining rapid kinetics in bioorthogonal reactions. ABC‐tagging works with a range of site‐selective bioconjugation methods with proteins tagged at the C‐terminus, N‐terminus or at internal positions. ABC‐tagged proteins can also be purified from complex mixtures including cell lysate. The combination of site‐selective conjugation and clean‐up with ABC‐tagged proteins also allows for facile on‐resin reactions to provide protein‐protein conjugates.

     
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  2. Abstract

    Class II major histocompatibility complex peptide (MHC‐IIp) multimers are precisely engineered reagents used to detect T cells specific for antigens from pathogens, tumors, and self‐proteins. While the related Class I MHC/peptide (MHC‐Ip) multimers are usually produced from subunits expressed inE. coli, most Class II MHC alleles cannot be produced in bacteria, and this has contributed to the perception that MHC‐IIp reagents are harder to produce. Herein, we present a robust constitutive expression system for soluble biotinylated MHC‐IIp proteins that uses stable lentiviral vector−transduced derivatives of HEK‐293T cells. The expression design includes allele‐specific peptide ligands tethered to the amino‐terminus of the MHC‐II β chain via a protease‐cleavable linker. Following cleavage of the linker, HLA‐DM is used to catalyze efficient peptide exchange, enabling high‐throughput production of many distinct MHC‐IIp complexes from a single production cell line. Peptide exchange is monitored using either of two label‐free methods, native isoelectric focusing gel electrophoresis or matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) mass spectrometry of eluted peptides. Together, these methods produce MHC‐IIp complexes that are highly homogeneous and that form the basis for excellent MHC‐IIp multimer reagents. © 2021 Wiley Periodicals LLC.

    This article was corrected on 19 July 2022. See the end of the full text for details.

    Basic Protocol 1: Lentivirus production and expression line creation

    Support Protocol 1: Six‐well assay for estimation of production cell line yield

    Support Protocol 2: Universal ELISA for quantifying proteins with fused leucine zippers and His‐tags

    Basic Protocol 2: Cultures for production of Class II MHC proteins

    Basic Protocol 3: Purification of Class II MHC proteins by anti‐leucine zipper affinity chromatography

    Alternate Protocol 1: IMAC purification of His‐tagged Class II MHC

    Support Protocol 3: Protein concentration measurements and adjustments

    Support Protocol 4: Polishing purification by anion‐exchange chromatography

    Support Protocol 5: Estimating biotinylation percentage by streptavidin precipitation

    Basic Protocol 4: Peptide exchange

    Basic Protocol 5: Analysis of peptide exchange by matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry

    Alternate Protocol 2: Native isoelectric focusing to validate MHC‐II peptide loading

    Basic Protocol 6: Multimerization

    Basic Protocol 7: Staining cells with Class II MHC tetramers

     
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  3. Abstract

    Protein labeling strategies have been explored for decades to study protein structure, function, and regulation. Fluorescent labeling of a protein enables the study of protein‐protein interactions through biophysical methods such as microscale thermophoresis (MST). MST measures the directed motion of a fluorescently labeled protein in response to microscopic temperature gradients, and the protein's thermal mobility can be used to determine binding affinity. However, the stoichiometry and site specificity of fluorescent labeling are hard to control, and heterogeneous labeling can generate inaccuracies in binding measurements. Here, we describe an easy‐to‐apply protocol for high‐stoichiometric, site‐specific labeling of a protein at its N‐terminus withN‐hydroxysuccinimide (NHS) esters as a means to measure protein‐protein interaction affinity by MST. This protocol includes guidelines for NHS ester labeling, fluorescent‐labeled protein purification, and MST measurement using a labeled protein. As an example of the entire workflow, we additionally provide a protocol for labeling a ubiquitin E3 enzyme and testing ubiquitin E2‐E3 enzyme binding affinity. These methods are highly adaptable and can be extended for protein interaction studies in various biological and biochemical circumstances. © 2021 Wiley Periodicals LLC.

    This article was corrected on 18 July 2022. See the end of the full text for details.

    Basic Protocol 1: Labeling a protein of interest at its N‐terminus with NHS esters through stepwise reaction

    Alternate Protocol: Labeling a protein of interest at its N‐terminus with NHS esters through a one‐pot reaction

    Basic Protocol 2: Purifying the N‐terminal fluorescent‐labeled protein and determining its concentration and labeling efficiency

    Basic Protocol 3: Using MST to determine the binding affinity of an N‐terminal fluorescent‐labeled protein to a binding partner.

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    Purification of recombinant proteins is a necessary step for functional or structural studies and other applications. Immobilized metal affinity chromatography is a common recombinant protein purification method. Mass spectrometry (MS) allows for confirmation of identity of expressed proteins and unambiguous detection of enzymatic substrates and reaction products. We demonstrate the detection of enzymes purified on immobilized metal affinity surfaces by direct or ambient ionization MS, and follow their enzymatic reactions by direct electrospray ionization (ESI) or desorption electrospray ionization (DESI).

    Methods

    A protein standard, His‐Ubq, and two recombinant proteins, His‐SHAN and His‐CS, expressed inEscherichia coliwere immobilized on two immobilized metal affinity systems, Cu–nitriloacetic acid (Cu‐NTA) and Ni‐NTA. The proteins were purified on surface, and released in the ESI spray solvent for direct infusion, when using the 96‐well plate form factor, or analyzed directly from immobilized metal affinity‐coated microscope slides by DESI‐MS. Enzyme activity was followed by incubating the substrates in wells or by depositing substrate on immobilized protein on coated slides for analysis.

    Results

    Small proteins (His‐Ubq) and medium proteins (His‐SAHN) could readily be detected from 96‐well plates by direct infusion ESI, or from microscope slides by DESI‐MS after purification on surface from clarifiedE. colicell lysate. Protein oxidation was observed for immobilized proteins on both Cu‐NTA and Ni‐NTA; however, this did not hamper the enzymatic reactions of these proteins. Both the nucleosidase reaction products for His‐SAHN and the methylation product of His‐CS (theobromine to caffeine) were detected.

    Conclusions

    The immobilization, purification, release and detection of His‐tagged recombinant proteins using immobilized metal affinity surfaces for direct infusion ESI‐MS or ambient DESI‐MS analyses were successfully demonstrated. Recombinant proteins were purified to allow identification directly out of clarified cell lysate. Biological activities of the recombinant proteins were preserved allowing the investigation of enzymatic activity via MS.

     
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