Site-Selective Enzymatic Labeling of Designed Ankyrin Repeat Proteins Using Protein Farnesyltransferase

Yi Zhang, Shelby Auger, Jonas V. Schaefer, Andreas Plückthun, Mark D Distefano

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Affinity agents coupled to a functional moiety play an ever-increasing role in modern medicine, ranging from radiolabeled selective binders in diagnosis to antibody–drug conjugates in targeted therapies. In biomedical research, protein coupling to fluorophores, surfaces and nanoparticles has become an integral part of many procedures. In addition to antibodies, small scaffold proteins with similar target binding properties are being widely explored as alternative targeting moieties. To label these binders of interest with different functional moieties, conventional chemical coupling methods can be employed, but often result in heterogeneously modified protein products. In contrast, enzymatic labeling methods are highly site-specific and efficient. Protein farnesyltransferase (PFTase) catalyzes the transfer of an isoprenoid moiety from farnesyl diphosphate (FPP) to a cysteine residue in a C-terminal CaaX motif at the C-terminus of a protein substrate. The addition of only four amino acid residues minimizes the influence on the native protein structure. In addition, a variety of isoprenoid analogs containing different bioorthogonal functional groups, including azides, alkynes, and aldehydes, have been developed to enable conjugation to various cargos after being incorporated onto the target protein by PFTase. In this protocol, we present a detailed procedure for labeling Designed Ankyrin Repeat Proteins (DARPins) engineered with a C-terminal CVIA sequence using an azide-containing FPP analog by yeast PFTase (yPFTase). In addition, procedures to subsequently conjugate the labeled DARPins to a TAMRA fluorophore using strained-promoted alkyne–azide cycloaddition (SPAAC) reactions as well as the sample preparation to evaluate the target binding ability of the conjugates by flow cytometry are described.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages207-219
Number of pages13
DOIs
StatePublished - Jan 1 2019

Publication series

NameMethods in Molecular Biology
Volume2033
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Fingerprint

Ankyrin Repeat
Proteins
Azides
Terpenes
Modern 1601-history
Fungal Proteins
Alkynes
p21(ras) farnesyl-protein transferase
Cycloaddition Reaction
Aldehydes
Nanoparticles
Cysteine
Biomedical Research
Flow Cytometry
Amino Acids
Antibodies

Keywords

  • DARPins
  • Enzymatic protein labeling
  • Flow cytometry
  • Isoprenoid analogs
  • Protein farnesyltransferase
  • Site-specific conjugation
  • SPACC

PubMed: MeSH publication types

  • Journal Article

Cite this

Zhang, Y., Auger, S., Schaefer, J. V., Plückthun, A., & Distefano, M. D. (2019). Site-Selective Enzymatic Labeling of Designed Ankyrin Repeat Proteins Using Protein Farnesyltransferase. In Methods in Molecular Biology (pp. 207-219). (Methods in Molecular Biology; Vol. 2033). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-9654-4_14

Site-Selective Enzymatic Labeling of Designed Ankyrin Repeat Proteins Using Protein Farnesyltransferase. / Zhang, Yi; Auger, Shelby; Schaefer, Jonas V.; Plückthun, Andreas; Distefano, Mark D.

Methods in Molecular Biology. Humana Press Inc., 2019. p. 207-219 (Methods in Molecular Biology; Vol. 2033).

Research output: Chapter in Book/Report/Conference proceedingChapter

Zhang, Y, Auger, S, Schaefer, JV, Plückthun, A & Distefano, MD 2019, Site-Selective Enzymatic Labeling of Designed Ankyrin Repeat Proteins Using Protein Farnesyltransferase. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 2033, Humana Press Inc., pp. 207-219. https://doi.org/10.1007/978-1-4939-9654-4_14
Zhang Y, Auger S, Schaefer JV, Plückthun A, Distefano MD. Site-Selective Enzymatic Labeling of Designed Ankyrin Repeat Proteins Using Protein Farnesyltransferase. In Methods in Molecular Biology. Humana Press Inc. 2019. p. 207-219. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-9654-4_14
Zhang, Yi ; Auger, Shelby ; Schaefer, Jonas V. ; Plückthun, Andreas ; Distefano, Mark D. / Site-Selective Enzymatic Labeling of Designed Ankyrin Repeat Proteins Using Protein Farnesyltransferase. Methods in Molecular Biology. Humana Press Inc., 2019. pp. 207-219 (Methods in Molecular Biology).
@inbook{ea51fef215b746aeb78793fe9cd8f666,
title = "Site-Selective Enzymatic Labeling of Designed Ankyrin Repeat Proteins Using Protein Farnesyltransferase",
abstract = "Affinity agents coupled to a functional moiety play an ever-increasing role in modern medicine, ranging from radiolabeled selective binders in diagnosis to antibody–drug conjugates in targeted therapies. In biomedical research, protein coupling to fluorophores, surfaces and nanoparticles has become an integral part of many procedures. In addition to antibodies, small scaffold proteins with similar target binding properties are being widely explored as alternative targeting moieties. To label these binders of interest with different functional moieties, conventional chemical coupling methods can be employed, but often result in heterogeneously modified protein products. In contrast, enzymatic labeling methods are highly site-specific and efficient. Protein farnesyltransferase (PFTase) catalyzes the transfer of an isoprenoid moiety from farnesyl diphosphate (FPP) to a cysteine residue in a C-terminal CaaX motif at the C-terminus of a protein substrate. The addition of only four amino acid residues minimizes the influence on the native protein structure. In addition, a variety of isoprenoid analogs containing different bioorthogonal functional groups, including azides, alkynes, and aldehydes, have been developed to enable conjugation to various cargos after being incorporated onto the target protein by PFTase. In this protocol, we present a detailed procedure for labeling Designed Ankyrin Repeat Proteins (DARPins) engineered with a C-terminal CVIA sequence using an azide-containing FPP analog by yeast PFTase (yPFTase). In addition, procedures to subsequently conjugate the labeled DARPins to a TAMRA fluorophore using strained-promoted alkyne–azide cycloaddition (SPAAC) reactions as well as the sample preparation to evaluate the target binding ability of the conjugates by flow cytometry are described.",
keywords = "DARPins, Enzymatic protein labeling, Flow cytometry, Isoprenoid analogs, Protein farnesyltransferase, Site-specific conjugation, SPACC",
author = "Yi Zhang and Shelby Auger and Schaefer, {Jonas V.} and Andreas Pl{\"u}ckthun and Distefano, {Mark D}",
year = "2019",
month = "1",
day = "1",
doi = "10.1007/978-1-4939-9654-4_14",
language = "English (US)",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "207--219",
booktitle = "Methods in Molecular Biology",

}

TY - CHAP

T1 - Site-Selective Enzymatic Labeling of Designed Ankyrin Repeat Proteins Using Protein Farnesyltransferase

AU - Zhang, Yi

AU - Auger, Shelby

AU - Schaefer, Jonas V.

AU - Plückthun, Andreas

AU - Distefano, Mark D

PY - 2019/1/1

Y1 - 2019/1/1

N2 - Affinity agents coupled to a functional moiety play an ever-increasing role in modern medicine, ranging from radiolabeled selective binders in diagnosis to antibody–drug conjugates in targeted therapies. In biomedical research, protein coupling to fluorophores, surfaces and nanoparticles has become an integral part of many procedures. In addition to antibodies, small scaffold proteins with similar target binding properties are being widely explored as alternative targeting moieties. To label these binders of interest with different functional moieties, conventional chemical coupling methods can be employed, but often result in heterogeneously modified protein products. In contrast, enzymatic labeling methods are highly site-specific and efficient. Protein farnesyltransferase (PFTase) catalyzes the transfer of an isoprenoid moiety from farnesyl diphosphate (FPP) to a cysteine residue in a C-terminal CaaX motif at the C-terminus of a protein substrate. The addition of only four amino acid residues minimizes the influence on the native protein structure. In addition, a variety of isoprenoid analogs containing different bioorthogonal functional groups, including azides, alkynes, and aldehydes, have been developed to enable conjugation to various cargos after being incorporated onto the target protein by PFTase. In this protocol, we present a detailed procedure for labeling Designed Ankyrin Repeat Proteins (DARPins) engineered with a C-terminal CVIA sequence using an azide-containing FPP analog by yeast PFTase (yPFTase). In addition, procedures to subsequently conjugate the labeled DARPins to a TAMRA fluorophore using strained-promoted alkyne–azide cycloaddition (SPAAC) reactions as well as the sample preparation to evaluate the target binding ability of the conjugates by flow cytometry are described.

AB - Affinity agents coupled to a functional moiety play an ever-increasing role in modern medicine, ranging from radiolabeled selective binders in diagnosis to antibody–drug conjugates in targeted therapies. In biomedical research, protein coupling to fluorophores, surfaces and nanoparticles has become an integral part of many procedures. In addition to antibodies, small scaffold proteins with similar target binding properties are being widely explored as alternative targeting moieties. To label these binders of interest with different functional moieties, conventional chemical coupling methods can be employed, but often result in heterogeneously modified protein products. In contrast, enzymatic labeling methods are highly site-specific and efficient. Protein farnesyltransferase (PFTase) catalyzes the transfer of an isoprenoid moiety from farnesyl diphosphate (FPP) to a cysteine residue in a C-terminal CaaX motif at the C-terminus of a protein substrate. The addition of only four amino acid residues minimizes the influence on the native protein structure. In addition, a variety of isoprenoid analogs containing different bioorthogonal functional groups, including azides, alkynes, and aldehydes, have been developed to enable conjugation to various cargos after being incorporated onto the target protein by PFTase. In this protocol, we present a detailed procedure for labeling Designed Ankyrin Repeat Proteins (DARPins) engineered with a C-terminal CVIA sequence using an azide-containing FPP analog by yeast PFTase (yPFTase). In addition, procedures to subsequently conjugate the labeled DARPins to a TAMRA fluorophore using strained-promoted alkyne–azide cycloaddition (SPAAC) reactions as well as the sample preparation to evaluate the target binding ability of the conjugates by flow cytometry are described.

KW - DARPins

KW - Enzymatic protein labeling

KW - Flow cytometry

KW - Isoprenoid analogs

KW - Protein farnesyltransferase

KW - Site-specific conjugation

KW - SPACC

UR - http://www.scopus.com/inward/record.url?scp=85070216266&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85070216266&partnerID=8YFLogxK

U2 - 10.1007/978-1-4939-9654-4_14

DO - 10.1007/978-1-4939-9654-4_14

M3 - Chapter

T3 - Methods in Molecular Biology

SP - 207

EP - 219

BT - Methods in Molecular Biology

PB - Humana Press Inc.

ER -