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ABPP Methodology: Introduction and Overview

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Activity-Based Protein Profiling

Part of the book series: Topics in Current Chemistry ((TOPCURRCHEM,volume 324))

Abstract

Activity-based protein profiling (ABPP) is emerging as a mature method for chemically interrogating the proteome of a cell. This chapter serves to introduce the reader to ABPP by providing overviews of the general principles of the technique, analytical methods used in ABPP, the classes of enzymes that can be specifically addressed by ABPP probes, and biological applications of ABPP.

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Abbreviations

(TOP)-ABPP:

Tandem orthogonal proteolysis ABPP

3-oxo-C12-HSL:

3-Oxo-dodecanoyl homoserine lactone

ABPP:

Activity-based protein profiling

ADP:

Adenosine diphosphate

AOMK:

Acyloxymethyl ketone

ASPP:

Active site peptide profiling

ATP:

Adenosine triphosphate

BODIPY:

Boron-dipyrromethane

CE:

Capillary electrophoresis

FDA:

Food and Drug Administration

FP:

Fluorophosphonate

HDAC:

Histone deacetylase

LC-MS:

Liquid chromatography–mass spectrometry

LIF:

Laser-induced fluorescence

ML:

Mixed lineage

MP:

Metalloprotease

MS:

Mass spectrometry

MudPIT:

Multidimensional protein identification technology

PAD4:

Protein arginine deiminase 4

PI3K:

Phosphoinositide 3-kinase

PKMT:

Protein lysine methyltransferase

PNA:

Peptide nucleic acid

RA:

Rheumatoid arthritis

SAHA:

Suberoylanilide hydroxamic acid

SAM:

S-Adenosyl-l-methionine

SDS:

Sodium dodecylsulfate

SDS-PAGE:

Sodium dodecylsulfate polyacrylamide gel electrophoresis

TEV:

Tobacco etch virus

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Acknowledgments

M. Nodwell thanks the Alexander von Humboldt foundation for a postdoctoral fellowship. S. Sieber is supported by the Deutsche Forschungsgemeinschaft (Emmy Noether), SFB749, FOR1406, an ERC starting grant, and the Center for Integrated Protein Science Munich CIPSM.

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  1. Department Chemie, Centre for Integrated Protein Science CIPSM, Institute of Advanced Studies, Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany

    Matthew B. Nodwell & Stephan A. Sieber

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  1. Technical University of Munich, Department of Organic Chemistry II, Lichtenbergstr. 4, Garching, 85747, Germany

    Stephan A. Sieber

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Nodwell, M.B., Sieber, S.A. (2011). ABPP Methodology: Introduction and Overview. In: Sieber, S. (eds) Activity-Based Protein Profiling. Topics in Current Chemistry, vol 324. Springer, Berlin, Heidelberg. https://doi.org/10.1007/128_2011_302

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