A new cross-linking strategy: protein interaction reporter (PIR) technology for protein–protein interaction studies

Tang, Xiaoting; Bruce, James E

doi:10.1039/b920876c

Cited by 143Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and ApplicationsClick Chemistry and Applications

A new cross-linking strategy: protein interaction reporter (PIR) technology for protein–protein interaction studies

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Tang, Xiaoting, Bruce, James E·2010·Molecular BioSystems

DOI 10.1039/b920876cPMC PMC3075923

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Abstract

Chemical cross-linking coupled with mass spectrometry, an emerging approach for protein topology and interaction studies, has gained increasing interest in the past few years. A number of recent proof-of-principle studies on model proteins or protein complex systems with improved cross-linking strategies have shown great promise. However, the heterogeneity and low abundance of the cross-linked products as well as data complexity continue to pose enormous challenges for large-scale application of cross-linking approaches. A novel mass spectrometry-cleavable cross-linking strategy embodied in Protein Interaction Reporter (PIR) technology, first reported in 2005, was recently successfully applied for in vivo identification of protein–protein interactions as well as actual regions of the interacting proteins that share close proximity while present within cells. PIR technology holds great promise for achieving the ultimate goal of mapping protein interaction network at systems level using chemical cross-linking. In this review, we will briefly describe the recent progress in the field of chemical cross-linking development with an emphasis on the PIR concepts, its applications and future directions.

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Chavez et al. utilized a cross-linking strategy, Protein Interaction Reporter technology, to generate cross-links that are cleaved within a mass spectrometer for the identification of interacting protein and peptide sequences.
“Chavez et al. utilized a remarkable cross-linking strategy, Protein Interaction Reporter technology, to generate cross-links that are cleaved within a mass spectrometer for the identification of interacting protein and peptide sequences [99,100].”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [99]

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Kojak: Efficient Analysis of Chemically Cross-Linked Protein Complexes
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Host-Microbe Protein Interactions during Bacterial Infection
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Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei
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XL-MS: protein cross-linking coupled with mass spectrometry
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Cross-linking Measurements of In Vivo Protein Complex Topologies
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Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein–Protein Interaction Networks in Vivo
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To Cleave or Not To Cleave in XL-MS?
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In Vivo Conformational Dynamics of Hsp90 and Its Interactors
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Protein interaction networks at the host–microbe interface inDiaphorina citri, the insect vector of the citrus greening pathogen
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Proteome-Wide Structural Biology: An Emerging Field for the Structural Analysis of Proteins on the Proteomic Scale
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Optimized Fragmentation Improves the Identification of Peptides Cross-Linked by MS-Cleavable Reagents
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Cross-linking Measurements of the <i>Potato leafroll virus</i> Reveal Protein Interaction Topologies Required for Virion Stability, Aphid Transmission, and Virus–Plant Interactions
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Systems structural biology measurements by in vivo cross-linking with mass spectrometry
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Mass Spectrometry Evidence for Cisplatin As a Protein Cross-Linking Reagent
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Topographic Studies of the GroEL-GroES Chaperonin Complex by Chemical Cross-linking Using Diformyl Ethynylbenzene
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Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable, Isotopically Coded, and Mass Spectrometry-cleavable Chemical Crosslinker
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Marked by association: techniques for proximity-dependent labeling of proteins in eukaryotic cells
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Structural mass spectrometry goes viral
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Comprehensive Cross-Linking Mass Spectrometry Reveals Parallel Orientation and Flexible Conformations of Plant HOP2–MND1
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Mitoproteomics: Tackling Mitochondrial Dysfunction in Human Disease
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MASS SPECTROMETRY IN VIROLOGICAL SCIENCES
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Structure-based validation can drastically underestimate error rate in proteome-wide cross-linking mass spectrometry studies
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The First MS-Cleavable, Photo-Thiol-Reactive Cross-Linker for Protein Structural Studies
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In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology
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A novel mass spectrometry-cleavable, phosphate-based enrichable and multi-targeting protein cross-linker
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Metabolization and sequestration of plant specialized metabolites in insect herbivores: Current and emerging approaches
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Prediction of an Upper Limit for the Fraction of Interprotein Cross-Links in Large-Scale In Vivo Cross-Linking Studies
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Identification of Putative Interactors of Arabidopsis Sugar Transporters
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Targeted cross-linker delivery for the in situ mapping of protein conformations and interactions in mitochondria
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Extending the cross-linking/mass spectrometry strategy: Facile incorporation of photo-activatable amino acids into the model protein calmodulin in Escherichia coli cells
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Combining Amine-Reactive Cross-Linkers and Photo-Reactive Amino Acids for 3D-Structure Analysis of Proteins and Protein Complexes
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In planta chemical cross‐linking and mass spectrometry analysis of protein structure and interaction in Arabidopsis
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Characterization of the Interaction between Heterodimeric αvβ6 Integrin and Urokinase Plasminogen Activator Receptor (uPAR) Using Functional Proteomics
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Progress toward Proteome-Wide Photo-Cross-Linking to Enable Residue-Level Visualization of Protein Structures and Networks In Vivo
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In Vivo Cross-Linking MS Reveals Conservation in OmpA Linkage to Different Classes of β-Lactamase Enzymes
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Fine Tuning of Proteomic Technologies to Improve Biological Findings: Advancements in 2011–2013
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Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa
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Mapping protein receptor–ligand interactions via in vivo chemical crosslinking, affinity purification, and differential mass spectrometry
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Dynamic Interactomics by Cross-Linking Mass Spectrometry: Mapping the Daily Cell Life in Postgenomic Era
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Characterization of the Interaction between Arginine Methyltransferase Hmt1 and Its Substrate Npl3: Use of Multiple Cross-Linkers, Mass Spectrometric Approaches, and Software Platforms
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Cross-linking and mass spectrometry as a tool for studying the structural biology of ribonucleoproteins
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Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS)
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Targeted cross-linking-mass spectrometry determines vicinal interactomes within heterogeneous RNP complexes
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Self-citation

Identification of Protein-Protein Interactions and Topologies in Living Cells with Chemical Cross-linking and Mass Spectrometry
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Self-citation
Improved Strategies for Rapid Identification of Chemically Cross-Linked Peptides Using Protein Interaction Reporter Technology
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Self-citation
In Vivo Application of Photocleavable Protein Interaction Reporter Technology
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Self-citation
Informatics Strategies for Large-Scale Novel Cross-Linking Analysis
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Self-citation
Mass Spectrometry Identifiable Cross-Linking Strategy for Studying Protein−Protein Interactions
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Self-citation

Authors: Tang, X., & Bruce, J. E.
Affiliations: Novo Nordisk (United States) (US)
University of Washington (US)
Corresponding author: Bruce, James E
ORCID: Tang, Xiaoting
Bruce, James E
Venue: Molecular BioSystems
Publisher: Oxford University Press (OUP)
Published: 2010-03-16
Volume: 6
Issue: 6
Pages: 939-947
ISSN: 1742-2051 (ISSN-L)
1742-206X
DOI: 10.1039/b920876c
PMC: PMC3075923
OpenAlex: W1995233241
Cited by: 143
References: 83
Citations by year: 2026: 1 · 2025: 5 · 2024: 6 · 2023: 9 · 2022: 11 · 2021: 10 · 2020: 13 · 2019: 19 · 2018: 15 · 2017: 5 · 2016: 5 · 2015: 12 · 2014: 6 · 2013: 6 · 2012: 11
FWCI: 0.68
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: academic.oup.com/pages/standard-publication-reuse-rights (vor)
Locations: Molecular BioSystems (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
Funders: National Institute of General Medical Sciences (R01GM086688)
National Center for Research Resources (R01RR023334, S10RR025107)
Topics: Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
Physical Sciences › Chemistry › Organic Chemistry › Click Chemistry and Applications
Keywords: crosslinking, protein-protein interaction, protein-protein interaction network
MeSH terms: Amino Acid Sequence, Binding Sites, Cross-Linking Reagents, Models, Chemical, Protein Binding, Proteins, Mass Spectrometry, Molecular Structure, Protein Interaction Mapping

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A new cross-linking strategy: protein interaction reporter (PIR) technology for protein–protein interaction studies

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