Cross-linking mass spectrometry for mapping protein complex topologies in situ

被引：29

作者：

Lee, Kitaik ^{[1
]}

O'Reilly, Francis J. ^{[1
]}

机构：

[1] NCI, Ctr Struct Biol, Ctr Canc Res, Frederick, MD 21702 USA

来源：

ESSAYS IN BIOCHEMISTRY | 2023年 / 67卷 / 02期

基金：

美国国家卫生研究院;

关键词：

LINKED PEPTIDES; SELECTIVE ENRICHMENT; INTERACTION NETWORK; IDENTIFICATION; INTERACTOME; PRODUCTS; CELLS; ARCHITECTURE; DYNAMICS;

D O I：

10.1042/EBC20220168

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Cross-linking mass spectrometry has become an established technology to provide struc-tural information on the topology and dynamics of protein complexes. Readily accessible workflows can provide detailed data on simplified systems, such as purified complexes. However, using this technology to study the structure of protein complexes in situ, such as in organelles, cells, and even tissues, is still a technological frontier. The complexity of these systems remains a considerable challenge, but there have been dramatic improve-ments in sample handling, data acquisition, and data processing. Here, we summarise these developments and describe the paths towards comprehensive and comparative structural interactomes by cross-linking mass spectrometry.

引用

页码：215 / 228

页数：14

共 110 条

[1] Suborganelle-Specific Protein Complex Analysis Enabled by in Vivo Cross-Linking Coupled with Proximal Labeling [J].

An, Yuxin ;

Zhao, Qun ;

Gong, Zhou ;

Zhao, Lili ;

Li, Yi ;

Liang, Zhen ;

Zou, Peng ;

Zhang, Yukui ;

Zhang, Lihua .

ANALYTICAL CHEMISTRY, 2022, :12051-12059

[2] Integrated Workflow for Structural Proteomics Studies Based on Cross-Linking/Mass Spectrometry with an MS/MS Cleavable Cross-Linker [J].

Arlt, Christian ;

Goetze, Michael ;

Ihling, Christian H. ;

Hage, Christoph ;

Schaefer, Mathias ;

Sinz, Andrea .

ANALYTICAL CHEMISTRY, 2016, 88 (16) :7930-7937

[3] Cross-linking Mass Spectrometry Analysis of the Yeast Nucleus Reveals Extensive Protein-Protein Interactions Not Detected by Systematic Two-Hybrid or Affinity Purification-Mass Spectrometry [J].

Bartolec, Tara K. ;

Smith, Daniela-Lee ;

Pang, Chi Nam Ignatius ;

Xu, You Dan ;

Hamey, Joshua J. ;

Wilkins, Marc R. .

ANALYTICAL CHEMISTRY, 2020, 92 (02) :1874-1882

[4]

Belsom Adam, 2021, Curr Opin Chem Biol, V60, P39, DOI 10.1016/j.cbpa.2020.07.008

[5] A synthetic peptide library for benchmarking crosslinking-mass spectrometry search engines for proteins and protein complexes [J].

Beveridge, Rebecca ;

Stadlmann, Johannes ;

Penninger, Josef M. ;

Mechtler, Karl .

NATURE COMMUNICATIONS, 2020, 11 (01)

[6] A gas phase cleavage reaction of cross-linked peptides for protein complex topology studies by peptide fragment fingerprinting from large sequence database [J].

Buncherd, Hansuk ;

Roseboom, Winfried ;

de Koning, Leo J. ;

de Koster, Chris G. ;

de Jong, Luitzen .

JOURNAL OF PROTEOMICS, 2014, 108 :65-77

[7] Selective enrichment and identification of cross-linked peptides to study 3-D structures of protein complexes by mass spectrometry [J].

Buncherd, Hansuk ;

Nessen, Mere A. ;

Nouse, Niels ;

Stelder, Sacha K. ;

Roseboom, Winfried ;

Dekker, Henk L. ;

Arents, Jos C. ;

Smeenk, Linde E. ;

Wanner, Martin J. ;

van Maarseveen, Jan H. ;

Yang, Xiao ;

Lewis, Peter J. ;

de Koning, Leo J. ;

de Koster, Chris G. ;

de Jong, Luitzen .

JOURNAL OF PROTEOMICS, 2012, 75 (07) :2205-2215

[8] Synthesis of two new enrichable and MS-cleavable cross-linkers to define protein-protein interactions by mass spectrometry [J].

Burke, Anthony M. ;

Kandur, Wynne ;

Novitsky, Eric J. ;

Kaake, Robyn M. ;

Yu, Clinton ;

Kao, Athit ;

Vellucci, Danielle ;

Huang, Lan ;

Rychnovsky, Scott D. .

ORGANIC & BIOMOLECULAR CHEMISTRY, 2015, 13 (17) :5030-5037

[9] Towards a structurally resolved human protein interaction network [J].

Burke, David F. ;

Bryant, Patrick ;

Barrio-Hernandez, Inigo ;

Memon, Danish ;

Pozzati, Gabriele ;

Shenoy, Aditi ;

Zhu, Wensi ;

Dunham, Alistair S. ;

Albanese, Pascal ;

Keller, Andrew ;

Scheltema, Richard A. ;

Bruce, James E. ;

Leitner, Alexander ;

Kundrotas, Petras ;

Beltrao, Pedro ;

Elofsson, Arne .

NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2023, 30 (02) :216-+

[10] Isobaric Quantitative Protein Interaction Reporter Technology for Comparative Interactome Studies [J].

Chavez, Juan D. ;

Keller, Andrew ;

Mohr, Jared P. ;

Bruce, James E. .

ANALYTICAL CHEMISTRY, 2020, 92 (20) :14094-14102

← 1 2 3 4 5 6 7 8 9 10 →