Genetically encoded selective cross-linkers and emerging applications

2020 ◽  
Vol 48 (4) ◽  
pp. 1807-1817
Author(s):  
Haiyan Ren
Keyword(s):  
Protein Interactions ◽  
Unnatural Amino Acids ◽  
Protein Complexes ◽  
Living Cells ◽  
Cross Linking ◽  
Protein Protein Interactions ◽  
New Class ◽  
Selective Reaction ◽  
Biological Studies ◽  
Lower Background

There has been a large amount of interest in the development of genetically encoded cross-linkers that target functional groups naturally present in cells. Recently, a new class of unnatural amino acids that specifically react with target residues were developed and genetically incorporated. The selective reaction shows higher cross-linking efficiency, lower background and predictable cross-linking sites. It has been applied to enhance protein/peptide stability, pinpoint protein–protein interactions, stabilize protein complexes, engineer covalent protein inhibitors, identify phosphatases in living cells, etc. These new covalent linkages provide excellent new tools for protein engineering and biological studies. Their applications in biotherapy will provide considerable opportunities for innovating and improving biomolecular medicines.

scholarly journals Mass spectrometry-based cross-linking study shows that the Psb28 protein binds to cytochrome b559 in Photosystem II

2017 ◽  
Vol 114 (9) ◽  
pp. 2224-2229 ◽  
Author(s):  
Daniel A. Weisz ◽  
Haijun Liu ◽  
Hao Zhang ◽  
Sundarapandian Thangapandian ◽  
Emad Tajkhorshid ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Photosystem Ii ◽  
Protein Interactions ◽  
Protein Complexes ◽  
Protein Docking ◽  
Cross Linking ◽  
Protein Protein Interactions ◽  
Cytochrome B559 ◽  
Reaction Center Complex ◽  
Assembly Intermediate

Photosystem II (PSII), a large pigment protein complex, undergoes rapid turnover under natural conditions. During assembly of PSII, oxidative damage to vulnerable assembly intermediate complexes must be prevented. Psb28, the only cytoplasmic extrinsic protein in PSII, protects the RC47 assembly intermediate of PSII and assists its efficient conversion into functional PSII. Its role is particularly important under stress conditions when PSII damage occurs frequently. Psb28 is not found, however, in any PSII crystal structure, and its structural location has remained unknown. In this study, we used chemical cross-linking combined with mass spectrometry to capture the transient interaction of Psb28 with PSII. We detected three cross-links between Psb28 and the α- and β-subunits of cytochrome b559, an essential component of the PSII reaction-center complex. These distance restraints enable us to position Psb28 on the cytosolic surface of PSII directly above cytochrome b559, in close proximity to the QB site. Protein–protein docking results also support Psb28 binding in this region. Determination of the Psb28 binding site and other biochemical evidence allow us to propose a mechanism by which Psb28 exerts its protective effect on the RC47 intermediate. This study also shows that isotope-encoded cross-linking with the “mass tags” selection criteria allows confident identification of more cross-linked peptides in PSII than has been previously reported. This approach thus holds promise to identify other transient protein–protein interactions in membrane protein complexes.

scholarly journals Mass spectrometry-based methods for analysing the mitochondrial interactome in mammalian cells

2019 ◽  
Vol 167 (3) ◽  
pp. 225-231 ◽  
Author(s):  
Takumi Koshiba ◽  
Hidetaka Kosako
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Mammalian Cells ◽  
Protein Complexes ◽  
Living Cells ◽  
Protein Protein Interactions ◽  
Cellular Functions ◽  
Protein Protein Interaction ◽  
Membrane Protein Complexes ◽  
Protein Protein Interaction Networks

Abstract Protein–protein interactions are essential biologic processes that occur at inter- and intracellular levels. To gain insight into the various complex cellular functions of these interactions, it is necessary to assess them under physiologic conditions. Recent advances in various proteomic technologies allow to investigate protein–protein interaction networks in living cells. The combination of proximity-dependent labelling and chemical cross-linking will greatly enhance our understanding of multi-protein complexes that are difficult to prepare, such as organelle-bound membrane proteins. In this review, we describe our current understanding of mass spectrometry-based proteomics mapping methods for elucidating organelle-bound membrane protein complexes in living cells, with a focus on protein–protein interactions in mitochondrial subcellular compartments.

scholarly journals Identification of Protein-Protein Interactions and Topologies in Living Cells with Chemical Cross-linking and Mass Spectrometry

2008 ◽  
Vol 8 (3) ◽  
pp. 409-420 ◽  
Author(s):  
Haizhen Zhang ◽  
Xiaoting Tang ◽  
Gerhard R. Munske ◽  
Nikola Tolic ◽  
Gordon A. Anderson ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Living Cells ◽  
Cross Linking ◽  
Protein Protein Interactions ◽  
Chemical Cross Linking

scholarly journals Recent advances in large-scale protein interactome mapping

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 782 ◽  
Author(s):  
Virja Mehta ◽  
Laura Trinkle-Mulcahy
Keyword(s):  
Protein Interactions ◽  
Large Scale ◽  
Protein Complexes ◽  
Specific Protein ◽  
Quality Data ◽  
Protein Protein Interactions ◽  
Cellular Functions ◽  
Biological Studies ◽  
Protein Interactome ◽  
Literature Curation

Protein-protein interactions (PPIs) underlie most, if not all, cellular functions. The comprehensive mapping of these complex networks of stable and transient associations thus remains a key goal, both for systems biology-based initiatives (where it can be combined with other ‘omics’ data to gain a better understanding of functional pathways and networks) and for focused biological studies. Despite the significant challenges of such an undertaking, major strides have been made over the past few years. They include improvements in the computation prediction of PPIs and the literature curation of low-throughput studies of specific protein complexes, but also an increase in the deposition of high-quality data from non-biased high-throughput experimental PPI mapping strategies into publicly available databases.

scholarly journals Synthesis of two new enrichable and MS-cleavable cross-linkers to define protein–protein interactions by mass spectrometry

2015 ◽  
Vol 13 (17) ◽  
pp. 5030-5037 ◽  
Author(s):  
Anthony M. Burke ◽  
Wynne Kandur ◽  
Eric J. Novitsky ◽  
Robyn M. Kaake ◽  
Clinton Yu ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Structural Information ◽  
Protein Complexes ◽  
Cross Linking ◽  
Protein Protein Interactions ◽  
The Cross

The cross-linking Mass Spectrometry (XL-MS) technique extracts structural information from protein complexes without requiring highly purified samples, crystallinity, or large amounts of material.

scholarly journals Cross-linking of the Endolysosomal System Reveals Flotillin Structures and Putative Cargo

2022 ◽  
Author(s):  
Jasjot Singh ◽  
Hadeer Elhabashy ◽  
Pathma Muthukottiappan ◽  
Markus Stepath ◽  
Martin Eisenacher ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Protein Complexes ◽  
Decisive Role ◽  
Cross Linking ◽  
Protein Protein Interactions ◽  
Lysosome Biogenesis ◽  
Early Endosomes ◽  
Cross Links ◽  
Related Proteins ◽  
G Protein Coupled

Lysosomes are well-established as the main cellular organelles for the degradation of macromolecules and emerging as regulatory centers of metabolism. They are of crucial importance for cellular homeostasis, which is exemplified by a plethora of disorders related to alterations in lysosomal function. In this context, protein complexes play a decisive role, regulating not only metabolic lysosomal processes, but also lysosome biogenesis, transport, and interaction with other organelles. Using cross-linking mass spectrometry, we analyzed lysosomes and early endosomes. Based on the identification of 5,376 cross-links, we investigated protein-protein interactions and structures of lysosome- and endosome-related proteins. In particular, we present evidence for a tetrameric assembly of the lysosomal hydrolase PPT1 and heterodimeric/-multimeric structures of FLOT1/FLOT2 at lysosomes and early endosomes. For FLOT1-/FLOT2-positive early endosomes, we identified >300 proteins presenting putative cargo, and confirm the latrophilin family of adhesion G protein-coupled receptors as substrates for flotillin-dependent endocytosis.

Inducing and Sensing Protein–Protein Interactions in Living Cells by Selective Cross-linking

2007 ◽  
Vol 119 (23) ◽  
pp. 4359-4362 ◽  
Author(s):  
Guillaume Lemercier ◽  
Susanne Gendreizig ◽  
Maik Kindermann ◽  
Kai Johnsson
Keyword(s):  
Protein Interactions ◽  
Living Cells ◽  
Cross Linking ◽  
Protein Protein Interactions

Genetically encoded releasable photo-cross-linking strategies for studying protein–protein interactions in living cells

2017 ◽  
Vol 12 (10) ◽  
pp. 2147-2168 ◽  
Author(s):  
Yi Yang ◽  
Haiping Song ◽  
Dan He ◽  
Shuai Zhang ◽  
Shizhong Dai ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Living Cells ◽  
Cross Linking ◽  
Protein Protein Interactions

scholarly journals Structure-based validation can drastically under-estimate error rate in proteome-wide cross-linking mass spectrometry studies

2019 ◽  
Author(s):  
Kumar Yugandhar ◽  
Ting-Yi Wang ◽  
Shayne D. Wierbowski ◽  
Elnur Elyar Shayhidin ◽  
Haiyuan Yu
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Protein Complexes ◽  
Error Rates ◽  
Cross Linking ◽  
Protein Protein Interactions ◽  
3D Structures ◽  
Cross Links ◽  
Assess Quality ◽  
Almost All

AbstractRecent, rapid advances in cross-linking mass spectrometry (XL-MS) has enabled detection of novel protein-protein interactions and their structural dynamics at the proteome scale. Given the importance and scale of the novel interactions identified in these proteome-wide XL-MS studies, thorough quality assessment is critical. Almost all current XL-MS studies validate cross-links against known 3D structures of representative protein complexes. However, current structure validation approach only includes cross-links where both peptides mapped to the 3D structures. Here we provide theoretical and experimental evidence demonstrating this approach can drastically underestimate error rates for proteome-wide XL-MS datasets. Addressing current shortcomings, we propose and demonstrate a comprehensive set of four metrics, including orthogonal experimental validation to thoroughly assess quality of proteome-wide XL-MS datasets.

Inducing and Sensing Protein–Protein Interactions in Living Cells by Selective Cross-linking

2007 ◽  
Vol 46 (23) ◽  
pp. 4281-4284 ◽  
Author(s):  
Guillaume Lemercier ◽  
Susanne Gendreizig ◽  
Maik Kindermann ◽  
Kai Johnsson
Keyword(s):  
Protein Interactions ◽  
Living Cells ◽  
Cross Linking ◽  
Protein Protein Interactions
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