1
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Cheng J, Wang H, Zhang Y, Wang X, Liu G. Advances in crosslinking chemistry and proximity-enabled strategies: deciphering protein complexes and interactions. Org Biomol Chem 2024; 22:7549-7559. [PMID: 39192765 DOI: 10.1039/d4ob01058b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Mass spectrometry, coupled with innovative crosslinking techniques to decode protein conformations and interactions through uninterrupted signal connections, has undergone remarkable progress in recent years. It is crucial to develop selective crosslinking reagents that minimally disrupt protein structure and dynamics, providing insights into protein network regulation and biological functions. Compared to traditional crosslinkers, new bifunctional chemical crosslinkers exhibit high selectivity and specificity in connecting proximal amino acid residues, resulting in stable molecular crosslinked products. The conjugation with specific amino acid residues like lysine, cysteine, arginine and tyrosine expands the XL-MS toolbox, enabling more precise modeling of target substrates and leading to improved data quality and reliability. Another emerging crosslinking method utilizes unnatural amino acids (UAAs) derived from proximity-enabled reactivity with specific amino acids or sulfur-fluoride exchange (SuFEx) reactions with nucleophilic residues. These UAAs are genetically encoded into proteins for the formation of specific covalent bonds. This technique combines the benefits of genetic encoding for live cell compatibility with chemical crosslinking, providing a valuable method for capturing transient and weak protein-protein interactions (PPIs) for mapping PPI coordinates and improving the pharmacological properties of proteins. With continued advancements in technology and applications, crosslinking mass spectrometry is poised to play an increasingly significant role in guiding our understanding of protein dynamics and function in the future.
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Affiliation(s)
- Jiongjia Cheng
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University, Nanjing, 211171, China.
| | - Haiying Wang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University, Nanjing, 211171, China.
| | - Yuchi Zhang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University, Nanjing, 211171, China.
| | - Xiaofeng Wang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University, Nanjing, 211171, China.
| | - Guangxiang Liu
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University, Nanjing, 211171, China.
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2
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Liu X, Abad L, Chatterjee L, Cristea IM, Varjosalo M. Mapping protein-protein interactions by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38742660 DOI: 10.1002/mas.21887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Protein-protein interactions (PPIs) are essential for numerous biological activities, including signal transduction, transcription control, and metabolism. They play a pivotal role in the organization and function of the proteome, and their perturbation is associated with various diseases, such as cancer, neurodegeneration, and infectious diseases. Recent advances in mass spectrometry (MS)-based protein interactomics have significantly expanded our understanding of the PPIs in cells, with techniques that continue to improve in terms of sensitivity, and specificity providing new opportunities for the study of PPIs in diverse biological systems. These techniques differ depending on the type of interaction being studied, with each approach having its set of advantages, disadvantages, and applicability. This review highlights recent advances in enrichment methodologies for interactomes before MS analysis and compares their unique features and specifications. It emphasizes prospects for further improvement and their potential applications in advancing our knowledge of PPIs in various biological contexts.
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Affiliation(s)
- Xiaonan Liu
- Department of Physiology, Faculty of Medical Sciences in Katowice, Medical University of Silesia in Katowice, Katowice, Poland
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Lawrence Abad
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Lopamudra Chatterjee
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Markku Varjosalo
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
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3
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Stahl K, Graziadei A, Dau T, Brock O, Rappsilber J. Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning. Nat Biotechnol 2023; 41:1810-1819. [PMID: 36941363 PMCID: PMC10713450 DOI: 10.1038/s41587-023-01704-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 02/06/2023] [Indexed: 03/23/2023]
Abstract
While AlphaFold2 can predict accurate protein structures from the primary sequence, challenges remain for proteins that undergo conformational changes or for which few homologous sequences are known. Here we introduce AlphaLink, a modified version of the AlphaFold2 algorithm that incorporates experimental distance restraint information into its network architecture. By employing sparse experimental contacts as anchor points, AlphaLink improves on the performance of AlphaFold2 in predicting challenging targets. We confirm this experimentally by using the noncanonical amino acid photo-leucine to obtain information on residue-residue contacts inside cells by crosslinking mass spectrometry. The program can predict distinct conformations of proteins on the basis of the distance restraints provided, demonstrating the value of experimental data in driving protein structure prediction. The noise-tolerant framework for integrating data in protein structure prediction presented here opens a path to accurate characterization of protein structures from in-cell data.
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Affiliation(s)
- Kolja Stahl
- Robotics and Biology Laboratory, Technische Universität Berlin, Berlin, Germany
| | - Andrea Graziadei
- Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany
| | - Therese Dau
- Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany
- Fritz Lipmann Institute, Leibniz Institute on Aging, Jena, Germany
| | - Oliver Brock
- Robotics and Biology Laboratory, Technische Universität Berlin, Berlin, Germany.
- Science of Intelligence, Research Cluster of Excellence, Berlin, Germany.
| | - Juri Rappsilber
- Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany.
- Si-M/'Der Simulierte Mensch', a Science Framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, Berlin, Germany.
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
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4
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Faustino AM, Sharma P, Manriquez-Sandoval E, Yadav D, Fried SD. Progress toward Proteome-Wide Photo-Cross-Linking to Enable Residue-Level Visualization of Protein Structures and Networks In Vivo. Anal Chem 2023; 95:10670-10685. [PMID: 37341467 DOI: 10.1021/acs.analchem.3c01369] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Cross-linking mass spectrometry (XL-MS) is emerging as a method at the crossroads of structural and cellular biology, uniquely capable of identifying protein-protein interactions with residue-level resolution and on the proteome-wide scale. With the development of cross-linkers that can form linkages inside cells and easily cleave during fragmentation on the mass spectrometer (MS-cleavable cross-links), it has become increasingly facile to identify contacts between any two proteins in complex samples, including in live cells or tissues. Photo-cross-linkers possess the advantages of high temporal resolution and high reactivity, thereby engaging all residue-types (rather than just lysine); nevertheless, photo-cross-linkers have not enjoyed widespread use and are yet to be employed for proteome-wide studies because their products are challenging to identify. Here, we demonstrate the synthesis and application of two heterobifunctional photo-cross-linkers that feature diazirines and N-hydroxy-succinimidyl carbamate groups, the latter of which unveil doubly fissile MS-cleavable linkages upon acyl transfer to protein targets. Moreover, these cross-linkers demonstrate high water-solubility and cell-permeability. Using these compounds, we demonstrate the feasibility of proteome-wide photo-cross-linking in cellulo. These studies elucidate a small portion of Escherichia coli's interaction network, albeit with residue-level resolution. With further optimization, these methods will enable the detection of protein quinary interaction networks in their native environment at residue-level resolution, and we expect that they will prove useful toward the effort to explore the molecular sociology of the cell.
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Affiliation(s)
- Anneliese M Faustino
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Piyoosh Sharma
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Edgar Manriquez-Sandoval
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Divya Yadav
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
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5
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Chen ZA, Rappsilber J. Protein structure dynamics by crosslinking mass spectrometry. Curr Opin Struct Biol 2023; 80:102599. [PMID: 37104977 DOI: 10.1016/j.sbi.2023.102599] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023]
Abstract
Crosslinking mass spectrometry captures protein structures in solution. The crosslinks reveal spatial proximities as distance restraints, but do not easily reveal which of these restraints derive from the same protein conformation. This superposition can be reduced by photo-crosslinking, and adding information from protein structure models, or quantitative crosslinking reveals conformation-specific crosslinks. As a consequence, crosslinking MS has proven useful already in the context of multiple dynamic protein systems. We foresee a breakthrough in the resolution and scale of studying protein dynamics when crosslinks are used to guide deep-learning-based protein modelling. Advances in crosslinking MS, such as photoactivatable crosslinking and in-situ crosslinking, will then reveal protein conformation dynamics in the cellular context, at a pseudo-atomic resolution, and plausibly in a time-resolved manner.
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Affiliation(s)
- Zhuo Angel Chen
- Technische Universität Berlin, Chair of Bioanalytics, 10623 Berlin, Germany
| | - Juri Rappsilber
- Technische Universität Berlin, Chair of Bioanalytics, 10623 Berlin, Germany; Si-M/"Der Simulierte Mensch", a Science Framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, 10623 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
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6
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Fedoryshchak RO, Gorelik A, Shen M, Shchepinova MM, Pérez-Dorado I, Tate EW. Discovery of lipid-mediated protein-protein interactions in living cells using metabolic labeling with photoactivatable clickable probes. Chem Sci 2023; 14:2419-2430. [PMID: 36873846 PMCID: PMC9977449 DOI: 10.1039/d2sc06116c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/29/2023] [Indexed: 01/31/2023] Open
Abstract
Protein-protein interactions (PPIs) are essential and pervasive regulatory elements in biology. Despite the development of a range of techniques to probe PPIs in living systems, there is a dearth of approaches to capture interactions driven by specific post-translational modifications (PTMs). Myristoylation is a lipid PTM added to more than 200 human proteins, where it may regulate membrane localization, stability or activity. Here we report the design and synthesis of a panel of novel photocrosslinkable and clickable myristic acid analog probes, and their characterization as efficient substrates for human N-myristoyltransferases NMT1 and NMT2, both biochemically and through X-ray crystallography. We demonstrate metabolic incorporation of probes to label NMT substrates in cell culture and in situ intracellular photoactivation to form a covalent crosslink between modified proteins and their interactors, capturing a snapshot of interactions in the presence of the lipid PTM. Proteomic analyses revealed both known and multiple novel interactors of a series of myristoylated proteins, including ferroptosis suppressor protein 1 (FSP1) and spliceosome-associated RNA helicase DDX46. The concept exemplified by these probes offers an efficient approach for exploring the PTM-specific interactome without the requirement for genetic modification, which may prove broadly applicable to other PTMs.
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Affiliation(s)
- Roman O Fedoryshchak
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK .,The Francis Crick Institute 1 Midland Road London NW1 1AT UK
| | - Andrii Gorelik
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK .,The Francis Crick Institute 1 Midland Road London NW1 1AT UK
| | - Mengjie Shen
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK
| | - Maria M Shchepinova
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK
| | - Inmaculada Pérez-Dorado
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK .,The Francis Crick Institute 1 Midland Road London NW1 1AT UK
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7
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Piersimoni L, Kastritis PL, Arlt C, Sinz A. Cross-Linking Mass Spectrometry for Investigating Protein Conformations and Protein-Protein Interactions─A Method for All Seasons. Chem Rev 2021; 122:7500-7531. [PMID: 34797068 DOI: 10.1021/acs.chemrev.1c00786] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mass spectrometry (MS) has become one of the key technologies of structural biology. In this review, the contributions of chemical cross-linking combined with mass spectrometry (XL-MS) for studying three-dimensional structures of proteins and for investigating protein-protein interactions are outlined. We summarize the most important cross-linking reagents, software tools, and XL-MS workflows and highlight prominent examples for characterizing proteins, their assemblies, and interaction networks in vitro and in vivo. Computational modeling plays a crucial role in deriving 3D-structural information from XL-MS data. Integrating XL-MS with other techniques of structural biology, such as cryo-electron microscopy, has been successful in addressing biological questions that to date could not be answered. XL-MS is therefore expected to play an increasingly important role in structural biology in the future.
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Affiliation(s)
- Lolita Piersimoni
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Kurt-Mothes-Strasse 3a, D-06120 Halle (Saale), Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Biozentrum, Weinbergweg 22, D-06120 Halle (Saale), Germany
| | - Christian Arlt
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
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8
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Grasso G. THE USE OF MASS SPECTROMETRY TO STUDY ZN-METALLOPROTEASE-SUBSTRATE INTERACTIONS. MASS SPECTROMETRY REVIEWS 2020; 39:574-585. [PMID: 31898821 DOI: 10.1002/mas.21621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/19/2019] [Indexed: 06/10/2023]
Abstract
Zinc metalloproteases (ZnMPs) participate in diverse biological reactions, encompassing the synthesis and degradation of all the major metabolites in living organisms. In particular, ZnMPs have been recognized to play a very important role in controlling the concentration level of several peptides and/or proteins whose homeostasis has to be finely regulated for the correct physiology of cells. Dyshomeostasis of aggregation-prone proteins causes pathological conditions and the development of several different diseases. For this reason, in recent years, many analytical approaches have been applied for studying the interaction between ZnMPs and their substrates and how environmental factors can affect enzyme activities. In this scenario, mass spectrometric methods occupy a very important role in elucidating different aspects of ZnMPs-substrates interaction. These range from identification of cleavage sites to quantitation of kinetic parameters. In this work, an overview of all the main achievements regarding the application of mass spectrometric methods to investigating ZnMPs-substrates interactions is presented. A general experimental protocol is also described which may prove useful to the study of similar interactions. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Giuseppe Grasso
- Department of Chemical Sciences, Università degli Studi di Catania, Viale Andrea Doria 6, Catania, 95125, Italy
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9
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Goehring A, Michin I, Gerdes T, Schulze N, Blueggel M, Rehic E, Kaschani F, Kaiser M, Bayer P. Targeting of parvulin interactors by diazirine mediated cross-linking discloses a cellular role of human Par14/17 in actin polymerization. Biol Chem 2020; 401:955-968. [PMID: 32142471 DOI: 10.1515/hsz-2019-0423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/04/2020] [Indexed: 11/15/2022]
Abstract
The peptidyl-prolyl cis/trans isomerases (PPIases) Parvulin 14 (Par14) and Parvulin 17 (Par17) result from alternative transcription initiation of the PIN4 gene. Whereas Par14 is present in all metazoan, Par17 is only expressed in Hominidae. Par14 resides mainly within the cellular nucleus, while Par17 is translocated into mitochondria. Using photo-affinity labeling, cross-linking and mass spectrometry (MS) we identified binding partners for both enzymes from HeLa lysates and disentangled their cellular roles. Par14 is involved in biogenesis of ribonucleoprotein (RNP)-complexes, RNA processing and DNA repair. Its elongated isoform Par17 participates in protein transport/translocation and in cytoskeleton organization. Nuclear magnetic resonance (NMR) spectroscopy reveals that Par17 binds to β-actin with its N-terminal region, while both parvulins initiate actin polymerization depending on their PPIase activity as monitored by fluorescence spectroscopy. The knockdown (KD) of Par17 in HCT116 cells results in a defect in cell motility and migration.
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Affiliation(s)
- Anna Goehring
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 2-5, D-45117 Essen, Germany
| | - Irina Michin
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 2-5, D-45117 Essen, Germany
| | - Tina Gerdes
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 2-5, D-45117 Essen, Germany
| | - Nina Schulze
- Imaging Centre Campus Essen (ICCE), Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 2-5, D-45117 Essen, Germany
| | - Mike Blueggel
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 2-5, D-45117 Essen, Germany
| | - Edisa Rehic
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 2-5, D-45117 Essen, Germany
| | - Farnusch Kaschani
- Chemical Biology, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 2-5, D-45117 Essen, Germany
| | - Markus Kaiser
- Chemical Biology, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 2-5, D-45117 Essen, Germany
| | - Peter Bayer
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 2-5, D-45117 Essen, Germany
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10
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Cross-linking/mass spectrometry to get a closer view on protein interaction networks. Curr Opin Biotechnol 2020; 63:48-53. [DOI: 10.1016/j.copbio.2019.12.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/02/2019] [Accepted: 12/09/2019] [Indexed: 12/21/2022]
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11
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Mass spectrometry-based methods for structural biology on a proteome-wide scale. Biochem Soc Trans 2020; 48:945-954. [DOI: 10.1042/bst20190794] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/14/2020] [Accepted: 04/16/2020] [Indexed: 11/17/2022]
Abstract
Mass spectrometry (MS) has long been used to study proteins mainly via sequence identification and quantitation of expression abundance. In recent years, MS has emerged as a tool for structural biology. Intact protein structural analysis has been enabled by the development of methods such as native MS, top-down proteomics, and ion mobility MS. Other MS-based structural methods include affinity purification MS, chemical cross-linking, and protein footprinting. These methods have enabled the study of protein–protein and protein–ligand interactions and regions of conformational change. The coupling of MS with liquid chromatography has permitted the analysis of complex samples. This bottom-up proteomics workflow enables the study of protein structure in the native cellular environment and provides structural information across the proteome. It has been demonstrated that the crowded environment of the cell affects protein binding interactions and affinities. Performing studies in this complex environment is essential for understanding the functional roles of proteins. MS-based structural methods permit analysis of samples such as cell lysates, intact cells, and tissue to provide a more physiological view of protein structure. This mini-review discusses the various MS-based methods that can be used for proteome-wide structural studies and highlights some of their application.
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12
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Abstract
Functions of intrinsically disordered proteins do not require structure. Such structure-independent functionality has melted away the classic rigid "lock and key" representation of structure-function relationships in proteins, opening a new page in protein science, where molten keys operate on melted locks and where conformational flexibility and intrinsic disorder, structural plasticity and extreme malleability, multifunctionality and binding promiscuity represent a new-fangled reality. Analysis and understanding of this new reality require novel tools, and some of the techniques elaborated for the examination of intrinsically disordered protein functions are outlined in this review.
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Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33620, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Russian Federation
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13
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Dülfer J, Kadek A, Kopicki JD, Krichel B, Uetrecht C. Structural mass spectrometry goes viral. Adv Virus Res 2019; 105:189-238. [PMID: 31522705 DOI: 10.1016/bs.aivir.2019.07.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Over the last 20 years, mass spectrometry (MS), with its ability to analyze small sample amounts with high speed and sensitivity, has more and more entered the field of structural virology, aiming to investigate the structure and dynamics of viral proteins as close to their native environment as possible. The use of non-perturbing labels in hydrogen-deuterium exchange MS allows for the analysis of interactions between viral proteins and host cell factors as well as their dynamic responses to the environment. Cross-linking MS, on the other hand, can analyze interactions in viral protein complexes and identify virus-host interactions in cells. Native MS allows transferring viral proteins, complexes and capsids into the gas phase and has broken boundaries to overcome size limitations, so that now even the analysis of intact virions is possible. Different MS approaches not only inform about size, stability, interactions and dynamics of virus assemblies, but also bridge the gap to other biophysical techniques, providing valuable constraints for integrative structural modeling of viral complex assemblies that are often inaccessible by single technique approaches. In this review, recent advances are highlighted, clearly showing that structural MS approaches in virology are moving towards systems biology and ever more experiments are performed on cellular level.
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Affiliation(s)
- Jasmin Dülfer
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Alan Kadek
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany; European XFEL GmbH, Schenefeld, Germany
| | - Janine-Denise Kopicki
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany; European XFEL GmbH, Schenefeld, Germany.
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14
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Götze M, Iacobucci C, Ihling CH, Sinz A. A Simple Cross-Linking/Mass Spectrometry Workflow for Studying System-wide Protein Interactions. Anal Chem 2019; 91:10236-10244. [DOI: 10.1021/acs.analchem.9b02372] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Michael Götze
- Institute for Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, D-06120 Halle (Saale), Germany
| | - Claudio Iacobucci
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, D-06120 Halle (Saale), Germany
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, D-06120 Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, D-06120 Halle (Saale), Germany
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15
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Kaur U, Johnson DT, Chea EE, Deredge DJ, Espino JA, Jones LM. Evolution of Structural Biology through the Lens of Mass Spectrometry. Anal Chem 2019; 91:142-155. [PMID: 30457831 PMCID: PMC6472977 DOI: 10.1021/acs.analchem.8b05014] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Upneet Kaur
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Danté T. Johnson
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Emily E. Chea
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Daniel J. Deredge
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Jessica A. Espino
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Lisa M. Jones
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
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16
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Proteomics. Mol Biol 2019. [DOI: 10.1016/b978-0-12-813288-3.00015-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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17
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Kaur U, Meng H, Lui F, Ma R, Ogburn RN, Johnson JHR, Fitzgerald MC, Jones LM. Proteome-Wide Structural Biology: An Emerging Field for the Structural Analysis of Proteins on the Proteomic Scale. J Proteome Res 2018; 17:3614-3627. [PMID: 30222357 DOI: 10.1021/acs.jproteome.8b00341] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past decade, a suite of new mass-spectrometry-based proteomics methods has been developed that now enables the conformational properties of proteins and protein-ligand complexes to be studied in complex biological mixtures, from cell lysates to intact cells. Highlighted here are seven of the techniques in this new toolbox. These techniques include chemical cross-linking (XL-MS), hydroxyl radical footprinting (HRF), Drug Affinity Responsive Target Stability (DARTS), Limited Proteolysis (LiP), Pulse Proteolysis (PP), Stability of Proteins from Rates of Oxidation (SPROX), and Thermal Proteome Profiling (TPP). The above techniques all rely on conventional bottom-up proteomics strategies for peptide sequencing and protein identification. However, they have required the development of unconventional proteomic data analysis strategies. Discussed here are the current technical challenges associated with these different data analysis strategies as well as the relative analytical capabilities of the different techniques. The new biophysical capabilities that the above techniques bring to bear on proteomic research are also highlighted in the context of several different application areas in which these techniques have been used, including the study of protein ligand binding interactions (e.g., protein target discovery studies and protein interaction network analyses) and the characterization of biological states.
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Affiliation(s)
- Upneet Kaur
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - He Meng
- Department of Chemistry , Duke University , Durham , North Carolina 27708-0346 , United States
| | | | - Renze Ma
- Department of Chemistry , Duke University , Durham , North Carolina 27708-0346 , United States
| | - Ryenne N Ogburn
- Department of Chemistry , Duke University , Durham , North Carolina 27708-0346 , United States
| | - Julia H R Johnson
- Department of Chemistry , Duke University , Durham , North Carolina 27708-0346 , United States
| | - Michael C Fitzgerald
- Department of Chemistry , Duke University , Durham , North Carolina 27708-0346 , United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
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18
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Chavez JD, Bruce JE. Chemical cross-linking with mass spectrometry: a tool for systems structural biology. Curr Opin Chem Biol 2018; 48:8-18. [PMID: 30172868 DOI: 10.1016/j.cbpa.2018.08.006] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/09/2018] [Accepted: 08/10/2018] [Indexed: 01/14/2023]
Abstract
Biological processes supporting life are orchestrated by a highly dynamic array of protein structures and interactions comprising the interactome. Defining the interactome, visualizing how structures and interactions change and function to support life is essential to improved understanding of fundamental molecular processes, but represents a challenge unmet by any single analytical technique. Chemical cross-linking with mass spectrometry provides identification of proximal amino acid residues within proteins and protein complexes, yielding low resolution structural information. This approach has predominantly been employed to provide structural insight on isolated protein complexes, and has been particularly useful for molecules that are recalcitrant to conventional structural biology studies. Here we discuss recent developments in cross-linking and mass spectrometry technologies that are providing large-scale or systems-level interactome data with successful applications to isolated organelles, cell lysates, virus particles, intact bacterial and mammalian cultured cells and tissue samples.
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Affiliation(s)
- Juan D Chavez
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - James E Bruce
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
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19
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Ge SS, Chen B, Wu YY, Long QS, Zhao YL, Wang PY, Yang S. Current advances of carbene-mediated photoaffinity labeling in medicinal chemistry. RSC Adv 2018; 8:29428-29454. [PMID: 35547988 PMCID: PMC9084484 DOI: 10.1039/c8ra03538e] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/07/2018] [Indexed: 12/21/2022] Open
Abstract
Photoaffinity labeling (PAL) in combination with a chemical probe to covalently bind its target upon UV irradiation has demonstrated considerable promise in drug discovery for identifying new drug targets and binding sites. In particular, carbene-mediated photoaffinity labeling (cmPAL) has been widely used in drug target identification owing to its excellent photolabeling efficiency, minimal steric interference and longer excitation wavelength. Specifically, diazirines, which are among the precursors of carbenes and have higher carbene yields and greater chemical stability than diazo compounds, have proved to be valuable photolabile reagents in a diverse range of biological systems. This review highlights current advances of cmPAL in medicinal chemistry, with a focus on structures and applications for identifying small molecule-protein and macromolecule-protein interactions and ligand-gated ion channels, coupled with advances in the discovery of targets and inhibitors using carbene precursor-based biological probes developed in recent decades.
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Affiliation(s)
- Sha-Sha Ge
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Biao Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Yuan-Yuan Wu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Qing-Su Long
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Yong-Liang Zhao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Pei-Yi Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University Guiyang 550025 China +86-851-8829-2170 +86-851-8829-2171
- College of Pharmacy, East China University of Science & Technology Shanghai 200237 China
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Hill JR, Robertson AAB. Fishing for Drug Targets: A Focus on Diazirine Photoaffinity Probe Synthesis. J Med Chem 2018; 61:6945-6963. [PMID: 29683660 DOI: 10.1021/acs.jmedchem.7b01561] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Target identification is a high-priority, albeit challenging, aspect of drug discovery. Diazirine-based photoaffinity probes (PAPs) can facilitate the process by covalently capturing transient molecular interactions. This can help identify target proteins and map the ligand's interactome. Diazirine probes have even been incorporated by cellular machinery into proteins. Embarking on the synthesis of customized PAPs, containing either an aliphatic or trifluoromethyl phenyl diazirine, can be a considerable endeavor, particularly for medicinal chemists and chemical biologists new to the field. This review takes a synthetic focus, aiming to summarize available routes, propose new avenues, and illuminate recent advances in diazirine synthesis. Select examples of diazirine photoaffinity labeling applications have been included throughout to provide instructive definition of the advantages and limitations of the technology while simultaneously highlighting how these reagents can be applied in a practical sense.
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Affiliation(s)
- James R Hill
- Institute for Molecular Bioscience , The University of Queensland , St. Lucia , Queensland 4072 , Australia
| | - Avril A B Robertson
- Institute for Molecular Bioscience , The University of Queensland , St. Lucia , Queensland 4072 , Australia.,School of Chemistry and Molecular Biosciences , The University of Queensland , St. Lucia QLD4072 , Australia
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21
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Piotrowski C, Sinz A. Structural Investigation of Proteins and Protein Complexes by Chemical Cross-Linking/Mass Spectrometry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1105:101-121. [PMID: 30617826 DOI: 10.1007/978-981-13-2200-6_8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
During the last two decades, cross-linking combined with mass spectrometry (MS) has evolved as a valuable tool to gain structural insights into proteins and protein assemblies. Structural information is obtained by introducing covalent connections between amino acids that are in spatial proximity in proteins and protein complexes. The distance constraints imposed by the cross-linking reagent provide information on the three-dimensional arrangement of the covalently connected amino acid residues and serve as basis for de-novo or homology modeling approaches. As cross-linking/MS allows investigating protein 3D-structures and protein-protein interactions not only in-vitro, but also in-vivo, it is especially appealing for studying protein systems in their native environment. In this chapter, we describe the principles of cross-linking/MS and illustrate its value for investigating protein 3D-structures and for unraveling protein interaction networks.
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Affiliation(s)
- Christine Piotrowski
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
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