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Manalastas-Cantos K, Adoni KR, Pfeifer M, Märtens B, Grünewald K, Thalassinos K, Topf M. Modeling Flexible Protein Structure With AlphaFold2 and Crosslinking Mass Spectrometry. Mol Cell Proteomics 2024; 23:100724. [PMID: 38266916 PMCID: PMC10884514 DOI: 10.1016/j.mcpro.2024.100724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/26/2024] Open
Abstract
We propose a pipeline that combines AlphaFold2 (AF2) and crosslinking mass spectrometry (XL-MS) to model the structure of proteins with multiple conformations. The pipeline consists of two main steps: ensemble generation using AF2 and conformer selection using XL-MS data. For conformer selection, we developed two scores-the monolink probability score (MP) and the crosslink probability score (XLP)-both of which are based on residue depth from the protein surface. We benchmarked MP and XLP on a large dataset of decoy protein structures and showed that our scores outperform previously developed scores. We then tested our methodology on three proteins having an open and closed conformation in the Protein Data Bank: Complement component 3 (C3), luciferase, and glutamine-binding periplasmic protein, first generating ensembles using AF2, which were then screened for the open and closed conformations using experimental XL-MS data. In five out of six cases, the most accurate model within the AF2 ensembles-or a conformation within 1 Å of this model-was identified using crosslinks, as assessed through the XLP score. In the remaining case, only the monolinks (assessed through the MP score) successfully identified the open conformation of glutamine-binding periplasmic protein, and these results were further improved by including the "occupancy" of the monolinks. This serves as a compelling proof-of-concept for the effectiveness of monolinks. In contrast, the AF2 assessment score was only able to identify the most accurate conformation in two out of six cases. Our results highlight the complementarity of AF2 with experimental methods like XL-MS, with the MP and XLP scores providing reliable metrics to assess the quality of the predicted models. The MP and XLP scoring functions mentioned above are available at https://gitlab.com/topf-lab/xlms-tools.
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Affiliation(s)
- Karen Manalastas-Cantos
- Center for Data and Computing in Natural Sciences, Universität Hamburg, Hamburg, Germany; Department of Integrative Virology, Leibniz-Institut für Virologie (LIV), Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Kish R Adoni
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK; Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Matthias Pfeifer
- Department of Integrative Virology, Leibniz-Institut für Virologie (LIV), Centre for Structural Systems Biology (CSSB), Hamburg, Germany; Universitätsklinikum Hamburg Eppendorf (UKE), Hamburg, Germany
| | - Birgit Märtens
- Department of Integrative Virology, Leibniz-Institut für Virologie (LIV), Centre for Structural Systems Biology (CSSB), Hamburg, Germany; Universitätsklinikum Hamburg Eppendorf (UKE), Hamburg, Germany
| | - Kay Grünewald
- Department of Integrative Virology, Leibniz-Institut für Virologie (LIV), Centre for Structural Systems Biology (CSSB), Hamburg, Germany; Department of Chemistry, Universität Hamburg, Hamburg, Germany
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK; Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Maya Topf
- Department of Integrative Virology, Leibniz-Institut für Virologie (LIV), Centre for Structural Systems Biology (CSSB), Hamburg, Germany; Universitätsklinikum Hamburg Eppendorf (UKE), Hamburg, Germany.
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2
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Park J, Son A, Kim H. A protein-protein interaction analysis tool for targeted cross-linking mass spectrometry. Sci Rep 2023; 13:22103. [PMID: 38092875 PMCID: PMC10719354 DOI: 10.1038/s41598-023-49663-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023] Open
Abstract
Protein networking is critical to understanding the biological functions of proteins and the underlying mechanisms of disease. However, identifying physical protein-protein interactions (PPIs) can be challenging. To gain insights into target proteins that interact with a particular disease, we need to profile all the proteins involved in the disease beforehand. Although the cross-linking mass spectrometry (XL-MS) method is a representative approach to identify physical interactions between proteins, calculating theoretical mass values for application to targeted mass spectrometry can be difficult. To address this challenge, our research team developed PPIAT, a web application that integrates information on reviewed human proteins, protein-protein interactions, cross-linkers, enzymes, and modifications. PPIAT leverages publicly accessible databases such as STRING to identify interactomes associated with target proteins. Moreover, it autonomously computes the theoretical mass value, accounting for all potential cross-linking scenarios pertinent to the application of XL-MS in SRM analysis. The outputs generated by PPIAT can be concisely represented in terms of protein interaction probabilities, complemented by findings from alternative analytical tools like Prego. These comprehensive summaries enable researchers to customize the results according to specific experimental conditions. All functions of PPIAT are available for free on the web application, making it a valuable tool for researchers studying protein-protein interactions.
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Affiliation(s)
- Jongham Park
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Ahrum Son
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, 92037, USA
| | - Hyunsoo Kim
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea.
- Department of Convergent Bioscience and Informatics, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea.
- SCICS, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea.
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3
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Lai YH, Wang YS. Advances in high-resolution mass spectrometry techniques for analysis of high mass-to-charge ions. MASS SPECTROMETRY REVIEWS 2023; 42:2426-2445. [PMID: 35686331 DOI: 10.1002/mas.21790] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/27/2022] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
A major challenge in modern mass spectrometry (MS) is achieving high mass resolving power and accuracy for precision analyses in high mass-to-charge (m/z) regions. To advance the capability of MS for increasingly demanding applications, understanding limitations of state-of-the-art techniques and their status in applied sciences is essential. This review summarizes important instruments in high-resolution mass spectrometry (HRMS) and related advances to extend their working range to high m/z regions. It starts with an overview of HRMS techniques that provide adequate performance for macromolecular analysis, including Fourier-transform, time-of-flight (TOF), quadrupole-TOF, and related data-processing techniques. Methodologies and applications of HRMS for characterizing macromolecules in biochemistry and material sciences are summarized, such as top-down proteomics, native MS, drug discovery, structural virology, and polymer analyses.
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Affiliation(s)
- Yin-Hung Lai
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, R.O.C
- Department of Chemical Engineering, National United University, Miaoli, Taiwan, R.O.C
- Institute of Food Safety and Health Risk Assessment, National Yang Ming Chiao Tung University, Taipei, Taiwan, R.O.C
| | - Yi-Sheng Wang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, R.O.C
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4
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Cao Y, Liu XT, Mao PZ, Chen ZL, Tarn C, Dong MQ. Comparative Analysis of Chemical Cross-Linking Mass Spectrometry Data Indicates That Protein STY Residues Rarely React with N-Hydroxysuccinimide Ester Cross-Linkers. J Proteome Res 2023; 22:2593-2607. [PMID: 37494005 DOI: 10.1021/acs.jproteome.3c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
When it comes to mass spectrometry data analysis for identification of peptide pairs linked by N-hydroxysuccinimide (NHS) ester cross-linkers, search engines bifurcate in their setting of cross-linkable sites. Some restrict NHS ester cross-linkable sites to lysine (K) and protein N-terminus, referred to as K only for short, whereas others additionally include serine (S), threonine (T), and tyrosine (Y) by default. Here, by setting amino acids with chemically inert side chains such as glycine (G), valine (V), and leucine (L) as cross-linkable sites, which serves as a negative control, we show that software-identified STY-cross-links are only as reliable as GVL-cross-links. This is true across different NHS ester cross-linkers including DSS, DSSO, and DSBU, and across different search engines including MeroX, xiSearch, and pLink. Using a published data set originated from synthetic peptides, we demonstrate that STY-cross-links indeed have a high false discovery rate. Further analysis revealed that depending on the data and the search engine used to analyze the data, up to 65% of the STY-cross-links identified are actually K-K cross-links of the same peptide pairs, up to 61% are actually K-mono-links, and the rest tend to contain short peptides at high risk of false identification.
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Affiliation(s)
- Yong Cao
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Xin-Tong Liu
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Peng-Zhi Mao
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen-Lin Chen
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ching Tarn
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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5
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Wang Z, Rabb JD, Lin Q. Orthogonal Crosslinking: A Strategy to Generate Novel Protein Topology and Function. Chemistry 2023; 29:e202202828. [PMID: 36251567 PMCID: PMC9839582 DOI: 10.1002/chem.202202828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Indexed: 11/27/2022]
Abstract
Compared to the disulfide bond, other naturally occurring intramolecular crosslinks have received little attention, presumably due to their rarity in the vast protein space. Here we presented examples of natural non-disulfide crosslinks, which we refer to as orthogonal crosslinks, emphasizing their effect on protein topology and function. We summarize recent efforts on expanding orthogonal crosslinks by using either the enzymes that catalyze protein circularization or the genetic code expansion strategy to add electrophilic amino acids site-specifically in proteins. The advantages and disadvantages of each method are discussed, along with their applications to generate novel protein topology and function. In particular, we highlight our recent work on spontaneous orthogonal crosslinking, in which a carbamate-based crosslink was generated in situ, and its applications in designing orthogonally crosslinked domain antibodies with their topology-mimicking bacterial adhesins.
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Affiliation(s)
- Zheng Wang
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA
| | - Johnathan D Rabb
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA
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6
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Mehta A, Kamal AHM, Cornelius S, Chowdhury SM. Protein-Protein Interaction Network Mapping by Affinity Purification Cross-Linking Mass Spectrometry (AP-XL-MS) based Proteomics. Methods Mol Biol 2023; 2690:255-267. [PMID: 37450153 DOI: 10.1007/978-1-0716-3327-4_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Protein-protein interactions (PPIs) are the physical interactions formed among proteins. These interactions are primarily functional, i.e., they arise from specific biomolecular events, and each interaction interface serves a specific purpose. A significant number of methods have been developed for protein interactions in the field of proteomics in the last decade. Advanced mass spectrometry technology significantly contributed to the development of these methods. The rapid advancement of groundbreaking MS technology has greatly aided the mapping of protein interaction from large-data sets comprehensively. This chapter describes the affinity purification (AP) mass spectrometry (MS)-based methods combined with chemical cross-linking (XL) of protein complexes. This chapter includes sample preparation methods involving cell culture, cell treatments with ligands, drugs, and cross-linkers, protein extractions, affinity purification, sodium dodecyl sulfate (SDS) polyacrylamide gel separation, in-solution or in-gel digestion, liquid-chromatography, and mass spectrometry analysis of samples (LC-MS/MS). Application of a cleavable cross-linker, dual cleavable cross-linking technology (DUCCT) in combination with the affinity purification (AP) method has also been described. Methods for data analysis using unmodified and cross-linked peptide analysis are discussed.
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Affiliation(s)
- Ashima Mehta
- Department of Chemistry and Biochemistry, University of Texas, Arlington, TX, USA
| | - Abu Hena Mostafa Kamal
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Sharel Cornelius
- Department of Chemistry and Biochemistry, University of Texas, Arlington, TX, USA
| | - Saiful M Chowdhury
- Department of Chemistry and Biochemistry, University of Texas, Arlington, TX, USA.
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7
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Santorelli L, Caterino M, Costanzo M. Dynamic Interactomics by Cross-Linking Mass Spectrometry: Mapping the Daily Cell Life in Postgenomic Era. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:633-649. [PMID: 36445175 DOI: 10.1089/omi.2022.0137] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The majority of processes that occur in daily cell life are modulated by hundreds to thousands of dynamic protein-protein interactions (PPI). The resulting protein complexes constitute a tangled network that, with its continuous remodeling, builds up highly organized functional units. Thus, defining the dynamic interactome of one or more proteins allows determining the full range of biological activities these proteins are capable of. This conceptual approach is poised to gain further traction and significance in the current postgenomic era wherein the treatment of severe diseases needs to be tackled at both genomic and PPI levels. This also holds true for COVID-19, a multisystemic disease affecting biological networks across the biological hierarchy from genome to proteome to metabolome. In this overarching context and the current historical moment of the COVID-19 pandemic where systems biology increasingly comes to the fore, cross-linking mass spectrometry (XL-MS) has become highly relevant, emerging as a powerful tool for PPI discovery and characterization. This expert review highlights the advanced XL-MS approaches that provide in vivo insights into the three-dimensional protein complexes, overcoming the static nature of common interactomics data and embracing the dynamics of the cell proteome landscape. Many XL-MS applications based on the use of diverse cross-linkers, MS detection methods, and predictive bioinformatic tools for single proteins or proteome-wide interactions were shown. We conclude with a future outlook on XL-MS applications in the field of structural proteomics and ways to sustain the remarkable flexibility of XL-MS for dynamic interactomics and structural studies in systems biology and planetary health.
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Affiliation(s)
- Lucia Santorelli
- Department of Oncology and Hematology-Oncology, University of Milano, Milan, Italy.,IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Marianna Caterino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.,CEINGE-Biotecnologie Avanzate s.c.ar.l., Naples, Italy
| | - Michele Costanzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.,CEINGE-Biotecnologie Avanzate s.c.ar.l., Naples, Italy
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8
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Yassaghi G, Kukačka Z, Fiala J, Kavan D, Halada P, Volný M, Novák P. Top-Down Detection of Oxidative Protein Footprinting by Collision-Induced Dissociation, Electron-Transfer Dissociation, and Electron-Capture Dissociation. Anal Chem 2022; 94:9993-10002. [PMID: 35797180 DOI: 10.1021/acs.analchem.1c05476] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fast photochemical oxidation of proteins (FPOP) footprinting is a structural mass spectrometry method that maps proteins by fast and irreversible chemical reactions. The position of oxidative modification reflects solvent accessibility and site reactivity and thus provides information about protein conformation, structural dynamics, and interactions. Bottom-up mass spectrometry is an established standard method to analyze FPOP samples. In the bottom-up approach, all forms of the protein are digested together by a protease of choice, which results in a mixture of peptides from various subpopulations of proteins with varying degrees of photochemical oxidation. Here, we investigate the possibility to analyze a specifically selected population of only singly oxidized proteins. This requires utilization of more specific top-down mass spectrometry approaches. The key element of any top-down experiment is the selection of a suitable method of ion isolation, excitation, and fragmentation. Here, we employ and compare collision-induced dissociation, electron-transfer dissociation, and electron-capture dissociation combined with multi-continuous accumulation of selected ions. A singly oxidized subpopulation of FPOP-labeled ubiquitin was used to optimize the method. The top-down approach in FPOP is limited to smaller proteins, but its usefulness was demonstrated by using it to visualize structural changes induced by co-factor removal from the holo/apo myoglobin system. The top-down data were compared with the literature and with the bottom-up data set obtained on the same samples. The top-down results were found to be in good agreement, which indicates that monitoring a singly oxidized FPOP ion population by the top-down approach is a functional workflow for oxidative protein footprinting.
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Affiliation(s)
- Ghazaleh Yassaghi
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic
| | - Zdeněk Kukačka
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic
| | - Jan Fiala
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic.,Faculty of Science, Charles University, Albertov 6, Prague 2 128 00, Czech Republic
| | - Daniel Kavan
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic.,Faculty of Science, Charles University, Albertov 6, Prague 2 128 00, Czech Republic
| | - Petr Halada
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic
| | - Michael Volný
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic
| | - Petr Novák
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic
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9
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Soluble TREM2 inhibits secondary nucleation of Aβ fibrillization and enhances cellular uptake of fibrillar Aβ. Proc Natl Acad Sci U S A 2022; 119:2114486119. [PMID: 35082148 PMCID: PMC8812518 DOI: 10.1073/pnas.2114486119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2021] [Indexed: 01/21/2023] Open
Abstract
Triggering receptor expressed on myeloid cells 2 (TREM2) is a single-pass transmembrane receptor of the immunoglobulin superfamily that is secreted in a soluble (sTREM2) form. Mutations in TREM2 have been linked to increased risk of Alzheimer's disease (AD). A prominent neuropathological component of AD is deposition of the amyloid-β (Aβ) into plaques, particularly Aβ40 and Aβ42. While the membrane-bound form of TREM2 is known to facilitate uptake of Aβ fibrils and the polarization of microglial processes toward amyloid plaques, the role of its soluble ectodomain, particularly in interactions with monomeric or fibrillar Aβ, has been less clear. Our results demonstrate that sTREM2 does not bind to monomeric Aβ40 and Aβ42, even at a high micromolar concentration, while it does bind to fibrillar Aβ42 and Aβ40 with equal affinities (2.6 ± 0.3 µM and 2.3 ± 0.4 µM). Kinetic analysis shows that sTREM2 inhibits the secondary nucleation step in the fibrillization of Aβ, while having little effect on the primary nucleation pathway. Furthermore, binding of sTREM2 to fibrils markedly enhanced uptake of fibrils into human microglial and neuroglioma derived cell lines. The disease-associated sTREM2 mutant, R47H, displayed little to no effect on fibril nucleation and binding, but it decreased uptake and functional responses markedly. We also probed the structure of the WT sTREM2-Aβ fibril complex using integrative molecular modeling based primarily on the cross-linking mass spectrometry data. The model shows that sTREM2 binds fibrils along one face of the structure, leaving a second, mutation-sensitive site free to mediate cellular binding and uptake.
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10
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Petrotchenko EV, Borchers CH. Protein Chemistry Combined with Mass Spectrometry for Protein Structure Determination. Chem Rev 2021; 122:7488-7499. [PMID: 34968047 DOI: 10.1021/acs.chemrev.1c00302] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The advent of soft-ionization mass spectrometry for biomolecules has opened up new possibilities for the structural analysis of proteins. Combining protein chemistry methods with modern mass spectrometry has led to the emergence of the distinct field of structural proteomics. Multiple protein chemistry approaches, such as surface modification, limited proteolysis, hydrogen-deuterium exchange, and cross-linking, provide diverse and often orthogonal structural information on the protein systems studied. Combining experimental data from these various structural proteomics techniques provides a more comprehensive examination of the protein structure and increases confidence in the ultimate findings. Here, we review various types of experimental data from structural proteomics approaches with an emphasis on the use of multiple complementary mass spectrometric approaches to provide experimental constraints for the solving of protein structures.
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Affiliation(s)
- Evgeniy V Petrotchenko
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia.,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada
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11
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Farooq QUA, Shaukat Z, Aiman S, Li CH. Protein-protein interactions: Methods, databases, and applications in virus-host study. World J Virol 2021; 10:288-300. [PMID: 34909403 PMCID: PMC8641042 DOI: 10.5501/wjv.v10.i6.288] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/19/2021] [Accepted: 07/30/2021] [Indexed: 02/06/2023] Open
Abstract
Almost all the cellular processes in a living system are controlled by proteins: They regulate gene expression, catalyze chemical reactions, transport small molecules across membranes, and transmit signal across membranes. Even, a viral infection is often initiated through virus-host protein interactions. Protein-protein interactions (PPIs) are the physical contacts between two or more proteins and they represent complex biological functions. Nowadays, PPIs have been used to construct PPI networks to study complex pathways for revealing the functions of unknown proteins. Scientists have used PPIs to find the molecular basis of certain diseases and also some potential drug targets. In this review, we will discuss how PPI networks are essential to understand the molecular basis of virus-host relationships and several databases which are dedicated to virus-host interaction studies. Here, we present a short but comprehensive review on PPIs, including the experimental and computational methods of finding PPIs, the databases dedicated to virus-host PPIs, and the associated various applications in protein interaction networks of some lethal viruses with their hosts.
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Affiliation(s)
- Qurat ul Ain Farooq
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Zeeshan Shaukat
- Faculty of Information Technology, Beijing University of Technology, Beijing 100124, China
| | - Sara Aiman
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Chun-Hua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
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12
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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: 81] [Impact Index Per Article: 27.0] [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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13
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Yugandhar K, Zhao Q, Gupta S, Xiong D, Yu H. Progress in methodologies and quality-control strategies in protein cross-linking mass spectrometry. Proteomics 2021; 21:e2100145. [PMID: 34647422 DOI: 10.1002/pmic.202100145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/04/2021] [Indexed: 11/10/2022]
Abstract
Deciphering the interaction networks and structural dynamics of proteins is pivotal to better understanding their biological functions. Cross-linking mass spectrometry (XL-MS) is a powerful and increasingly popular technology that provides information about protein-protein interactions and their structural constraints for individual proteins and multiprotein complexes on a proteome-scale. In this review, we first assess the coverage and depth of the XL-MS technique by utilizing publicly available datasets. We then delve into the progress in XL-MS experimental and computational methodologies and examine different quality-control strategies reported in the literature. Finally, we discuss the progress in XL-MS applications along with the scope for future improvements.
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Affiliation(s)
- Kumar Yugandhar
- Department of Computational Biology, Cornell University, New York, USA.,Weill Institute for Cell and Molecular Biology, Cornell University, New York, USA
| | - Qiuye Zhao
- Department of Computational Biology, Cornell University, New York, USA.,Weill Institute for Cell and Molecular Biology, Cornell University, New York, USA
| | - Shobhita Gupta
- Department of Computational Biology, Cornell University, New York, USA.,Weill Institute for Cell and Molecular Biology, Cornell University, New York, USA
| | - Dapeng Xiong
- Department of Computational Biology, Cornell University, New York, USA.,Weill Institute for Cell and Molecular Biology, Cornell University, New York, USA
| | - Haiyuan Yu
- Department of Computational Biology, Cornell University, New York, USA.,Weill Institute for Cell and Molecular Biology, Cornell University, New York, USA
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14
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Kogut M, Gong Z, Tang C, Liwo A. Pseudopotentials for coarse-grained cross-link-assisted modeling of protein structures. J Comput Chem 2021; 42:2054-2067. [PMID: 34402552 DOI: 10.1002/jcc.26736] [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: 04/13/2021] [Revised: 07/09/2021] [Accepted: 08/03/2021] [Indexed: 11/08/2022]
Abstract
Pseudopotentials for the chemical cross-links comprising the glutamic- and aspartic-acid side chains bridged with adipic- (ADH) or pimelic-acid hydrazide (PDH), and the lysine side chains bridged with glutaric (BS2 G) or suberic acid (BS3 ) for coarse-grained cross-link-assisted simulations were determined by canonical molecular dynamics with the Amber14sb force field. The potentials depend on the distance between side-chain ends and on side-chain orientation, this preventing from making cross-link contacts across the globule in simulations. The potentials were implemented in the UNRES coarse-grained force field and their effect on the quality of models was assessed with 11 monomeric and 1 dimeric proteins, using synthetic or experimental cross-link data. Simulations with the new potentials resulted in improvement of the generated models compared to unrestrained simulations in more instances compared to those with the statistical potentials.
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Affiliation(s)
- Mateusz Kogut
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Zhou Gong
- Innovation Academy of Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Chun Tang
- College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
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15
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14-3-3-protein regulates Nedd4-2 by modulating interactions between HECT and WW domains. Commun Biol 2021; 4:899. [PMID: 34294877 PMCID: PMC8298602 DOI: 10.1038/s42003-021-02419-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/05/2021] [Indexed: 11/16/2022] Open
Abstract
Neural precursor cell expressed developmentally down-regulated 4 ligase (Nedd4-2) is an E3 ubiquitin ligase that targets proteins for ubiquitination and endocytosis, thereby regulating numerous ion channels, membrane receptors and tumor suppressors. Nedd4-2 activity is regulated by autoinhibition, calcium binding, oxidative stress, substrate binding, phosphorylation and 14-3-3 protein binding. However, the structural basis of 14-3-3-mediated Nedd4-2 regulation remains poorly understood. Here, we combined several techniques of integrative structural biology to characterize Nedd4-2 and its complex with 14-3-3. We demonstrate that phosphorylated Ser342 and Ser448 are the key residues that facilitate 14-3-3 protein binding to Nedd4-2 and that 14-3-3 protein binding induces a structural rearrangement of Nedd4-2 by inhibiting interactions between its structured domains. Overall, our findings provide the structural glimpse into the 14-3-3-mediated Nedd4-2 regulation and highlight the potential of the Nedd4-2:14-3-3 complex as a pharmacological target for Nedd4-2-associated diseases such as hypertension, epilepsy, kidney disease and cancer. Pohl et al. investigated the structural basis of Nedd4-2 regulation by 14-3-3 and found that phosphorylated Ser342 and Ser448 are the main residues that facilitate 14-3-3 binding to Nedd4-2. The authors propose that the Nedd4-2:14-3-3 complex then stimulates a structural rearrangement of Nedd4-2 through inhibiting interaction of its structured domains.
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16
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Low TY, Syafruddin SE, Mohtar MA, Vellaichamy A, A Rahman NS, Pung YF, Tan CSH. Recent progress in mass spectrometry-based strategies for elucidating protein-protein interactions. Cell Mol Life Sci 2021; 78:5325-5339. [PMID: 34046695 PMCID: PMC8159249 DOI: 10.1007/s00018-021-03856-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/03/2021] [Accepted: 05/14/2021] [Indexed: 02/07/2023]
Abstract
Protein-protein interactions are fundamental to various aspects of cell biology with many protein complexes participating in numerous fundamental biological processes such as transcription, translation and cell cycle. MS-based proteomics techniques are routinely applied for characterising the interactome, such as affinity purification coupled to mass spectrometry that has been used to selectively enrich and identify interacting partners of a bait protein. In recent years, many orthogonal MS-based techniques and approaches have surfaced including proximity-dependent labelling of neighbouring proteins, chemical cross-linking of two interacting proteins, as well as inferring PPIs from the co-behaviour of proteins such as the co-fractionating profiles and the thermal solubility profiles of proteins. This review discusses the underlying principles, advantages, limitations and experimental considerations of these emerging techniques. In addition, a brief account on how MS-based techniques are used to investigate the structural and functional properties of protein complexes, including their topology, stoichiometry, copy number and dynamics, are discussed.
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Affiliation(s)
- Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Jalan Yaacob Latiff, Bandar Tun Razak, 56000, Kuala Lumpur, Malaysia.
| | - Saiful Effendi Syafruddin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Jalan Yaacob Latiff, Bandar Tun Razak, 56000, Kuala Lumpur, Malaysia
| | - M Aiman Mohtar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Jalan Yaacob Latiff, Bandar Tun Razak, 56000, Kuala Lumpur, Malaysia
| | | | - Nisa Syakila A Rahman
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Jalan Yaacob Latiff, Bandar Tun Razak, 56000, Kuala Lumpur, Malaysia
| | - Yuh-Fen Pung
- Division of Biomedical Science, University of Nottingham Malaysia, 43500, Semenyih, Malaysia
| | - Chris Soon Heng Tan
- Department of Chemistry, College of Science , Southern University of Science and Technology, Shenzhen, 518055, China.
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17
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Del Amo-Maestro L, Sagar A, Pompach P, Goulas T, Scavenius C, Ferrero DS, Castrillo-Briceño M, Taulés M, Enghild JJ, Bernadó P, Gomis-Rüth FX. An Integrative Structural Biology Analysis of Von Willebrand Factor Binding and Processing by ADAMTS-13 in Solution. J Mol Biol 2021; 433:166954. [PMID: 33771572 DOI: 10.1016/j.jmb.2021.166954] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/16/2021] [Accepted: 03/16/2021] [Indexed: 10/21/2022]
Abstract
Von Willebrand Factor (vWF), a 300-kDa plasma protein key to homeostasis, is cleaved at a single site by multi-domain metallopeptidase ADAMTS-13. vWF is the only known substrate of this peptidase, which circulates in a latent form and becomes allosterically activated by substrate binding. Herein, we characterised the complex formed by a competent peptidase construct (AD13-MDTCS) comprising metallopeptidase (M), disintegrin-like (D), thrombospondin (T), cysteine-rich (C), and spacer (S) domains, with a 73-residue functionally relevant vWF-peptide, using nine complementary techniques. Pull-down assays, gel electrophoresis, and surface plasmon resonance revealed tight binding with sub-micromolar affinity. Cross-linking mass spectrometry with four reagents showed that, within the peptidase, domain D approaches M, C, and S. S is positioned close to M and C, and the peptide contacts all domains. Hydrogen/deuterium exchange mass spectrometry revealed strong and weak protection for C/D and M/S, respectively. Structural analysis by multi-angle laser light scattering and small-angle X-ray scattering in solution revealed that the enzyme adopted highly flexible unbound, latent structures and peptide-bound, active structures that differed from the AD13-MDTCS crystal structure. Moreover, the peptide behaved like a self-avoiding random chain. We integrated the results with computational approaches, derived an ensemble of structures that collectively satisfied all experimental restraints, and discussed the functional implications. The interaction conforms to a 'fuzzy complex' that follows a 'dynamic zipper' mechanism involving numerous reversible, weak but additive interactions that result in strong binding and cleavage. Our findings contribute to illuminating the biochemistry of the vWF:ADAMTS-13 axis.
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Affiliation(s)
- Laura Del Amo-Maestro
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
| | - Amin Sagar
- Centre de Biochimie Structurale, INSERM, CNRS and Université de Montpellier, 34090 Montpellier, France
| | - Petr Pompach
- Institute of Microbiology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czechia; Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czechia
| | - Theodoros Goulas
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
| | - Carsten Scavenius
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Diego S Ferrero
- Laboratory for Viruses and Large Biological Complexes, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
| | - Mariana Castrillo-Briceño
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
| | - Marta Taulés
- Scientific and Technological Centers (CCiTUB), University of Barcelona, Lluís Solé i Sabaris, 1-3, 08028 Barcelona, Catalonia, Spain
| | - Jan J Enghild
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM, CNRS and Université de Montpellier, 34090 Montpellier, France.
| | - F Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain.
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18
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Kukačka Z, Rosůlek M, Jelínek J, Slavata L, Kavan D, Novák P. LinX: A Software Tool for Uncommon Cross-Linking Chemistry. J Proteome Res 2021; 20:2021-2027. [PMID: 33657806 DOI: 10.1021/acs.jproteome.0c00858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chemical cross-linking mass spectrometry has become a popular tool in structural biology. Although several algorithms exist that efficiently analyze data-dependent mass spectrometric data, the algorithm to identify and quantify intermolecular cross-links located at the interaction interface of homodimer molecules was missing. The algorithm in LinX utilizes high mass accuracy for ion identification. In contrast with standard data-dependent analysis, LinX enables the elucidation of cross-linked peptides originating from the interaction interface of homodimers labeled by 14N/15N, including their ratio or cross-links from protein-nucleic acid complexes. The software is written in Java language, and its source code and a detailed user's guide are freely available at https://github.com/KukackaZ/LinX or https://ms-utils.org/LinX. Data are accessible via the ProteomeXchange server with the data set identifier PXD023522.
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Affiliation(s)
- Zdeněk Kukačka
- Institute of Microbiology, v.v.i., The Czech Academy of Sciences, Videnska 1083, Prague 14220, Czech Republic
| | - Michal Rosůlek
- Institute of Microbiology, v.v.i., The Czech Academy of Sciences, Videnska 1083, Prague 14220, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Albertov 6, 12800 Prague 2, Czech Republic
| | - Jan Jelínek
- Institute of Microbiology, v.v.i., The Czech Academy of Sciences, Videnska 1083, Prague 14220, Czech Republic.,Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 12000 Prague 2, Czech Republic
| | - Lukáš Slavata
- Institute of Microbiology, v.v.i., The Czech Academy of Sciences, Videnska 1083, Prague 14220, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Albertov 6, 12800 Prague 2, Czech Republic
| | - Daniel Kavan
- Institute of Microbiology, v.v.i., The Czech Academy of Sciences, Videnska 1083, Prague 14220, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Albertov 6, 12800 Prague 2, Czech Republic
| | - Petr Novák
- Institute of Microbiology, v.v.i., The Czech Academy of Sciences, Videnska 1083, Prague 14220, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Albertov 6, 12800 Prague 2, Czech Republic
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19
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Tang X, Wippel HH, Chavez JD, Bruce JE. Crosslinking mass spectrometry: A link between structural biology and systems biology. Protein Sci 2021; 30:773-784. [PMID: 33594738 DOI: 10.1002/pro.4045] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/12/2022]
Abstract
Protein structure underpins functional roles in all biological processes; therefore, improved understanding of protein structures is of fundamental importance in nearly all biological and biomedical research areas. Traditional techniques such as X-ray crystallography and more recently, cryo-EM, can reveal structural features on isolated proteins/protein complexes at atomic resolution level and have become indispensable tools for structural biology. Crosslinking mass spectrometry (XL-MS), on the other hand, is an emerging technique capable of capturing transient and dynamic information on protein interactions and assemblies in their native environment. The combination of XL-MS with traditional techniques holds potential for bridging the gap between structural biology and systems biology approaches. Such a combination will enable visualization of protein structures and interactions within the crowded macromolecular environment in living systems that can dramatically increase understanding of biological functions. In this review, we first discuss general strategies of XL-MS and then survey recent examples to show how qualitative and quantitative XL-MS studies can be integrated with available protein structural data to better understand biological function at systems level.
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Affiliation(s)
- Xiaoting Tang
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Helisa H Wippel
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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20
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Sinnott M, Malhotra S, Madhusudhan MS, Thalassinos K, Topf M. Combining Information from Crosslinks and Monolinks in the Modeling of Protein Structures. Structure 2020; 28:1061-1070.e3. [DOI: 10.1016/j.str.2020.05.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 05/08/2020] [Accepted: 05/22/2020] [Indexed: 11/30/2022]
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21
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Natural Killer Cell Activation Receptor NKp30 Oligomerization Depends on Its N-Glycosylation. Cancers (Basel) 2020; 12:cancers12071998. [PMID: 32708305 PMCID: PMC7409301 DOI: 10.3390/cancers12071998] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/22/2020] [Accepted: 07/14/2020] [Indexed: 12/29/2022] Open
Abstract
NKp30 is one of the main human natural killer (NK) cell activating receptors used in directed immunotherapy. The oligomerization of the NKp30 ligand binding domain depends on the length of the C-terminal stalk region, but our structural knowledge of NKp30 oligomerization and its role in signal transduction remains limited. Moreover, ligand binding of NKp30 is affected by the presence and type of N-glycosylation. In this study, we assessed whether NKp30 oligomerization depends on its N-glycosylation. Our results show that NKp30 forms oligomers when expressed in HEK293S GnTI- cell lines with simple N-glycans. However, NKp30 was detected only as monomers after enzymatic deglycosylation. Furthermore, we characterized the interaction between NKp30 and its best-studied cognate ligand, B7-H6, with respect to glycosylation and oligomerization, and we solved the crystal structure of this complex with glycosylated NKp30, revealing a new glycosylation-induced mode of NKp30 dimerization. Overall, this study provides new insights into the structural basis of NKp30 oligomerization and explains how the stalk region and glycosylation of NKp30 affect its ligand affinity. This furthers our understanding of the molecular mechanisms involved in NK cell activation, which is crucial for the successful design of novel NK cell-based targeted immunotherapeutics.
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22
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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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23
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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24
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Zhao B, Zhuang J, Xu M, Liu T, Limpikirati P, Thayumanavan S, Vachet RW. Covalent Labeling with an α,β-Unsaturated Carbonyl Scaffold for Studying Protein Structure and Interactions by Mass Spectrometry. Anal Chem 2020; 92:6637-6644. [PMID: 32250591 PMCID: PMC7207043 DOI: 10.1021/acs.analchem.0c00463] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new covalent labeling (CL) reagent based on an α,β-unsaturated carbonyl scaffold has been developed for studying protein structure and protein-protein interactions when coupled with mass spectrometry. We show that this new reagent scaffold can react with up to 13 different types of residues on protein surfaces, thereby providing excellent structural resolution. To illustrate the value of this reagent scaffold, it is used to identify the residues involved in the protein-protein interface that is formed upon Zn(II) binding to the protein β-2-microglobulin. The modular design of the α,β-unsaturated carbonyl scaffold allows facile variation of the functional groups, enabling labeling kinetics and selectivity to be tuned. Moreover, by introducing isotopically enriched functional groups into the reagent structure, labeling sites can be more easily identified by MS and MS/MS. Overall, this reagent scaffold should be a valuable CL reagent for protein higher order structure characterization by MS.
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Affiliation(s)
- Bo Zhao
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Jiaming Zhuang
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Miaowei Xu
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Tianying Liu
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | | | - S. Thayumanavan
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Center for Bioactive Delivery – Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Richard W. Vachet
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Center for Bioactive Delivery – Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
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25
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Influence of cross-linker polarity on selectivity towards lysine side chains. J Proteomics 2020; 218:103716. [DOI: 10.1016/j.jprot.2020.103716] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/02/2020] [Accepted: 02/19/2020] [Indexed: 11/19/2022]
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26
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Evaluation of chemical cross-linkers for in-depth structural analysis of G protein-coupled receptors through cross-linking mass spectrometry. Anal Chim Acta 2020; 1102:53-62. [DOI: 10.1016/j.aca.2019.12.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/12/2019] [Accepted: 12/15/2019] [Indexed: 01/05/2023]
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27
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Chakrabarty JK, Sadananda SC, Bhat A, Naik AJ, Ostwal DV, Chowdhury SM. High Confidence Identification of Cross-Linked Peptides by an Enrichment-Based Dual Cleavable Cross-Linking Technology and Data Analysis tool Cleave-XL. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:173-182. [PMID: 32031390 DOI: 10.1021/jasms.9b00111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cleavable cross-linking technology requires further MS/MS of the cleavable fragments for unambiguous identification of cross-linked peptides. These spectra are sometimes very ambiguous due to the sensitivity and complex fragmentation pattern of the peptides with the cross-linked residues. We recently reported a dual cleavable cross-linking technology (DUCCT), which can enhance the confidence in the identification of cross-linked peptides. The heart of this strategy is a novel dual mass spectrometry cleavable cross linker that can be cleaved preferentially by two differential tandem mass spectrometry methods, collision induced dissociation and electron transfer dissociation (CID and ETD). Different signature ions from two different mass spectra for the same cross-linked peptide helped identify the cross-linked peptides with high confidence. In this study, we developed an enrichment-based photocleavable DUCCT (PC-DUCCT-biotin), where cross-linked products were enriched from biological samples using affinity purification, and subsequently, two sequential tandem (CID and ETD) mass spectrometry processes were utilized. Furthermore, we developed a prototype software called Cleave-XL to analyze cross-linked products generated by DUCCT. Photocleavable DUCCT was demonstrated in standard peptides and proteins. Efficiency of the software tools to search and compare CID and ETD data of photocleavable DUCCT biotin in standard peptides and proteins as well as regular DUCCT in protein complexes from immune cells were tested. The software is efficient in pinpointing cross-linked sites using CID and ETD cross-linking data. We believe this new DUCCT and associated software tool Cleave-XL will advance high confidence identification of protein cross-linking sites and automated identification of low-resolution protein structures.
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Affiliation(s)
- Jayanta K Chakrabarty
- Department of Chemistry and Biochemistry , University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Sandhya C Sadananda
- Department of Computer Science , University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Apeksha Bhat
- Department of Computer Science , University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Aishwarya J Naik
- Department of Computer Science , University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Dhanashri V Ostwal
- Department of Computer Science , University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Saiful M Chowdhury
- Department of Chemistry and Biochemistry , University of Texas at Arlington , Arlington , Texas 76019 , United States
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28
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Steigenberger B, Albanese P, Heck AJR, Scheltema RA. To Cleave or Not To Cleave in XL-MS? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:196-206. [PMID: 32031400 DOI: 10.1021/jasms.9b00085] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cross-linking mass spectrometry (XL-MS) is an efficient technique for uncovering structural features and interactions of the in-solution state of the proteins under investigation. Distance constraints obtained by this technique are highly complementary to classical structural biology approaches like X-ray crystallography and cryo-EM and have successfully been leveraged to shed light on protein structures of increasing size and complexity. To accomplish this, small reagents are used that typically incorporate two amine reactive moieties connected by a spacer arm and that can be applied in solution to protein structures of any size. Over the years, many reagents initially developed for different applications were adopted, and others were specifically developed for XL-MS. This has resulted in a vast array of options, making it difficult to make the right choice for specific experiments. Here, we delve into the previous decade of published XL-MS literature to uncover which workflows have been predominantly applied. We focus on application papers as these represent proof that biologically valid results can be extracted. This ignores some more recent approaches that did not have sufficient time to become more widely applied, for which we supply a separate discussion. From our selection, we extract information on the types of samples, cross-linking reagent, prefractionation, instruments, and data analysis, to highlight widely used workflows. All of the results are summarized in an easy-to-use flow chart defined by selection points resulting from our analysis. Although potentially biased by our own experiences, we expect this overview to be useful for novices stepping into this rapidly expanding field.
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Affiliation(s)
- B Steigenberger
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands
- Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - P Albanese
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands
- Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - A J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands
- Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - R A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands
- Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
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Reese HR, Shanahan CC, Proulx C, Menegatti S. Peptide science: A "rule model" for new generations of peptidomimetics. Acta Biomater 2020; 102:35-74. [PMID: 31698048 DOI: 10.1016/j.actbio.2019.10.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/17/2019] [Accepted: 10/30/2019] [Indexed: 02/07/2023]
Abstract
Peptides have been heavily investigated for their biocompatible and bioactive properties. Though a wide array of functionalities can be introduced by varying the amino acid sequence or by structural constraints, properties such as proteolytic stability, catalytic activity, and phase behavior in solution are difficult or impossible to impart upon naturally occurring α-L-peptides. To this end, sequence-controlled peptidomimetics exhibit new folds, morphologies, and chemical modifications that create new structures and functions. The study of these new classes of polymers, especially α-peptoids, has been highly influenced by the analysis, computational, and design techniques developed for peptides. This review examines techniques to determine primary, secondary, and tertiary structure of peptides, and how they have been adapted to investigate peptoid structure. Computational models developed for peptides have been modified to predict the morphologies of peptoids and have increased in accuracy in recent years. The combination of in vitro and in silico techniques have led to secondary and tertiary structure design principles that mirror those for peptides. We then examine several important developments in peptoid applications inspired by peptides such as pharmaceuticals, catalysis, and protein-binding. A brief survey of alternative backbone structures and research investigating these peptidomimetics shows how the advancement of peptide and peptoid science has influenced the growth of numerous fields of study. As peptide, peptoid, and other peptidomimetic studies continue to advance, we will expect to see higher throughput structural analyses, greater computational accuracy and functionality, and wider application space that can improve human health, solve environmental challenges, and meet industrial needs. STATEMENT OF SIGNIFICANCE: Many historical, chemical, and functional relations draw a thread connecting peptides to their recent cognates, the "peptidomimetics". This review presents a comprehensive survey of this field by highlighting the width and relevance of these familial connections. In the first section, we examine the experimental and computational techniques originally developed for peptides and their morphing into a broader analytical and predictive toolbox. The second section presents an excursus of the structures and properties of prominent peptidomimetics, and how the expansion of the chemical and structural diversity has returned new exciting properties. The third section presents an overview of technological applications and new families of peptidomimetics. As the field grows, new compounds emerge with clear potential in medicine and advanced manufacturing.
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Piotrowski C, Moretti R, Ihling CH, Haedicke A, Liepold T, Lipstein N, Meiler J, Jahn O, Sinz A. Delineating the Molecular Basis of the Calmodulin‒bMunc13-2 Interaction by Cross-Linking/Mass Spectrometry-Evidence for a Novel CaM Binding Motif in bMunc13-2. Cells 2020; 9:cells9010136. [PMID: 31936129 PMCID: PMC7017353 DOI: 10.3390/cells9010136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/23/2019] [Accepted: 01/02/2020] [Indexed: 01/20/2023] Open
Abstract
Exploring the interactions between the Ca2+ binding protein calmodulin (CaM) and its target proteins remains a challenging task. Members of the Munc13 protein family play an essential role in short-term synaptic plasticity, modulated via the interaction with CaM at the presynaptic compartment. In this study, we focus on the bMunc13-2 isoform expressed in the brain, as strong changes in synaptic transmission were observed upon its mutagenesis or deletion. The CaM–bMunc13-2 interaction was previously characterized at the molecular level using short bMunc13-2-derived peptides only, revealing a classical 1–5–10 CaM binding motif. Using larger protein constructs, we have now identified for the first time a novel and unique CaM binding site in bMunc13-2 that contains an N-terminal extension of a classical 1–5–10 CaM binding motif. We characterize this motif using a range of biochemical and biophysical methods and highlight its importance for the CaM–bMunc13-2 interaction.
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Affiliation(s)
- Christine Piotrowski
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, D-06120 Halle/Saale, Germany
| | - Rocco Moretti
- Center for Structural Biology, Department of Chemistry, Vanderbilt University, Nashville, TN 37221, USA
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, D-06120 Halle/Saale, Germany
| | - André Haedicke
- Biophysical Chemistry, Institute of Chemistry, Martin Luther University Halle-Wittenberg, D-06120 Halle/Saale, Germany
| | - Thomas Liepold
- Proteomics Group, Max Planck Institute of Experimental Medicine, D-37075 Göttingen, Germany
| | - Noa Lipstein
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, D-37075 Göttingen, Germany
| | - Jens Meiler
- Center for Structural Biology, Department of Chemistry, Vanderbilt University, Nashville, TN 37221, USA
| | - Olaf Jahn
- Proteomics Group, Max Planck Institute of Experimental Medicine, D-37075 Göttingen, Germany
- Correspondence: (O.J.); (A.S.); Tel.: +49-551-3899-313 (O.J.); +49-345-5525170 (A.S.)
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, D-06120 Halle/Saale, Germany
- Correspondence: (O.J.); (A.S.); Tel.: +49-551-3899-313 (O.J.); +49-345-5525170 (A.S.)
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31
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Xiang Y, Shen Z, Shi Y. Chemical Cross-Linking and Mass Spectrometric Analysis of the Endogenous Yeast Exosome Complexes. Methods Mol Biol 2020; 2062:383-400. [PMID: 31768986 DOI: 10.1007/978-1-4939-9822-7_18] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chemical cross-linking and mass spectrometric readout (CX-MS) has become a useful toolkit for structural analysis of protein complexes. CX-MS enables rapid detection of a larger number of cross-link peptides from the chemically cross-linked protein assembly, providing invaluable cross-link spatial restraints to understand the architecture of the complex. Since CX-MS is complementary with other structural and computational modeling tools, it can be used for integrative structural determination of large native protein assemblies. However, due to technical limitations, current CX-MS applications have still been predominantly confined to complexes reconstituted from recombinant proteins where large amount of purified materials are available. Cross-linking and hybrid structural proteomic analysis of endogenous protein complexes remains a challenge. In this chapter, we present a protocol that efficiently couples affinity capture of endogenous complexes with sensitive CX-MS analysis, with particular application to the yeast RNA processing exosome complexes.
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Affiliation(s)
- Yufei Xiang
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Zhuolun Shen
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Yi Shi
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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32
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Zeman J, Itoh Y, Kukačka Z, Rosůlek M, Kavan D, Kouba T, Jansen ME, Mohammad MP, Novák P, Valášek LS. Binding of eIF3 in complex with eIF5 and eIF1 to the 40S ribosomal subunit is accompanied by dramatic structural changes. Nucleic Acids Res 2019; 47:8282-8300. [PMID: 31291455 PMCID: PMC6735954 DOI: 10.1093/nar/gkz570] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/12/2019] [Accepted: 07/05/2019] [Indexed: 12/31/2022] Open
Abstract
eIF3 is a large multiprotein complex serving as an essential scaffold promoting binding of other eIFs to the 40S subunit, where it coordinates their actions during translation initiation. Perhaps due to a high degree of flexibility of multiple eIF3 subunits, a high-resolution structure of free eIF3 from any organism has never been solved. Employing genetics and biochemistry, we previously built a 2D interaction map of all five yeast eIF3 subunits. Here we further improved the previously reported in vitro reconstitution protocol of yeast eIF3, which we cross-linked and trypsin-digested to determine its overall shape in 3D by advanced mass-spectrometry. The obtained cross-links support our 2D subunit interaction map and reveal that eIF3 is tightly packed with its WD40 and RRM domains exposed. This contrasts with reported cryo-EM structures depicting eIF3 as a molecular embracer of the 40S subunit. Since the binding of eIF1 and eIF5 further fortified the compact architecture of eIF3, we suggest that its initial contact with the 40S solvent-exposed side makes eIF3 to open up and wrap around the 40S head with its extended arms. In addition, we mapped the position of eIF5 to the region below the P- and E-sites of the 40S subunit.
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Affiliation(s)
- Jakub Zeman
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Yuzuru Itoh
- Institute of Genetics and Molecular and Cellular Biology, CNRS UMR7104, INSERM UMR964, Illkirch, France
| | - Zdeněk Kukačka
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Michal Rosůlek
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Daniel Kavan
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Tomáš Kouba
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Myrte E Jansen
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Mahabub P Mohammad
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Petr Novák
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Leoš S Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
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33
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Psenakova K, Hexnerova R, Srb P, Obsilova V, Veverka V, Obsil T. The redox‐active site of thioredoxin is directly involved in apoptosis signal‐regulating kinase 1 binding that is modulated by oxidative stress. FEBS J 2019; 287:1626-1644. [DOI: 10.1111/febs.15101] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/10/2019] [Accepted: 10/16/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Katarina Psenakova
- Department of Physical and Macromolecular Chemistry Faculty of Science Charles University Prague Czech Republic
- Department of Structural Biology of Signaling Proteins, Division BIOCEV Institute of Physiology of the Czech Academy of Sciences Vestec Czech Republic
| | - Rozalie Hexnerova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague Czech Republic
| | - Pavel Srb
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague Czech Republic
| | - Veronika Obsilova
- Department of Structural Biology of Signaling Proteins, Division BIOCEV Institute of Physiology of the Czech Academy of Sciences Vestec Czech Republic
| | - Vaclav Veverka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague Czech Republic
- Department of Cell Biology Faculty of Science Charles University Prague Czech Republic
| | - Tomas Obsil
- Department of Physical and Macromolecular Chemistry Faculty of Science Charles University Prague Czech Republic
- Department of Structural Biology of Signaling Proteins, Division BIOCEV Institute of Physiology of the Czech Academy of Sciences Vestec Czech Republic
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34
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Hu W, Yuan Y, Wang CH, Tian HT, Guo AD, Nie HJ, Hu H, Tan M, Tang Z, Chen XH. Genetically Encoded Residue-Selective Photo-Crosslinker to Capture Protein-Protein Interactions in Living Cells. Chem 2019. [DOI: 10.1016/j.chempr.2019.08.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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35
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Pompach P, Viola CM, Radosavljević J, Lin J, Jiráček J, Brzozowski AM, Selicharová I. Cross-Linking/Mass Spectrometry Uncovers Details of Insulin-Like Growth Factor Interaction With Insect Insulin Binding Protein Imp-L2. Front Endocrinol (Lausanne) 2019; 10:695. [PMID: 31649623 PMCID: PMC6794382 DOI: 10.3389/fendo.2019.00695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 09/25/2019] [Indexed: 11/13/2022] Open
Abstract
Structural details of changes accompanying interaction between insulin-related hormones and their binding partners are often enigmatic. Here, cross-linking/mass spectrometry could complement structural techniques and reveal details of these protein-protein interfaces. We used such approach to clarify missing structural description of the interface in human insulin-like growth factor (IGF-1): Drosophila melanogaster imaginal morphogenesis protein-late 2 protein (Imp-L2) complex which we studied previously by X-ray crystallography. We crosslinked these proteins by heterobifunctional cross-linker sulfosuccinimidyl 4,4'-azidopentanoate (Sulfo-SDA) for the subsequent mass spectrometry (MS) analysis. The MS analysis revealed IGF-1:Imp-L2 interactions which were not resolved in the crystal structure of this assembly, and they converged with X-ray results, indicating the importance of the IGF-1 N-terminus interaction with the C-terminal (185-242) part of the Imp-L2 for stability of this complex. Here, we also showed the advantage and reliability of MS approach in solving details of protein-protein interactions that are too flexible for solid state structural methods.
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Affiliation(s)
- Petr Pompach
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
| | - Cristina M. Viola
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, United Kingdom
| | - Jelena Radosavljević
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Jingjing Lin
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Jiří Jiráček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Andrzej M. Brzozowski
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, United Kingdom
| | - Irena Selicharová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
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36
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MS-Based Approaches Enable the Structural Characterization of Transcription Factor/DNA Response Element Complex. Biomolecules 2019; 9:biom9100535. [PMID: 31561554 PMCID: PMC6843354 DOI: 10.3390/biom9100535] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/18/2019] [Accepted: 09/24/2019] [Indexed: 02/06/2023] Open
Abstract
The limited information available on the structure of complexes involving transcription factors and cognate DNA response elements represents a major obstacle in the quest to understand their mechanism of action at the molecular level. We implemented a concerted structural proteomics approach, which combined hydrogen-deuterium exchange (HDX), quantitative protein-protein and protein-nucleic acid cross-linking (XL), and homology analysis, to model the structure of the complex between the full-length DNA binding domain (DBD) of Forkhead box protein O4 (FOXO4) and its DNA binding element (DBE). The results confirmed that FOXO4-DBD assumes the characteristic forkhead topology shared by these types of transcription factors, but its binding mode differs significantly from those of other members of the family. The results showed that the binding interaction stabilized regions that were rather flexible and disordered in the unbound form. Surprisingly, the conformational effects were not limited only to the interface between bound components, but extended also to distal regions that may be essential to recruiting additional factors to the transcription machinery. In addition to providing valuable new insights into the binding mechanism, this project provided an excellent evaluation of the merits of structural proteomics approaches in the investigation of systems that are not directly amenable to traditional high-resolution techniques.
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37
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Jones AX, Cao Y, Tang YL, Wang JH, Ding YH, Tan H, Chen ZL, Fang RQ, Yin J, Chen RC, Zhu X, She Y, Huang N, Shao F, Ye K, Sun RX, He SM, Lei X, Dong MQ. Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers. Nat Commun 2019; 10:3911. [PMID: 31477730 PMCID: PMC6718413 DOI: 10.1038/s41467-019-11917-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 08/05/2019] [Indexed: 02/07/2023] Open
Abstract
Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) is widely used to study protein-protein interactions (PPI), protein structures, and even protein dynamics. However, structural information provided by CXMS is still limited, partly because most CXMS experiments use lysine-lysine (K-K) cross-linkers. Although superb in selectivity and reactivity, they are ineffective for lysine deficient regions. Herein, we develop aromatic glyoxal cross-linkers (ArGOs) for arginine-arginine (R-R) cross-linking and the lysine-arginine (K-R) cross-linker KArGO. The R-R or K-R cross-links generated by ArGO or KArGO fit well with protein crystal structures and provide information not attainable by K-K cross-links. KArGO, in particular, is highly valuable for CXMS, with robust performance on a variety of samples including a kinase and two multi-protein complexes. In the case of the CNGP complex, KArGO cross-links covered as much of the PPI interface as R-R and K-K cross-links combined and improved the accuracy of Rosetta docking substantially. Cross-linking mass spectrometry can provide insights into protein structures and interactions but its scope depends on the reactivity of the cross-linker. Here, the authors develop Arg-Arg and Lys-Arg cross-linkers, which provide structural information elusive to the widely used Lys-Lys cross-linkers.
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Affiliation(s)
- Alexander X Jones
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Yong Cao
- School of Life Sciences, Peking University, 100871, Beijing, China.,National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Yu-Liang Tang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Jian-Hua Wang
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Yue-He Ding
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Hui Tan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Zhen-Lin Chen
- Key Lab of Intelligent Information Processing, Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, 100049, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Run-Qian Fang
- Key Lab of Intelligent Information Processing, Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, 100049, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jili Yin
- Key Lab of Intelligent Information Processing, Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, 100049, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Rong-Chang Chen
- University of Chinese Academy of Sciences, 100049, Beijing, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Xing Zhu
- University of Chinese Academy of Sciences, 100049, Beijing, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yang She
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Niu Huang
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Feng Shao
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Keqiong Ye
- University of Chinese Academy of Sciences, 100049, Beijing, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Rui-Xiang Sun
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Si-Min He
- Key Lab of Intelligent Information Processing, Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, 100049, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China.
| | - Meng-Qiu Dong
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China. .,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 102206, Beijing, China.
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38
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Zhao B, Reilly CP, Reilly JP. ETD-Cleavable Linker for Confident Cross-linked Peptide Identifications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1631-1642. [PMID: 31098958 DOI: 10.1007/s13361-019-02227-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/12/2019] [Accepted: 04/13/2019] [Indexed: 06/09/2023]
Abstract
Peptide cross-links formed using the homobifunctional-linker diethyl suberthioimidate (DEST) are shown to be ETD-cleavable. DEST has a spacer arm consisting of a 6-carbon alkyl chain and it cleaves at the amidino groups created upon reaction with primary amines. In ETD MS2 spectra, DEST cross-links can be recognized based on mass pairs consisting of peptide-NH2• and peptide+linker+NH3 ions, and backbone cleavages are more equally distributed over the two constituent peptides compared with collisional activation. Dead ends that are often challenging to distinguish from cross-links are diagnosed by intense reporter ions. ETD mass pairs can be used in MS3 experiments to confirm cross-link identifications. These features provide a simple but reliable approach to identify cross-links that should facilitate studies of protein complexes.
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Affiliation(s)
- Bingqing Zhao
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Colin P Reilly
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - James P Reilly
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA.
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39
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Carter R, Luchini A, Liotta L, Haymond A. Next Generation Techniques for Determination of Protein-Protein Interactions: Beyond the Crystal Structure. CURRENT PATHOBIOLOGY REPORTS 2019; 7:61-71. [PMID: 33094031 PMCID: PMC7577580 DOI: 10.1007/s40139-019-00198-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PURPOSE OF REVIEW We discuss recent advancements in structural biology methods for investigating sites of protein-protein interactions. We will inform readers outside the field of structural biology about techniques beyond crystallography, and how these different technologies can be utilized for drug development. RECENT FINDINGS Advancements in cryo-electron microscopy (cryoEM) and micro-electron diffraction (microED) may change how we view atomic resolution structural biology, such that well-ordered macrocrystals of protein complexes are not required for interface identification. However, some drug discovery applications, such as lead peptide compound generation, may not require atomic resolution; mass spectrometry techniques can provide an expedited path to generation of lead compounds. New crosslinking compounds, more user-friendly data analysis, and novel protocols such as protein painting can advance drug discovery programs, even in the absence of atomic resolution structural data. Finally, artificial intelligence and machine learning methods, while never truly replacing experimental methods, may provide rational ways to stratify potential druggable regions identified with mass spectrometry into higher and lower priority candidates. SUMMARY Electron diffraction of nanocrystals combines the benefits of both x-ray diffraction and cryoEM, and may prove to be the next generation of atomic resolution protein-protein interface identification. However, in situations such as peptide drug discovery, mass spectrometry techniques supported by advancements in computational methods will likely prove sufficient to support drug discovery efforts. In addition, these methods can be significantly faster than any crystallographic or cryoEM methods for identification of interacting regions.
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Affiliation(s)
- Rachel Carter
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA
| | - Alessandra Luchini
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA
| | - Lance Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA
| | - Amanda Haymond
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA
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40
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Chen ZL, Meng JM, Cao Y, Yin JL, Fang RQ, Fan SB, Liu C, Zeng WF, Ding YH, Tan D, Wu L, Zhou WJ, Chi H, Sun RX, Dong MQ, He SM. A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides. Nat Commun 2019; 10:3404. [PMID: 31363125 PMCID: PMC6667459 DOI: 10.1038/s41467-019-11337-z] [Citation(s) in RCA: 238] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 06/20/2019] [Indexed: 01/05/2023] Open
Abstract
We describe pLink 2, a search engine with higher speed and reliability for proteome-scale identification of cross-linked peptides. With a two-stage open search strategy facilitated by fragment indexing, pLink 2 is ~40 times faster than pLink 1 and 3~10 times faster than Kojak. Furthermore, using simulated datasets, synthetic datasets, 15N metabolically labeled datasets, and entrapment databases, four analysis methods were designed to evaluate the credibility of ten state-of-the-art search engines. This systematic evaluation shows that pLink 2 outperforms these methods in precision and sensitivity, especially at proteome scales. Lastly, re-analysis of four published proteome-scale cross-linking datasets with pLink 2 required only a fraction of the time used by pLink 1, with up to 27% more cross-linked residue pairs identified. pLink 2 is therefore an efficient and reliable tool for cross-linking mass spectrometry analysis, and the systematic evaluation methods described here will be useful for future software development. The identification of cross-linked peptides at a proteome scale for interactome analyses represents a complex challenge. Here the authors report an efficient and reliable search engine pLink 2 for proteome-scale cross-linking mass spectrometry analyses, and demonstrate how to systematically evaluate the credibility of search engines.
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Affiliation(s)
- Zhen-Lin Chen
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jia-Ming Meng
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong Cao
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Ji-Li Yin
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Run-Qian Fang
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sheng-Bo Fan
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Liu
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Feng Zeng
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yue-He Ding
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Dan Tan
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Long Wu
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Jing Zhou
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Chi
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rui-Xiang Sun
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, 102206, China.
| | - Si-Min He
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, 100190, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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41
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Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews P, Bernfur K, Borchers C, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis T, Degliesposti G, Dong MQ, Edinger N, Emanuelsson C, Gay M, Götze M, Gomes-Neto F, Gozzo FC, Gutierrez C, Haupt C, Heck AJR, Herzog F, Huang L, Hoopmann MR, Kalisman N, Klykov O, Kukačka Z, Liu F, MacCoss MJ, Mechtler K, Mesika R, Moritz RL, Nagaraj N, Nesati V, Neves-Ferreira AGC, Ninnis R, Novák P, O'Reilly FJ, Pelzing M, Petrotchenko E, Piersimoni L, Plasencia M, Pukala T, Rand KD, Rappsilber J, Reichmann D, Sailer C, Sarnowski CP, Scheltema RA, Schmidt C, Schriemer DC, Shi Y, Skehel JM, Slavin M, Sobott F, Solis-Mezarino V, Stephanowitz H, Stengel F, Stieger CE, Trabjerg E, Trnka M, Vilaseca M, Viner R, Xiang Y, Yilmaz S, Zelter A, Ziemianowicz D, Leitner A, Sinz A. First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study. Anal Chem 2019; 91:6953-6961. [PMID: 31045356 PMCID: PMC6625963 DOI: 10.1021/acs.analchem.9b00658] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein-protein interactions has increased during the last years. As the technique is now becoming routine for in vitro and in vivo applications in proteomics and structural biology there is a pressing need to define protocols as well as data analysis and reporting formats. Such consensus formats should become accepted in the field and be shown to lead to reproducible results. This first, community-based harmonization study on XL-MS is based on the results of 32 groups participating worldwide. The aim of this paper is to summarize the status quo of XL-MS and to compare and evaluate existing cross-linking strategies. Our study therefore builds the framework for establishing best practice guidelines to conduct cross-linking experiments, perform data analysis, and define reporting formats with the ultimate goal of assisting scientists to generate accurate and reproducible XL-MS results.
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Affiliation(s)
- Claudio Iacobucci
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
| | - Christine Piotrowski
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich , Otto-Stern-Weg 3 , 8093 Zurich , Switzerland.,Faculty of Science , University of Zurich , 8006 Zurich , Switzerland
| | - Bruno C Amaral
- Institute of Chemistry , University of Campinas , Campinas São Paulo 13083-970 , Brazil
| | - Philip Andrews
- Departments of Biological Chemistry, Bioinformatics, and Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Katja Bernfur
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science , Lund University , 221 00 Lund , Sweden
| | - Christoph Borchers
- University of Victoria-Genome British Columbia Proteomics Centre , Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada.,Department of Biochemistry and Microbiology , University of Victoria , Petch Building, Room 270d, 3800 Finnerty Road , Victoria , British Columbia V8P 5C2 , Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital , McGill University , 3755 Côte Ste-Catherine Road , Montréal , Quebec H3T 1E2 , Canada.,Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital , McGill University , 3755 Côte Ste-Catherine Road , Montréal , Quebec H3T 1E2 , Canada
| | - Nicolas I Brodie
- University of Victoria-Genome British Columbia Proteomics Centre , Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada
| | - James E Bruce
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - Yong Cao
- National Institute of Biological Sciences , Beijing 7 Science Park Road, ZGC Life Science Park , 102206 Beijing , China
| | - Stéphane Chaignepain
- CBMN, UMR 5248, CNRS , Université de Bordeaux, INP Bordeaux , Pessac 33607 , France
| | - Juan D Chavez
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - Stéphane Claverol
- Centre de Génomique Fonctionnelle, Plateforme Protéome , Université de Bordeaux , Bordeaux 33000 , France
| | - Jürgen Cox
- Computational Systems Biochemistry Research Group , Max-Planck-Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Trisha Davis
- Department of Biochemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Gianluca Degliesposti
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Meng-Qiu Dong
- National Institute of Biological Sciences , Beijing 7 Science Park Road, ZGC Life Science Park , 102206 Beijing , China
| | - Nufar Edinger
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Cecilia Emanuelsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science , Lund University , 221 00 Lund , Sweden
| | - Marina Gay
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology (BIST) , Baldiri Reixac 10 , 08028 Barcelona , Spain
| | - Michael Götze
- Institute for Biochemistry and Biotechnology, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
| | - Francisco Gomes-Neto
- Laboratory of Toxinology , Oswaldo Cruz Institute , Fiocruz, Avenida Brasil 4365 (Moorish Castle) , Manguinhos, Rio de Janeiro , Rio de Janeiro 21040-900 , Brazil
| | - Fabio C Gozzo
- Institute of Chemistry , University of Campinas , Campinas São Paulo 13083-970 , Brazil
| | - Craig Gutierrez
- Department of Physiology & Biophysics , University of California , Irvine , California 92697 , United States
| | - Caroline Haupt
- Interdisciplinary Research Center HALOmem, Institute for Biochemistry and Biotechnology, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , University of Utrecht and Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Franz Herzog
- Gene Center Munich, Department of Biochemistry, Faculty of Chemistry and Pharmacy , Ludwig Maximilians University of Munich , Feodor-Lynen-Strasse 25 , 81377 Munich , Germany
| | - Lan Huang
- Department of Physiology & Biophysics , University of California , Irvine , California 92697 , United States
| | - Michael R Hoopmann
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109 , United States
| | - Nir Kalisman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Oleg Klykov
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , University of Utrecht and Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Zdeněk Kukačka
- Institute of Microbiology , BIOCEV , Prumyslova 595 , 252 50 Vestec , Czech Republic
| | - Fan Liu
- Leibniz Institute of Molecular Pharmacology (FMP) , Robert-Rössle-Strasse 10 , 13125 Berlin , Germany
| | - Michael J MacCoss
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - Karl Mechtler
- Protein Chemistry Facility, Research Institute of Molecular Pathology (IMP) and Institute of Molecular Biotechnology (IMBA) , Vienna Biocenter (VBC) , Dr. Bohr-Gasse 3 , 1030 Vienna , Austria
| | - Ravit Mesika
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Robert L Moritz
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109 , United States
| | - Nagarjuna Nagaraj
- Biochemistry Core Facility , Max-Planck-Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Victor Nesati
- Analytical Biochemistry, CSL Limited , Bio21 Institute , 30 Flemington Road , 3010 Parkville, Melbourne , Australia
| | - Ana G C Neves-Ferreira
- Laboratory of Toxinology , Oswaldo Cruz Institute , Fiocruz, Avenida Brasil 4365 (Moorish Castle) , Manguinhos, Rio de Janeiro , Rio de Janeiro 21040-900 , Brazil
| | - Robert Ninnis
- Analytical Biochemistry, CSL Limited , Bio21 Institute , 30 Flemington Road , 3010 Parkville, Melbourne , Australia
| | - Petr Novák
- Institute of Microbiology , BIOCEV , Prumyslova 595 , 252 50 Vestec , Czech Republic
| | - Francis J O'Reilly
- Chair of Bioanalytics, Institute of Biotechnology Technische Universität Berlin , 13355 Berlin , Germany
| | - Matthias Pelzing
- Analytical Biochemistry, CSL Limited , Bio21 Institute , 30 Flemington Road , 3010 Parkville, Melbourne , Australia
| | - Evgeniy Petrotchenko
- University of Victoria-Genome British Columbia Proteomics Centre , Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada
| | - Lolita Piersimoni
- Departments of Biological Chemistry, Bioinformatics, and Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Manolo Plasencia
- Departments of Biological Chemistry, Bioinformatics, and Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Tara Pukala
- Discipline of Chemistry, Faculty of Sciences , University of Adelaide , North Terrace, Adelaide , South Australia 5005 , Australia
| | - Kasper D Rand
- Department of Pharmacy , University of Copenhagen , 2100 Copenhagen , Denmark
| | - Juri Rappsilber
- Chair of Bioanalytics, Institute of Biotechnology Technische Universität Berlin , 13355 Berlin , Germany.,Wellcome Trust Centre for Cell Biology, School of Biological Sciences , University of Edinburgh , EH9 3BF Edinburgh , U.K
| | - Dana Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Carolin Sailer
- University of Konstanz , Department of Biology , Universitätsstrasse 10 , 78457 Konstanz , Germany
| | - Chris P Sarnowski
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich , Otto-Stern-Weg 3 , 8093 Zurich , Switzerland.,PhD Program in Systems Biology , University of Zurich and ETH Zurich , 8092 Zurich , Switzerland
| | - Richard A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , University of Utrecht and Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Institute for Biochemistry and Biotechnology, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
| | - David C Schriemer
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre , University of Calgary , 3330 Hospital Drive North West , Calgary , Alberta T2N 4N1 , Canada
| | - Yi Shi
- Department of Cell Biology , University of Pittsburgh, School of Medicine , Pittsburgh , Pennsylvania 15213 , United States
| | - J Mark Skehel
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Moriya Slavin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Frank Sobott
- Department of Chemistry , University of Antwerp , Groenenborgerlaan 171 , 2020 Antwerp , Belgium.,The Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology , University of Leeds , LS2 9JT Leeds , U.K
| | - Victor Solis-Mezarino
- Gene Center Munich, Department of Biochemistry, Faculty of Chemistry and Pharmacy , Ludwig Maximilians University of Munich , Feodor-Lynen-Strasse 25 , 81377 Munich , Germany
| | - Heike Stephanowitz
- Leibniz Institute of Molecular Pharmacology (FMP) , Robert-Rössle-Strasse 10 , 13125 Berlin , Germany
| | - Florian Stengel
- University of Konstanz , Department of Biology , Universitätsstrasse 10 , 78457 Konstanz , Germany
| | - Christian E Stieger
- Protein Chemistry Facility, Research Institute of Molecular Pathology (IMP) and Institute of Molecular Biotechnology (IMBA) , Vienna Biocenter (VBC) , Dr. Bohr-Gasse 3 , 1030 Vienna , Austria
| | - Esben Trabjerg
- Department of Pharmacy , University of Copenhagen , 2100 Copenhagen , Denmark
| | - Michael Trnka
- UCSF Mass Spectrometry Facility , Genentech Hall, 600 16th Street , San Francisco , California 94158 , United States
| | - Marta Vilaseca
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology (BIST) , Baldiri Reixac 10 , 08028 Barcelona , Spain
| | - Rosa Viner
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Yufei Xiang
- Department of Cell Biology , University of Pittsburgh, School of Medicine , Pittsburgh , Pennsylvania 15213 , United States
| | - Sule Yilmaz
- Computational Systems Biochemistry Research Group , Max-Planck-Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Alex Zelter
- Department of Biochemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Daniel Ziemianowicz
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre , University of Calgary , 3330 Hospital Drive North West , Calgary , Alberta T2N 4N1 , Canada
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich , Otto-Stern-Weg 3 , 8093 Zurich , Switzerland
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
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42
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Fang Z, Baghdady YZ, Schug KA, Chowdhury SM. Evaluation of Different Stationary Phases in the Separation of Inter-Cross-Linked Peptides. J Proteome Res 2019; 18:1916-1925. [PMID: 30786713 DOI: 10.1021/acs.jproteome.9b00114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Chemical cross-linking coupled with mass spectrometry (MS) is becoming a routinely and widely used technique for depicting and constructing protein structures and protein interaction networks. One major challenge for cross-linking/MS is the determination of informative low-abundant inter-cross-linked products, generated within a sample of high complexity. A C18 stationary phase is the conventional means for reversed-phase (RP) separation of inter-cross-linked peptides. Various RP stationary phases, which provide different selectivities and retentions, have been developed as alternatives to C18 stationary phases. In this study, two phenyl-based columns, biphenyl and fluorophenyl, were investigated and compared with a C18 phase for separating BS3 (bis(sulfosuccinimidyl)suberate) cross-linked bovine serum albumin (BSA) and myoglobin by bottom-up proteomics. Fractions from the three columns were collected and analyzed in a linear ion trap (LIT) mass spectrometer for improving detection of low abundant inter-cross-linked peptides. Among these three columns, the fluorophenyl column provides additional ion-exchange interaction and exhibits unique retention in separating the cross-linked peptides. The fractioned data was analyzed in pLink, showing the fluorophenyl column consistently obtained more inter-cross-linked peptide identifications than both C18 and biphenyl columns. For the BSA cross-linked sample, the identified inter-cross-linked peptide numbers of the fluorophenyl to C18 column are 136 to 102 in "low confident" results and 11 to 6 in "high confident" results. The fluorophenyl column could potentially be a better alternative for targeting the low stoichiometric inter-cross-linked peptides.
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Affiliation(s)
- Zixiang Fang
- Department of Chemistry & Biochemistry , The University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Yehia Z Baghdady
- Department of Chemistry & Biochemistry , The University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Kevin A Schug
- Department of Chemistry & Biochemistry , The University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Saiful M Chowdhury
- Department of Chemistry & Biochemistry , The University of Texas at Arlington , Arlington , Texas 76019 , United States
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43
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Hernychová L, Rosůlek M, Kádek A, Mareška V, Chmelík J, Adámková L, Grobárová V, Šebesta O, Kukačka Z, Skála K, Spiwok V, Černý J, Novák P. The C-type lectin-like receptor Nkrp1b: Structural proteomics reveals features affecting protein conformation and interactions. J Proteomics 2019; 196:162-172. [DOI: 10.1016/j.jprot.2018.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/31/2018] [Accepted: 11/05/2018] [Indexed: 11/24/2022]
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44
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Computational modeling of RNA 3D structure based on experimental data. Biosci Rep 2019; 39:BSR20180430. [PMID: 30670629 PMCID: PMC6367127 DOI: 10.1042/bsr20180430] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 01/02/2023] Open
Abstract
RNA molecules are master regulators of cells. They are involved in a variety of molecular processes: they transmit genetic information, sense cellular signals and communicate responses, and even catalyze chemical reactions. As in the case of proteins, RNA function is dictated by its structure and by its ability to adopt different conformations, which in turn is encoded in the sequence. Experimental determination of high-resolution RNA structures is both laborious and difficult, and therefore the majority of known RNAs remain structurally uncharacterized. To address this problem, predictive computational methods were developed based on the accumulated knowledge of RNA structures determined so far, the physical basis of the RNA folding, and taking into account evolutionary considerations, such as conservation of functionally important motifs. However, all theoretical methods suffer from various limitations, and they are generally unable to accurately predict structures for RNA sequences longer than 100-nt residues unless aided by additional experimental data. In this article, we review experimental methods that can generate data usable by computational methods, as well as computational approaches for RNA structure prediction that can utilize data from experimental analyses. We outline methods and data types that can be potentially useful for RNA 3D structure modeling but are not commonly used by the existing software, suggesting directions for future development.
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45
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Downard KM, Maleknia SD. Mass spectrometry in structural proteomics: The case for radical probe protein footprinting. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.11.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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46
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A cross-linking/mass spectrometry workflow based on MS-cleavable cross-linkers and the MeroX software for studying protein structures and protein–protein interactions. Nat Protoc 2018; 13:2864-2889. [DOI: 10.1038/s41596-018-0068-8] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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47
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Cross-linking mass spectrometry: methods and applications in structural, molecular and systems biology. Nat Struct Mol Biol 2018; 25:1000-1008. [PMID: 30374081 DOI: 10.1038/s41594-018-0147-0] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/19/2018] [Indexed: 01/11/2023]
Abstract
Over the past decade, cross-linking mass spectrometry (CLMS) has developed into a robust and flexible tool that provides medium-resolution structural information. CLMS data provide a measure of the proximity of amino acid residues and thus offer information on the folds of proteins and the topology of their complexes. Here, we highlight notable successes of this technique as well as common pipelines. Novel CLMS applications, such as in-cell cross-linking, probing conformational changes and tertiary-structure determination, are now beginning to make contributions to molecular biology and the emerging fields of structural systems biology and interactomics.
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48
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Smidova A, Alblova M, Kalabova D, Psenakova K, Rosulek M, Herman P, Obsil T, Obsilova V. 14-3-3 protein masks the nuclear localization sequence of caspase-2. FEBS J 2018; 285:4196-4213. [PMID: 30281929 DOI: 10.1111/febs.14670] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 09/28/2018] [Indexed: 12/13/2022]
Abstract
Caspase-2 is an apical protease responsible for the proteolysis of cellular substrates directly involved in mediating apoptotic signaling cascades. Caspase-2 activation is inhibited by phosphorylation followed by binding to the scaffolding protein 14-3-3, which recognizes two phosphoserines located in the linker between the caspase recruitment domain and the p19 domains of the caspase-2 zymogen. However, the structural details of this interaction and the exact role of 14-3-3 in the regulation of caspase-2 activation remain unclear. Moreover, the caspase-2 region with both 14-3-3-binding motifs also contains the nuclear localization sequence (NLS), thus suggesting that 14-3-3 binding may regulate the subcellular localization of caspase-2. Here, we report a structural analysis of the 14-3-3ζ:caspase-2 complex using a combined approach based on small angle X-ray scattering, NMR, chemical cross-linking, and fluorescence spectroscopy. The structural model proposed in this study suggests that phosphorylated caspase-2 and 14-3-3ζ form a compact and rigid complex in which the p19 and the p12 domains of caspase-2 are positioned within the central channel of the 14-3-3 dimer and stabilized through interactions with the C-terminal helices of both 14-3-3ζ protomers. In this conformation, the surface of the p12 domain, which is involved in caspase-2 activation by dimerization, is sterically occluded by the 14-3-3 dimer, thereby likely preventing caspase-2 activation. In addition, 14-3-3 protein binding to caspase-2 masks its NLS. Therefore, our results suggest that 14-3-3 protein binding to caspase-2 may play a key role in regulating caspase-2 activation. DATABASE: The atomic coordinates and structure factors have been deposited in the Protein Data Bank, www.ww pdb.org (PDB ID codes 6GKF and 6GKG).
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Affiliation(s)
- Aneta Smidova
- Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Miroslava Alblova
- Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Dana Kalabova
- Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, Vestec, Czech Republic.,2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Katarina Psenakova
- Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, Vestec, Czech Republic.,Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michal Rosulek
- Division BIOCEV, Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Herman
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Tomas Obsil
- Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, Vestec, Czech Republic.,Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Veronika Obsilova
- Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, Vestec, Czech Republic
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Proximity-enhanced SuFEx chemical cross-linker for specific and multitargeting cross-linking mass spectrometry. Proc Natl Acad Sci U S A 2018; 115:11162-11167. [PMID: 30322930 DOI: 10.1073/pnas.1813574115] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Chemical cross-linking mass spectrometry (CXMS) is being increasingly used to study protein assemblies and complex protein interaction networks. Existing CXMS chemical cross-linkers target only Lys, Cys, Glu, and Asp residues, limiting the information measurable. Here we report a "plant-and-cast" cross-linking strategy that employs a heterobifunctional cross-linker that contains a highly reactive succinimide ester as well as a less reactive sulfonyl fluoride. The succinimide ester reacts rapidly with surface Lys residues "planting" the reagent at fixed locations on protein. The pendant aryl sulfonyl fluoride is then "cast" across a limited range of the protein surface, where it can react with multiple weakly nucleophilic amino acid sidechains in a proximity-enhanced sulfur-fluoride exchange (SuFEx) reaction. Using proteins of known structures, we demonstrated that the heterobifunctional agent formed cross-links between Lys residues and His, Ser, Thr, Tyr, and Lys sidechains. This geometric specificity contrasts with current bis-succinimide esters, which often generate nonspecific cross-links between lysines brought into proximity by rare thermal fluctuations. Thus, the current method can provide diverse and robust distance restraints to guide integrative modeling. This work provides a chemical cross-linker targeting unactivated Ser, Thr, His, and Tyr residues using sulfonyl fluorides. In addition, this methodology yielded a variety of cross-links when applied to the complex Escherichia coli cell lysate. Finally, in combination with genetically encoded chemical cross-linking, cross-linking using this reagent markedly increased the identification of weak and transient enzyme-substrate interactions in live cells. Proximity-dependent cross-linking will dramatically expand the scope and power of CXMS for defining the identities and structures of protein complexes.
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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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