51
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Hawkins CL, Davies MJ. Detection, identification, and quantification of oxidative protein modifications. J Biol Chem 2019; 294:19683-19708. [PMID: 31672919 PMCID: PMC6926449 DOI: 10.1074/jbc.rev119.006217] [Citation(s) in RCA: 205] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Exposure of biological molecules to oxidants is inevitable and therefore commonplace. Oxidative stress in cells arises from both external agents and endogenous processes that generate reactive species, either purposely (e.g. during pathogen killing or enzymatic reactions) or accidentally (e.g. exposure to radiation, pollutants, drugs, or chemicals). As proteins are highly abundant and react rapidly with many oxidants, they are highly susceptible to, and major targets of, oxidative damage. This can result in changes to protein structure, function, and turnover and to loss or (occasional) gain of activity. Accumulation of oxidatively-modified proteins, due to either increased generation or decreased removal, has been associated with both aging and multiple diseases. Different oxidants generate a broad, and sometimes characteristic, spectrum of post-translational modifications. The kinetics (rates) of damage formation also vary dramatically. There is a pressing need for reliable and robust methods that can detect, identify, and quantify the products formed on amino acids, peptides, and proteins, especially in complex systems. This review summarizes several advances in our understanding of this complex chemistry and highlights methods that are available to detect oxidative modifications-at the amino acid, peptide, or protein level-and their nature, quantity, and position within a peptide sequence. Although considerable progress has been made in the development and application of new techniques, it is clear that further development is required to fully assess the relative importance of protein oxidation and to determine whether an oxidation is a cause, or merely a consequence, of injurious processes.
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Affiliation(s)
- Clare L Hawkins
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen 2200, Denmark
| | - Michael J Davies
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen 2200, Denmark
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52
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Irwin MJ, Gupta R, Gao XZ, Cahill KB, Chu F, Cote RH. The molecular architecture of photoreceptor phosphodiesterase 6 (PDE6) with activated G protein elucidates the mechanism of visual excitation. J Biol Chem 2019; 294:19486-19497. [PMID: 31690623 DOI: 10.1074/jbc.ra119.011002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 10/25/2019] [Indexed: 11/06/2022] Open
Abstract
Photoreceptor phosphodiesterase 6 (PDE6) is the central effector of the visual excitation pathway in both rod and cone photoreceptors, and PDE6 mutations that alter PDE6 structure or regulation can result in several human retinal diseases. The rod PDE6 holoenzyme consists of two catalytic subunits (Pαβ) whose activity is suppressed in the dark by binding of two inhibitory γ-subunits (Pγ). Upon photoactivation of rhodopsin, the heterotrimeric G protein (transducin) is activated, resulting in binding of the activated transducin α-subunit (Gtα) to PDE6, displacement of Pγ from the PDE6 active site, and enzyme activation. Although the biochemistry of this pathway is understood, a lack of detailed structural information about the PDE6 activation mechanism hampers efforts to develop therapeutic interventions for managing PDE6-associated retinal diseases. To address this gap, here we used a cross-linking MS-based approach to create a model of the entire interaction surface of Pγ with the regulatory and catalytic domains of Pαβ in its nonactivated state. Following reconstitution of PDE6 and activated Gtα with liposomes and identification of cross-links between Gtα and PDE6 subunits, we determined that the PDE6-Gtα protein complex consists of two Gtα-binding sites per holoenzyme. Each Gtα interacts with the catalytic domains of both catalytic subunits and induces major changes in the interaction sites of the Pγ subunit with the catalytic subunits. These results provide the first structural model for the activated state of the transducin-PDE6 complex during visual excitation, enhancing our understanding of the molecular etiology of inherited retinal diseases.
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Affiliation(s)
- Michael J Irwin
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824
| | - Richa Gupta
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824
| | - Xiong-Zhuo Gao
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824
| | - Karyn B Cahill
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824
| | - Feixia Chu
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824
| | - Rick H Cote
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824
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53
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Sanulli S, Trnka MJ, Dharmarajan V, Tibble RW, Pascal BD, Burlingame AL, Griffin PR, Gross JD, Narlikar GJ. HP1 reshapes nucleosome core to promote phase separation of heterochromatin. Nature 2019; 575:390-394. [PMID: 31618757 PMCID: PMC7039410 DOI: 10.1038/s41586-019-1669-2] [Citation(s) in RCA: 288] [Impact Index Per Article: 57.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 09/17/2019] [Indexed: 12/24/2022]
Abstract
Heterochromatin affects genome function at many levels. It enables heritable gene repression, maintains chromosome integrity and provides mechanical rigidity to the nucleus1,2. These diverse functions are proposed to arise in part from compaction of the underlying chromatin2. A major type of heterochromatin contains at its core the complex formed between HP1 proteins and chromatin that is methylated on histone H3, lysine 9 (H3K9me). HP1 is proposed to use oligomerization to compact chromatin into phase-separated condensates3-6. Yet, how HP1-mediated phase separation relates to chromatin compaction remains unclear. Here we show that chromatin compaction by the Schizosaccharomyces pombe HP1 protein Swi6 results in phase-separated liquid condensates. Unexpectedly, we find that Swi6 substantially increases the accessibility and dynamics of buried histone residues within a nucleosome. Restraining these dynamics impairs compaction of chromatin into liquid droplets by Swi6. Our results indicate that Swi6 couples its oligomerization to the phase separation of chromatin by a counterintuitive mechanism, namely the dynamic exposure of buried nucleosomal regions. We propose that such reshaping of the octamer core by Swi6 increases opportunities for multivalent interactions between nucleosomes, thereby promoting phase separation. This mechanism may more generally drive chromatin organization beyond heterochromatin.
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Affiliation(s)
- S Sanulli
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - M J Trnka
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - V Dharmarajan
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - R W Tibble
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.,Program in Chemistry and Chemical Biology, University of California San Francisco, San Francisco, CA, USA
| | - B D Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - A L Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - P R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - J D Gross
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
| | - G J Narlikar
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
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54
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Lexhaller B, Ludwig C, Scherf KA. Comprehensive Detection of Isopeptides between Human Tissue Transglutaminase and Gluten Peptides. Nutrients 2019; 11:nu11102263. [PMID: 31547042 PMCID: PMC6835481 DOI: 10.3390/nu11102263] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/03/2019] [Accepted: 09/15/2019] [Indexed: 01/02/2023] Open
Abstract
Celiac disease (CD) is a chronic inflammation of the small intestine triggered by the ingestion of gluten in genetically predisposed individuals. Tissue transglutaminase (TG2) is a key factor in CD pathogenesis, because it catalyzes both the deamidation of specific glutamine residues and the formation of covalent Nε-(γ-glutamyl)-lysine isopeptide crosslinks resulting in TG2–gluten peptide complexes. These complexes are thought to activate B cells causing the secretion of anti-TG2 autoantibodies that serve as diagnostic markers for CD, although their pathogenic role remains unclear. To gain more insight into the molecular structures of TG2-gluten peptide complexes, we used different proteomics software tools that enable the comprehensive identification of isopeptides. Thus, 34 different isopeptides involving 20 TG2 lysine residues were identified in a model system, only six of which were previously known. Additionally, 36 isopeptides of TG2-TG2 multimers were detected. Experiments with different TG2-gluten peptide molar ratios revealed the most preferred lysine residues involved in isopeptide crosslinking. Expanding the model system to three gluten peptides with more glutamine residues allowed the localization of the preferred glutamine crosslinking sites. These new insights into the structure of TG2-gluten peptide complexes may help clarify the role of extracellular TG2 in CD autoimmunity and in other inflammatory diseases.
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Affiliation(s)
- Barbara Lexhaller
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Str. 34, 85354 Freising, Germany.
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Gregor-Mendel-Str. 4, 85354 Freising, Germany.
| | - Katharina A Scherf
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Str. 34, 85354 Freising, Germany.
- Department of Bioactive and Functional Food Chemistry, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Adenauerring 20a, 76131 Karlsruhe, Germany.
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55
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Mukherjee S, Fang M, Kok WM, Kapp EA, Thombare VJ, Huguet R, Hutton CA, Reid GE, Roberts BR. Establishing Signature Fragments for Identification and Sequencing of Dityrosine Cross-Linked Peptides Using Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2019; 91:12129-12133. [DOI: 10.1021/acs.analchem.9b02986] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Soumya Mukherjee
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Mengxuan Fang
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - W. Mei Kok
- University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland 4072, Australia
| | - Eugene A. Kapp
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Varsha J. Thombare
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Craig A. Hutton
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - Gavin E. Reid
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Blaine R. Roberts
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
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56
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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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57
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Chu F, Hogan D, Gupta R, Gao XZ, Nguyen HT, Cote RH. Allosteric Regulation of Rod Photoreceptor Phosphodiesterase 6 (PDE6) Elucidated by Chemical Cross-Linking and Quantitative Mass Spectrometry. J Mol Biol 2019; 431:3677-3689. [PMID: 31394113 DOI: 10.1016/j.jmb.2019.07.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 06/29/2019] [Accepted: 07/30/2019] [Indexed: 12/31/2022]
Abstract
Photoreceptor phosphodiesterase (PDE6) is the central effector enzyme in the visual excitation pathway in rod and cone photoreceptors. Its tight regulation is essential for the speed, sensitivity, recovery, and adaptation of visual signaling. The rod PDE6 holoenzyme (Pαβγ2) is composed of a catalytic heterodimer (Pαβ) that binds two inhibitory γ subunits. Each of the two catalytic subunits (Pα and Pβ) contains a catalytic domain responsible for cGMP hydrolysis and two tandem GAF domains, one of which binds cGMP noncatalytically. Unlike related GAF-containing PDEs where cGMP binding allosterically activates catalysis, the physiological significance of cGMP binding to the GAF domains of PDE6 is unknown. To elucidate the structural determinants of PDE6 allosteric regulators, we biochemically characterized PDE6 complexes in various allosteric states (Pαβ, Pαβ-cGMP, Pαβγ2, and Pαβγ2-cGMP) with a quantitative cross-linking/mass spectrometry approach. We employed a normalization strategy to dissect the cross-linking reactivity of individual residues in order to assess the spatial cross-linking propensity of detected pairs. In addition to identifying cross-linked pairs that undergo conformational changes upon ligand binding, we observed an asymmetric binding of the inhibitory γ-subunit and the noncatalytic cGMP to the GAFa domains of rod PDE6, as well as a stable open conformation of Pαβ catalytic dimer in different allosteric states. These results advance our understanding of the exquisite regulatory control of the lifetime of rod PDE6 activation/deactivation during visual signaling, as well as providing a structural basis for interpreting how mutations in rod PDE6 subunits can lead to retinal diseases.
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Affiliation(s)
- Feixia Chu
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, USA.
| | - Donna Hogan
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Richa Gupta
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Xiong-Zhuo Gao
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Hieu T Nguyen
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Rick H Cote
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, USA
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58
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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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59
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Keller A, Chavez JD, Felt KC, Bruce JE. Prediction of an Upper Limit for the Fraction of Interprotein Cross-Links in Large-Scale In Vivo Cross-Linking Studies. J Proteome Res 2019; 18:3077-3085. [PMID: 31267744 DOI: 10.1021/acs.jproteome.9b00189] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chemical cross-linking and mass spectrometry is of growing use for establishment of distance constraints on protein conformations and interactions. Whereas intraprotein cross-links can arise from proteins in isolation, interprotein cross-links reflect proximity of two interacting proteins in the sample. Prediction of expected ratios of the number of interprotein to intraprotein cross-links is hindered by lacking comprehensive knowledge on the interactome network and global occupancy levels for all interacting complex subunits. Here we determine the theoretical number of possible inter- and intraprotein cross-links in available PDB structures of proteins bound in complexes to predict a maximum expected fraction of interprotein cross-links in large scale in vivo cross-linking studies. We show how the maximum fraction can guide interpretation of reported interprotein fractions with respect to the extent of sample protein binding, comparing whole cell and lysate cross-linked samples as an example. We also demonstrate how an observation of interprotein cross-link fractions greater than the maximum value can result from the presence of false positive cross-links which are predominantly interprotein, their number estimable from the observed surplus fraction of interprotein cross-links.
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Affiliation(s)
- Andrew Keller
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 United States
| | - Juan D Chavez
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 United States
| | - Kevin C Felt
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 United States
| | - James E Bruce
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 United States
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60
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Structural underpinnings of Ric8A function as a G-protein α-subunit chaperone and guanine-nucleotide exchange factor. Nat Commun 2019; 10:3084. [PMID: 31300652 PMCID: PMC6625990 DOI: 10.1038/s41467-019-11088-x] [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: 12/11/2018] [Accepted: 06/21/2019] [Indexed: 02/03/2023] Open
Abstract
Resistance to inhibitors of cholinesterase 8A (Ric8A) is an essential regulator of G protein α-subunits (Gα), acting as a guanine nucleotide exchange factor and a chaperone. We report two crystal structures of Ric8A, one in the apo form and the other in complex with a tagged C-terminal fragment of Gα. These structures reveal two principal domains of Ric8A: an armadillo-fold core and a flexible C-terminal tail. Additionally, they show that the Gα C-terminus binds to a highly-conserved patch on the concave surface of the Ric8A armadillo-domain, with selectivity determinants residing in the Gα sequence. Biochemical analysis shows that the Ric8A C-terminal tail is critical for its stability and function. A model of the Ric8A/Gα complex derived from crosslinking mass spectrometry and molecular dynamics simulations suggests that the Ric8A C-terminal tail helps organize the GTP-binding site of Gα. This study lays the groundwork for understanding Ric8A function at the molecular level. Ric8A regulates G protein α-subunits (Gα) by acting as a guanine nucleotide exchange factor (GEF) and a Gα chaperone. Here, the authors solve the crystal structures of free and Gα fragment bound Ric8A, and provide insights into the structural basis for Ric8A’s GEF and chaperone functions.
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61
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Bergkessel M, Babin BM, VanderVelde D, Sweredoski MJ, Moradian A, Eggleston-Rangel R, Hess S, Tirrell DA, Artsimovitch I, Newman DK. The dormancy-specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa. Mol Microbiol 2019; 112:992-1009. [PMID: 31254296 DOI: 10.1111/mmi.14337] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2019] [Indexed: 11/27/2022]
Abstract
Though most bacteria in nature are nutritionally limited and grow slowly, our understanding of core processes like transcription comes largely from studies in model organisms doubling rapidly. We previously identified a small protein of unknown function, SutA, in a screen of proteins synthesized in Pseudomonas aeruginosa during dormancy. SutA binds RNA polymerase (RNAP), causing widespread changes in gene expression, including upregulation of the ribosomal RNA genes. Here, using biochemical and structural methods, we examine how SutA interacts with RNAP and the functional consequences of these interactions. We show that SutA comprises a central α-helix with unstructured N- and C-terminal tails, and binds to the β1 domain of RNAP. It activates transcription from the rrn promoter by both the housekeeping sigma factor holoenzyme (Eσ70 ) and the stress sigma factor holoenzyme (EσS ) in vitro, but has a greater impact on EσS . In both cases, SutA appears to affect intermediates in the open complex formation and its N-terminal tail is required for activation. The small magnitudes of in vitro effects are consistent with a role in maintaining activity required for homeostasis during dormancy. Our results add SutA to a growing list of transcription regulators that use their intrinsically disordered regions to remodel transcription complexes.
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Affiliation(s)
- Megan Bergkessel
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Brett M Babin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - David VanderVelde
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Annie Moradian
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Roxana Eggleston-Rangel
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Sonja Hess
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Irina Artsimovitch
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
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62
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Chavez JD, Mohr JP, Mathay M, Zhong X, Keller A, Bruce JE. Systems structural biology measurements by in vivo cross-linking with mass spectrometry. Nat Protoc 2019; 14:2318-2343. [PMID: 31270507 DOI: 10.1038/s41596-019-0181-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 04/18/2019] [Indexed: 12/23/2022]
Abstract
This protocol describes a workflow for utilizing large-scale cross-linking with mass spectrometry (XL-MS) to make systems-level structural biology measurements in complex biological samples, including cells, isolated organelles, and tissue samples. XL-MS is a structural biology technique that provides information on the molecular structure of proteins and protein complexes using chemical probes that report the proximity of probe-reactive amino acids within proteins, typically lysine residues. Information gained through XL-MS studies is often complementary to more traditional methods, such as X-ray crystallography, nuclear magnetic resonance, and cryo-electron microscopy. The use of MS-cleavable cross-linkers, including protein interaction reporter (PIR) technologies, enables XL-MS studies on protein structures and interactions in extremely complex biological samples, including intact living cells. PIR cross-linkers are designed to contain chemical bonds at specific locations within the cross-linker molecule that can be selectively cleaved by collision-induced dissociation or UV light. When broken, these bonds release the intact peptides that were cross-linked, as well as a reporter ion. Conservation of mass dictates that the sum of the two released peptide masses and the reporter mass equals the measured precursor mass. This relationship is used to identify cross-linked peptide pairs. Release of the individual peptides permits accurate measurement of their masses and independent amino acid sequence determination by tandem MS, allowing the use of standard proteomics search engines such as Comet for peptide sequence assignment, greatly simplifying data analysis of cross-linked peptide pairs. Search results are processed with XLinkProphet for validation and can be uploaded into XlinkDB for interaction network and structural analysis.
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Affiliation(s)
- Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jared P Mohr
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Martin Mathay
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Xuefei Zhong
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Andrew Keller
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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63
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Inferring Protein-Protein Interaction Networks From Mass Spectrometry-Based Proteomic Approaches: A Mini-Review. Comput Struct Biotechnol J 2019; 17:805-811. [PMID: 31316724 PMCID: PMC6611912 DOI: 10.1016/j.csbj.2019.05.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/20/2019] [Accepted: 05/26/2019] [Indexed: 01/06/2023] Open
Abstract
Studying protein-protein interaction networks provide key evidence for the underlying molecular mechanisms. Mass spectrometry-based proteomic approaches have been playing a pivotal role in deciphering these interaction networks, along with precise quantification for individual interactions. In this mini-review we discuss the available techniques and methods for qualitative and quantitative elucidation of protein-protein interaction networks. We then summarize the down-stream computational strategies for identification and quantification of interactions from those techniques. Finally, we highlight the challenges and limitations of current computational pipelines in eliminating false positive interactors, followed by a summary of the innovative algorithms to address these issues, along with the scope for future improvements.
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64
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Trnka MJ, Pellarin R, Robinson PJ. Role of integrative structural biology in understanding transcriptional initiation. Methods 2019; 159-160:4-22. [PMID: 30890443 PMCID: PMC6617507 DOI: 10.1016/j.ymeth.2019.03.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/14/2019] [Accepted: 03/15/2019] [Indexed: 12/12/2022] Open
Abstract
Integrative structural biology combines data from multiple experimental techniques to generate complete structural models for the biological system of interest. Most commonly cross-linking data sets are employed alongside electron microscopy maps, crystallographic structures, and other data by computational methods that integrate all known information and produce structural models at a level of resolution that is appropriate to the input data. The precision of these modelled solutions is limited by the sparseness of cross-links observed, the length of the cross-linking reagent, the ambiguity arisen from the presence of multiple copies of the same protein, and structural and compositional heterogeneity. In recent years integrative structural biology approaches have been successfully applied to a range of RNA polymerase II complexes. Here we will provide a general background to integrative structural biology, a description of how it should be practically implemented and how it has furthered our understanding of the biology of large transcriptional assemblies. Finally, in the context of recent breakthroughs in microscope and direct electron detector technology, where increasingly EM is capable of resolving structural features directly without the aid of other structural techniques, we will discuss the future role of integrative structural techniques.
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Affiliation(s)
- Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Riccardo Pellarin
- Institut Pasteur, Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, CNRS UMR 3528, C3BI USR 3756 CNRS & IP, Paris, France
| | - Philip J Robinson
- Department of Biological Sciences, Birkbeck University of London, Institute of Structural and Molecular Biology, London, United Kingdom.
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65
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McKerchar HJ, Clerens S, Dobson RC, Dyer JM, Maes E, Gerrard JA. Protein-protein crosslinking in food: Proteomic characterisation methods, consequences and applications. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.02.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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66
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Mass Spectrometry Identifies Isopeptide Cross-Links Promoted by Diethylphosphorylated Lysine in Proteins Treated with Chlorpyrifos Oxon. Chem Res Toxicol 2019; 32:762-772. [DOI: 10.1021/acs.chemrestox.9b00001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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67
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James JMB, Cryar A, Thalassinos K. Optimization Workflow for the Analysis of Cross-Linked Peptides Using a Quadrupole Time-of-Flight Mass Spectrometer. Anal Chem 2019; 91:1808-1814. [PMID: 30620560 PMCID: PMC6383985 DOI: 10.1021/acs.analchem.8b02319] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
Cross-linking
mass spectrometry is an emerging structural biology
technique. Almost exclusively, the analyzer of choice for such an
experiment has been the Orbitrap. We present an optimized protocol
for the use of a Synapt G2-Si for the analysis of cross-linked peptides.
We first tested six different energy ramps and analyzed the fragmentation
behavior of cross-linked peptides identified by xQuest. By combining
the most successful energy ramps, cross-link yield can be increased
by up to 40%. When compared to previously published Orbitrap data,
the Synapt G2-Si also offers improved fragmentation of the β
peptide. In order to improve cross-link quality control we have also
developed ValidateXL, a programmatic solution that works with existing
cross-linking software to improve cross-link quality control.
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Affiliation(s)
- Juliette M B James
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology , University College London , Gower Street , London , WC1E 6BT , United Kingdom
| | - Adam Cryar
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology , University College London , Gower Street , London , WC1E 6BT , United Kingdom.,LGC Group , Queen's Road , Teddington , TW11 0LY , United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology , University College London , Gower Street , London , WC1E 6BT , United Kingdom.,Institute of Structural and Molecular Biology, Department of Biological Sciences , Birkbeck, University of London , London , WC1E 7HX , United Kingdom
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68
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Mirzakhanyan Y, Gershon P. The Vaccinia virion: Filling the gap between atomic and ultrastructure. PLoS Pathog 2019; 15:e1007508. [PMID: 30615658 PMCID: PMC6336343 DOI: 10.1371/journal.ppat.1007508] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 01/17/2019] [Accepted: 12/06/2018] [Indexed: 01/19/2023] Open
Abstract
We have investigated the molecular-level structure of the Vaccinia virion in situ by protein-protein chemical crosslinking, identifying 4609 unique-mass crosslink ions at an effective FDR of 0.33%, covering 2534 unique pairs of crosslinked protein positions, 625 of which were inter-protein. The data were statistically non-random and rational in the context of known structures, and showed biological rationality. Crosslink density strongly tracked the individual proteolytic maturation products of p4a and p4b, the two major virion structural proteins, and supported the prediction of transmembrane domains within membrane proteins. A clear sub-network of four virion structural proteins provided structural insights into the virion core wall, and proteins VP8 and A12 formed a strongly-detected crosslinked pair with an apparent structural role. A strongly-detected sub-network of membrane proteins A17, H3, A27 and A26 represented an apparent interface of the early-forming virion envelope with structures added later during virion morphogenesis. Protein H3 seemed to be the central hub not only for this sub-network but also for an 'attachment protein' sub-network comprising membrane proteins H3, ATI, CAHH(D8), A26, A27 and G9. Crosslinking data lent support to a number of known interactions and interactions within known complexes. Evidence is provided for the membrane targeting of genome telomeres. In covering several orders of magnitude in protein abundance, this study may have come close to the bottom of the protein-protein crosslinkome of an intact organism, namely a complex animal virus.
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Affiliation(s)
- Yeva Mirzakhanyan
- Department of Molecular Biology & Biochemistry, UC-Irvine, Irvine, California, United States of America
| | - Paul Gershon
- Department of Molecular Biology & Biochemistry, UC-Irvine, Irvine, California, United States of America
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69
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Iacobucci C, Piotrowski C, Rehkamp A, Ihling CH, Sinz A. The First MS-Cleavable, Photo-Thiol-Reactive Cross-Linker for Protein Structural Studies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:139-148. [PMID: 29679287 DOI: 10.1007/s13361-018-1952-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 06/08/2023]
Abstract
Cleavable cross-linkers are gaining increasing importance for chemical cross-linking/mass spectrometry (MS) as they permit a reliable and automated data analysis in structural studies of proteins and protein assemblies. Here, we introduce 1,3-diallylurea (DAU) as the first CID-MS/MS-cleavable, photo-thiol-reactive cross-linker. DAU is a commercially available, inexpensive reagent that efficiently undergoes an anti-Markovnikov hydrothiolation with cysteine residues in the presence of a radical initiator upon UV-A irradiation. Radical cysteine cross-linking proceeds via an orthogonal "click reaction" and yields stable alkyl sulfide products. DAU reacts at physiological pH and cross-linking reactions with peptides, and proteins can be performed at temperatures as low as 4 °C. The central urea bond is efficiently cleaved upon collisional activation during tandem MS experiments generating characteristic product ions. This improves the reliability of automated cross-link identification. Different radical initiators have been screened for the cross-linking reaction of DAU using the thiol-containing compounds cysteine and glutathione. Our concept has also been exemplified for the biologically relevant proteins bMunc13-2 and retinal guanylyl cyclase-activating protein-2. Graphical abstract ᅟ.
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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-Str. 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-Str. 3a, 06120, Halle (Saale), Germany
| | - Anne Rehkamp
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany.
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70
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Myers SA, Klaeger S, Satpathy S, Viner R, Choi J, Rogers J, Clauser K, Udeshi ND, Carr SA. Evaluation of Advanced Precursor Determination for Tandem Mass Tag (TMT)-Based Quantitative Proteomics across Instrument Platforms. J Proteome Res 2018; 18:542-547. [PMID: 30351145 DOI: 10.1021/acs.jproteome.8b00611] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Tandem mass tag (TMT)-based quantitation is a strong modality for quantitative proteomics, as samples can be multiplexed, creating large-scale data sets with high precision and minimal missing values. However, coisolation/cofragmentation of near isobaric, coeluting precursor peptide analytes has been well-documented to show ratio compression, compromising the accuracy of peptide/protein quantitation. Advanced peak determination (APD) is a new peak-picking algorithm that shows improved identification of peak detection in survey scans (MS1) to increase the number of precursors selected for unimolecular dissociation (MS2). To increase the number of these "features" selected for MS2 APD purposefully selects multiple peptide precursors of very similar m/ z that often derive from different proteins-a major source of ratio compression in TMT quantification. Here, we evaluate the effects of various data acquisition parameters combined with APD on ratio compression. We find that data acquisition with APD enabled results in more coisolated precursors, more mixed spectra, and in turn, fewer peptide spectral matches, especially at standard on-column loads. We conclude that APD should not be utilized for isobaric tagging, MS2-based experiments.
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Affiliation(s)
- Samuel A Myers
- The Broad Institute of MIT and Harvard , Cambridge , Massachusetts , United States
| | - Susan Klaeger
- The Broad Institute of MIT and Harvard , Cambridge , Massachusetts , United States
| | - Shankha Satpathy
- The Broad Institute of MIT and Harvard , Cambridge , Massachusetts , United States
| | - Rosa Viner
- Thermo Fisher Scientific , San Jose , California , United States
| | - Jae Choi
- Thermo Fisher Scientific , Rockford , Illinois , United States
| | - John Rogers
- Thermo Fisher Scientific , Rockford , Illinois , United States
| | - Karl Clauser
- The Broad Institute of MIT and Harvard , Cambridge , Massachusetts , United States
| | - Namrata D Udeshi
- The Broad Institute of MIT and Harvard , Cambridge , Massachusetts , United States
| | - Steven A Carr
- The Broad Institute of MIT and Harvard , Cambridge , Massachusetts , United States
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71
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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: 196] [Impact Index Per Article: 32.7] [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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72
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Minic Z, Dahms TES, Babu M. Chromatographic separation strategies for precision mass spectrometry to study protein-protein interactions and protein phosphorylation. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1102-1103:96-108. [PMID: 30380468 DOI: 10.1016/j.jchromb.2018.10.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 11/30/2022]
Abstract
Investigating protein-protein interactions and protein phosphorylation can be of great significance when studying biological processes and human diseases at the molecular level. However, sample complexity, presence of low abundance proteins, and dynamic nature of the proteins often impede in achieving sufficient analytical depth in proteomics research. In this regard, chromatographic separation methodologies have played a vital role in the identification and quantification of proteins in complex sample mixtures. The combination of peptide and protein fractionation techniques with advanced high-performance mass spectrometry has allowed the researchers to successfully study the protein-protein interactions and protein phosphorylation. Several new fractionation strategies for large scale analysis of proteins and peptides have been developed to study protein-protein interactions and protein phosphorylation. These emerging chromatography methodologies have enabled the identification of several hundred protein complexes and even thousands of phosphorylation sites in a single study. In this review, we focus on current workflow strategies and chromatographic tools, highlighting their advantages and disadvantages, and examining their associated challenges and future potential.
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Affiliation(s)
- Zoran Minic
- Department of Chemistry and Biomolecular Science, University of Ottawa, John L. Holmes, Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, Room 02, Ottawa, ON K1N 1A2, Canada.
| | - Tanya E S Dahms
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
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73
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Gaber A, Kim SJ, Kaake RM, Benčina M, Krogan N, Šali A, Pavšič M, Lenarčič B. EpCAM homo-oligomerization is not the basis for its role in cell-cell adhesion. Sci Rep 2018; 8:13269. [PMID: 30185875 PMCID: PMC6125409 DOI: 10.1038/s41598-018-31482-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 08/20/2018] [Indexed: 01/01/2023] Open
Abstract
Cell-surface tumor marker EpCAM plays a key role in proliferation, differentiation and adhesion processes in stem and epithelial cells. It is established as a cell-cell adhesion molecule, forming intercellular interactions through homophilic association. However, the mechanism by which such interactions arise has not yet been fully elucidated. Here, we first show that EpCAM monomers do not associate into oligomers that would resemble an inter-cellular homo-oligomer, capable of mediating cell-cell adhesion, by using SAXS, XL-MS and bead aggregation assays. Second, we also show that EpCAM forms stable dimers on the surface of a cell with pre-formed cell-cell contacts using FLIM-FRET; however, no inter-cellular homo-oligomers were detectable. Thus, our study provides clear evidence that EpCAM indeed does not function as a homophilic cell adhesion molecule and therefore calls for a significant revision of its role in both normal and cancerous tissues. In the light of this, we strongly support the previously suggested name Epithelial Cell Activating Molecule instead of the Epithelial Cell Adhesion Molecule.
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Affiliation(s)
- Aljaž Gaber
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana, SI 1000, Slovenia
| | - Seung Joong Kim
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, 1700 4th Street, Suite 503B, San Francisco, CA, 94158, USA
| | - Robyn M Kaake
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, SI 1000, Slovenia
| | - Nevan Krogan
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute, QBI, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Andrej Šali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, 1700 4th Street, Suite 503B, San Francisco, CA, 94158, USA
| | - Miha Pavšič
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana, SI 1000, Slovenia.
| | - Brigita Lenarčič
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana, SI 1000, Slovenia.
- Department of Biochemistry, Molecular and Structural Biology, Institute Jožef Stefan, Jamova 39, Ljubljana, SI 1000, Slovenia.
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74
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Hägglund P, Mariotti M, Davies MJ. Identification and characterization of protein cross-links induced by oxidative reactions. Expert Rev Proteomics 2018; 15:665-681. [DOI: 10.1080/14789450.2018.1509710] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Per Hägglund
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Michele Mariotti
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael J. Davies
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
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75
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Schopfer LM, Lockridge O. Chlorpyrifos oxon promotes tubulin aggregation via isopeptide cross-linking between diethoxyphospho-Lys and Glu or Asp: Implications for neurotoxicity. J Biol Chem 2018; 293:13566-13577. [PMID: 30006344 PMCID: PMC6120212 DOI: 10.1074/jbc.ra118.004172] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/09/2018] [Indexed: 11/06/2022] Open
Abstract
Exposure to organophosphorus toxicants (OP) can have chronic adverse effects that are not explained by inhibition of acetylcholinesterase, the cause of acute OP toxicity. We therefore hypothesized that OP-induced chronic illness is initiated by the formation of organophosphorus adducts on lysine residues in proteins, followed by protein cross-linking and aggregation. Here, Western blots revealed that exposure to the OP chlorpyrifos oxon converted porcine tubulin from its original 55-kDa mass to high-molecular-weight aggregates. Liquid chromatography–tandem MS analysis of trypsin-digested samples identified several diethoxyphospho-lysine residues in the OP-treated tubulin. Using a search approach based on the Batch Tag program, we identified cross-linked peptides and found that these chemically activated lysines reacted with acidic amino acid residues creating γ-glutamyl-ϵ-lysine or aspartyl-ϵ-lysine isopeptide bonds between β- and α-tubulin. Of note, these cross-linked tubulin molecules accounted for the high-molecular-weight aggregates. To the best of our knowledge, this is the first report indicating that chlorpyrifos oxon–exposed tubulin protein forms intermolecular cross-links with other tubulin molecules, resulting in high-molecular-weight protein aggregates. It is tempting to speculate that chronic illness from OP exposure may be explained by a mechanism that starts with OP adduct formation on protein lysines followed by protein cross-linking. We further speculate that OP-modified or cross-linked tubulin can impair axonal transport, reduce neuron connections, and result in neurotoxicity.
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Affiliation(s)
- Lawrence M Schopfer
- From the Eppley Institute, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900
| | - Oksana Lockridge
- From the Eppley Institute, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900
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76
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Lu L, Millikin RJ, Solntsev SK, Rolfs Z, Scalf M, Shortreed MR, Smith LM. Identification of MS-Cleavable and Noncleavable Chemically Cross-Linked Peptides with MetaMorpheus. J Proteome Res 2018; 17:2370-2376. [PMID: 29793340 DOI: 10.1021/acs.jproteome.8b00141] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein chemical cross-linking combined with mass spectrometry has become an important technique for the analysis of protein structure and protein-protein interactions. A variety of cross-linkers are well developed, but reliable, rapid, and user-friendly tools for large-scale analysis of cross-linked proteins are still in need. Here we report MetaMorpheusXL, a new search module within the MetaMorpheus software suite that identifies both MS-cleavable and noncleavable cross-linked peptides in MS data. MetaMorpheusXL identifies MS-cleavable cross-linked peptides with an ion-indexing algorithm, which enables an efficient large database search. The identification does not require the presence of signature fragment ions, an advantage compared with similar programs such as XlinkX. One complication associated with the need for signature ions from cleavable cross-linkers such as DSSO (disuccinimidyl sulfoxide) is the requirement for multiple fragmentation types and energy combinations, which is not necessary for MetaMorpheusXL. The ability to perform proteome-wide analysis is another advantage of MetaMorpheusXL compared with programs such as MeroX and DXMSMS. MetaMorpheusXL is also faster than other currently available MS-cleavable cross-link search software programs. It is imbedded in MetaMorpheus, an open-source and freely available software suite that provides a reliable, fast, user-friendly graphical user interface that is readily accessible to researchers.
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77
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Pap A, Klement E, Hunyadi-Gulyas E, Darula Z, Medzihradszky KF. Status Report on the High-Throughput Characterization of Complex Intact O-Glycopeptide Mixtures. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1210-1220. [PMID: 29730764 DOI: 10.1007/s13361-018-1945-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 06/08/2023]
Abstract
A very complex mixture of intact, human N- and O-glycopeptides, enriched from the tryptic digest of urinary proteins of three healthy donors using a two-step lectin affinity enrichment, was analyzed by LC-MS/MS, leading to approximately 45,000 glycopeptide EThcD spectra. Two search engines, Byonic and Protein Prospector, were used for the interpretation of the data, and N- and O-linked glycopeptides were assigned from separate searches. The identification rate was very low in all searches, even when results were combined. Thus, we investigated the reasons why was it so, to help to improve the identification success rate. Focusing on O-linked glycopeptides, we noticed that in EThcD, larger glycan oxonium ions better survive the activation than those in HCD. These fragments, combined with reducing terminal Y ions, provide important information about the glycan(s) present, so we investigated whether filtering the peaklists for glycan oxonium ions indicating the presence of a tetra- or hexasaccharide structure would help to reveal all molecules containing such glycans. Our study showed that intact glycans frequently do not survive even mild supplemental activation, meaning one cannot rely on these oxonium ions exclusively. We found that ETD efficiency is still a limiting factor, and for highly glycosylated peptides, the only information revealed in EThcD was related to the glycan structures. The limited overlap of results delivered by the two search engines draws attention to the fact that automated data interpretation of O-linked glycopeptides is not even close to being solved. Graphical abstract ᅟ.
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Affiliation(s)
- Adam Pap
- Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Eva Klement
- Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Eva Hunyadi-Gulyas
- Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Zsuzsanna Darula
- Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.
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78
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Chu F, Thornton DT, Nguyen HT. Chemical cross-linking in the structural analysis of protein assemblies. Methods 2018; 144:53-63. [PMID: 29857191 DOI: 10.1016/j.ymeth.2018.05.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/22/2018] [Accepted: 05/25/2018] [Indexed: 12/31/2022] Open
Abstract
For decades, chemical cross-linking of proteins has been an established method to study protein interaction partners. The chemical cross-linking approach has recently been revived by mass spectrometric analysis of the cross-linking reaction products. Chemical cross-linking and mass spectrometric analysis (CXMS) enables the identification of residues that are close in three-dimensional (3D) space but not necessarily close in primary sequence. Therefore, this approach provides medium resolution information to guide de novo structure prediction, protein interface mapping and protein complex model building. The robustness and compatibility of the CXMS approach with multiple biochemical methods have made it especially appealing for challenging systems with multiple biochemical compositions and conformation states. This review provides an overview of the CXMS approach, describing general procedures in sample processing, data acquisition and analysis. Selection of proper chemical cross-linking reagents, strategies for cross-linked peptide identification, and successful application of CXMS in structural characterization of proteins and protein complexes are discussed.
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Affiliation(s)
- Feixia Chu
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States; Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, United States.
| | - Daniel T Thornton
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States
| | - Hieu T Nguyen
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States
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79
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Mohr JP, Perumalla P, Chavez JD, Eng JK, Bruce JE. Mango: A General Tool for Collision Induced Dissociation-Cleavable Cross-Linked Peptide Identification. Anal Chem 2018; 90:6028-6034. [PMID: 29676898 PMCID: PMC5959040 DOI: 10.1021/acs.analchem.7b04991] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Chemical cross-linking combined with mass spectrometry provides a method to study protein structures and interactions. The introduction of cleavable bonds in a cross-linker provides an avenue to decouple released peptide masses from their precursor species, greatly simplifying the downstream search, allowing for whole proteome investigations to be performed. Typically, these experiments have been challenging to carry out, often utilizing nonstandard methods to fully identify cross-linked peptides. Mango is an open source software tool that extracts precursor masses from chimeric spectra generated using cleavable cross-linkers, greatly simplifying the downstream search. As it is designed to work with chimeric spectra, Mango can be used on traditional high-resolution tandem mass spectrometry (MS/MS) capable mass spectrometers without the need for additional modifications. When paired with a traditional proteomics search engine, Mango can be used to identify several thousand cross-linked peptide pairs searching against the entire Escherichia coli proteome. Mango provides an avenue to perform whole proteome cross-linking experiments without specialized instrumentation or access to nonstandard methods.
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Affiliation(s)
- Jared P. Mohr
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - Poorna Perumalla
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - Juan D. Chavez
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - Jimmy K. Eng
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - James E. Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
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80
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Gamarra N, Johnson SL, Trnka MJ, Burlingame AL, Narlikar GJ. The nucleosomal acidic patch relieves auto-inhibition by the ISWI remodeler SNF2h. eLife 2018; 7:35322. [PMID: 29664398 PMCID: PMC5976439 DOI: 10.7554/elife.35322] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/16/2018] [Indexed: 12/12/2022] Open
Abstract
ISWI family chromatin remodeling motors use sophisticated autoinhibition mechanisms to control nucleosome sliding. Yet how the different autoinhibitory domains are regulated is not well understood. Here we show that an acidic patch formed by histones H2A and H2B of the nucleosome relieves the autoinhibition imposed by the AutoN and the NegC regions of the human ISWI remodeler SNF2h. Further, by single molecule FRET we show that the acidic patch helps control the distance travelled per translocation event. We propose a model in which the acidic patch activates SNF2h by providing a landing pad for the NegC and AutoN auto-inhibitory domains. Interestingly, the INO80 complex is also strongly dependent on the acidic patch for nucleosome sliding, indicating that this substrate feature can regulate remodeling enzymes with substantially different mechanisms. We therefore hypothesize that regulating access to the acidic patch of the nucleosome plays a key role in coordinating the activities of different remodelers in the cell. Every human cell contains nearly two meters of DNA, which is carefully packaged to form a dense structure known as chromatin. The building block of chromatin is the nucleosome, a unit composed of a short section of DNA tightly wound up around a spool-like core of proteins called histones. The tight structure of the nucleosome prevents the cell from accessing and ‘reading’ the genes in the packaged DNA, effectively switching off these genes. So the exact placement of nucleosomes helps manage which genes are turned on. Changing the position of the nucleosomes can ‘free’ the DNA and make genes available to the cell. Enzymes called chromatin remodelers move nucleosomes around – for example, they can make the histone core slide on the DNA strand. However, it is still unclear how these enzymes recognize nucleosomes. Previous research indicates that many proteins bind to nucleosomes by using a surface on the histone proteins called the acidic patch. Could chromatin remodelers also work by interacting with this acidic patch? To address this further, Gamarra et al. investigate how a chromatin remodeler enzyme known as SNF2h interacts with a nucleosome. By default, SNF2h is inactive because two of its regions called AutoN and NegC act as brakes. The experiments show that the acidic patch helps to bypass this inactivation and switches on SNF2h. Gamarra et al. propose that, when SNF2h docks on to the nucleosome, the patch provides a landing pad for the AutoN and NegC modules; this interaction activates the enzyme, which can then start remodeling the nucleosome. However, another type of chromatin remodeler also uses the patch to interact with nucleosomes but it does not have the AutoN and NegC regions. This suggests that chromatin remodelers work with the acidic patch in different ways. Overall, the findings deepen our understanding of how DNA is packaged in cells, and how this process may go wrong and cause disease.
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Affiliation(s)
- Nathan Gamarra
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.,Tetrad Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Stephanie L Johnson
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
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81
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Mariotti M, Leinisch F, Leeming DJ, Svensson B, Davies MJ, Hägglund P. Mass-Spectrometry-Based Identification of Cross-Links in Proteins Exposed to Photo-Oxidation and Peroxyl Radicals Using 18O Labeling and Optimized Tandem Mass Spectrometry Fragmentation. J Proteome Res 2018; 17:2017-2027. [DOI: 10.1021/acs.jproteome.7b00881] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Michele Mariotti
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, Kongens Lyngby, DK 2800 Denmark
| | - Fabian Leinisch
- Department of Biomedical Sciences, University of Copenhagen, Nørregade 10, Copenhagen, DK-1017 Denmark
| | | | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, Kongens Lyngby, DK 2800 Denmark
| | - Michael J. Davies
- Department of Biomedical Sciences, University of Copenhagen, Nørregade 10, Copenhagen, DK-1017 Denmark
| | - Per Hägglund
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, Kongens Lyngby, DK 2800 Denmark
- Department of Biomedical Sciences, University of Copenhagen, Nørregade 10, Copenhagen, DK-1017 Denmark
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82
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Wysoczynski-Horita CL, Boursier ME, Hill R, Hansen K, Blackwell HE, Churchill MEA. Mechanism of agonism and antagonism of the Pseudomonas aeruginosa quorum sensing regulator QscR with non-native ligands. Mol Microbiol 2018; 108:240-257. [PMID: 29437248 DOI: 10.1111/mmi.13930] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2018] [Indexed: 12/25/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that uses the process of quorum sensing (QS) to coordinate the expression of many virulence genes. During quorum sensing, N-acyl-homoserine lactone (AHL) signaling molecules regulate the activity of three LuxR-type transcription factors, LasR, RhlR and QscR. To better understand P. aeruginosa QS signal reception, we examined the mechanism underlying the response of QscR to synthetic agonists and antagonists using biophysical and structural approaches. The structure of QscR bound to a synthetic agonist reveals a novel mode of ligand binding supporting a general mechanism for agonist activity. In turn, antagonists of QscR with partial agonist activity were found to destabilize and greatly impair QscR dimerization and DNA binding. These results highlight the diversity of LuxR-type receptor responses to small molecule agonists and antagonists and demonstrate the potential for chemical strategies for the selective targeting of individual QS systems.
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Affiliation(s)
- Christina L Wysoczynski-Horita
- Department of Pharmacology and Program in Structural Biology and Biochemistry, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | | | - Ryan Hill
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kirk Hansen
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Mair E A Churchill
- Department of Pharmacology and Program in Structural Biology and Biochemistry, University of Colorado School of Medicine, Aurora, CO 80045, USA
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83
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Zhou CY, Stoddard CI, Johnston JB, Trnka MJ, Echeverria I, Palovcak E, Sali A, Burlingame AL, Cheng Y, Narlikar GJ. Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones. Cell Rep 2018; 19:2033-2044. [PMID: 28591576 DOI: 10.1016/j.celrep.2017.05.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 04/05/2017] [Accepted: 05/09/2017] [Indexed: 12/18/2022] Open
Abstract
The hexameric AAA+ ATPases Rvb1 and Rvb2 (Rvbs) are essential for diverse processes ranging from metabolic signaling to chromatin remodeling, but their functions are unknown. While originally thought to act as helicases, recent proposals suggest that Rvbs act as protein assembly chaperones. However, experimental evidence for chaperone-like behavior is lacking. Here, we identify a potent protein activator of the Rvbs, a domain in the Ino80 ATPase subunit of the INO80 chromatin-remodeling complex, termed Ino80INS. Ino80INS stimulates Rvbs' ATPase activity by 16-fold while concomitantly promoting their dodecamerization. Using mass spectrometry, cryo-EM, and integrative modeling, we find that Ino80INS binds asymmetrically along the dodecamerization interface, resulting in a conformationally flexible dodecamer that collapses into hexamers upon ATP addition. Our results demonstrate the chaperone-like potential of Rvb1/Rvb2 and suggest a model where binding of multiple clients such as Ino80 stimulates ATP-driven cycling between hexamers and dodecamers, providing iterative opportunities for correct subunit assembly.
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Affiliation(s)
- Coral Y Zhou
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Caitlin I Stoddard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jonathan B Johnston
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ignacia Echeverria
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Eugene Palovcak
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute of Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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84
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Zhang J, Ye ZW, Chen W, Manevich Y, Mehrotra S, Ball L, Janssen-Heininger Y, Tew KD, Townsend DM. S-Glutathionylation of estrogen receptor α affects dendritic cell function. J Biol Chem 2018; 293:4366-4380. [PMID: 29374060 DOI: 10.1074/jbc.m117.814327] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 01/18/2018] [Indexed: 12/27/2022] Open
Abstract
Glutathione S-transferase Pi (GSTP) is a thiolase that catalyzes the addition of glutathione (GSH) to receptive cysteines in target proteins, producing an S-glutathionylated residue. Accordingly, previous studies have reported that S-glutathionylation is constitutively decreased in cells from mice lacking GSTP (Gstp1/p2-/-). Here, we found that bone marrow-derived dendritic cells (BMDDCs) from Gstp1/p2-/- mice have proliferation rates that are greater than those in their WT counterparts (Gstp1/p2+/+). Moreover, Gstp1/p2-/- BMDDCs had increased reactive oxygen species (ROS) levels and decreased GSH:glutathione disulfide (GSSG) ratios. Estrogen receptor α (ERα) is linked to myeloproliferation and differentiation, and we observed that its steady-state levels are elevated in Gstp1/p2-/- BMDDCs, indicating a link between GSTP and ERα activities. BMDDCs differentiated by granulocyte-macrophage colony-stimulating factor had elevated ERα levels, which were more pronounced in Gstp1/p2-/- than WT mice. When stimulated with lipopolysaccharide for maturation, Gstp1/p2-/- BMDDCs exhibited augmented endocytosis, maturation rate, cytokine secretion, and T-cell activation; heightened glucose uptake and glycolysis; increased Akt signaling (in the mTOR pathway); and decreased AMPK-mediated phosphorylation of proteins. Of note, GSTP formed a complex with ERα, stimulating ERα S-glutathionylation at cysteines 221, 245, 417, and 447; altering ERα's binding affinity for estradiol; and reducing overall binding potential (receptor density and affinity) 3-fold. Moreover, in Gstp1/p2-/- BMDDCs, ERα S-glutathionylation was constitutively decreased. Taken together, these findings suggest that GSTP-mediated S-glutathionylation of ERα controls BMDDC differentiation and affects metabolic function in dendritic cells.
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Affiliation(s)
- Jie Zhang
- From the Departments of Cell and Molecular Pharmacology and Experimental Therapeutics
| | - Zhi-Wei Ye
- From the Departments of Cell and Molecular Pharmacology and Experimental Therapeutics
| | - Wei Chen
- Department of Infectious Disease, the Second Affiliated Hospital of Medical School of the Southeast University, 1-1 Zhongfu Road, Nanjing 210003, China, and
| | - Yefim Manevich
- From the Departments of Cell and Molecular Pharmacology and Experimental Therapeutics
| | - Shikhar Mehrotra
- Surgery, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Lauren Ball
- From the Departments of Cell and Molecular Pharmacology and Experimental Therapeutics
| | - Yvonne Janssen-Heininger
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont 05405
| | - Kenneth D Tew
- From the Departments of Cell and Molecular Pharmacology and Experimental Therapeutics,
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85
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Yu C, Huang L. Cross-Linking Mass Spectrometry: An Emerging Technology for Interactomics and Structural Biology. Anal Chem 2018; 90:144-165. [PMID: 29160693 PMCID: PMC6022837 DOI: 10.1021/acs.analchem.7b04431] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Clinton Yu
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697
| | - Lan Huang
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697
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86
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Chavez JD, Lee CF, Caudal A, Keller A, Tian R, Bruce JE. Chemical Crosslinking Mass Spectrometry Analysis of Protein Conformations and Supercomplexes in Heart Tissue. Cell Syst 2017; 6:136-141.e5. [PMID: 29199018 DOI: 10.1016/j.cels.2017.10.017] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 09/05/2017] [Accepted: 10/25/2017] [Indexed: 12/16/2022]
Abstract
While modern structural biology technologies have greatly expanded the size and type of protein complexes that can now be studied, the ability to derive large-scale structural information on proteins and complexes as they exist within tissues is practically nonexistent. Here, we demonstrate the application of crosslinking mass spectrometry to identify protein structural features and interactions in tissue samples, providing systems structural biology insight into protein complexes as they exist in the mouse heart. This includes insights into multiple conformational states of sarcomere proteins, as well as interactions among OXPHOS complexes indicative of supercomplex assembly. The extension of crosslinking mass spectrometry analysis into the realm of tissues opens the door to increasing our understanding of protein structures and interactions within the context of the greater biological system.
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Affiliation(s)
- Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Chi Fung Lee
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA; Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98105, USA; Mitochondria and Metabolism Center, University of Washington, Seattle, WA 98105, USA
| | - Arianne Caudal
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA; Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98105, USA; Mitochondria and Metabolism Center, University of Washington, Seattle, WA 98105, USA
| | - Andrew Keller
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Rong Tian
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA; Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98105, USA; Mitochondria and Metabolism Center, University of Washington, Seattle, WA 98105, USA
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA.
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87
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Yang H, Chi H, Zhou WJ, Zeng WF, Liu C, Wang RM, Wang ZW, Niu XN, Chen ZL, He SM. pSite: Amino Acid Confidence Evaluation for Quality Control of De Novo Peptide Sequencing and Modification Site Localization. J Proteome Res 2017; 17:119-128. [DOI: 10.1021/acs.jproteome.7b00428] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hao Yang
- Key
Lab 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
| | - Hao Chi
- Key
Lab of Intelligent Information Processing of Chinese Academy of Sciences
(CAS), Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Wen-Jing Zhou
- Key
Lab 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
| | - Wen-Feng Zeng
- Key
Lab 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
| | - Chao Liu
- Key
Lab of Intelligent Information Processing of Chinese Academy of Sciences
(CAS), Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Rui-Min Wang
- Key
Lab 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
| | - Zhao-Wei Wang
- Key
Lab 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
| | - Xiu-Nan Niu
- Key
Lab 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
Lab 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
| | - Si-Min He
- Key
Lab 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
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88
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Webb B, Viswanath S, Bonomi M, Pellarin R, Greenberg CH, Saltzberg D, Sali A. Integrative structure modeling with the Integrative Modeling Platform. Protein Sci 2017; 27:245-258. [PMID: 28960548 DOI: 10.1002/pro.3311] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/23/2017] [Accepted: 09/25/2017] [Indexed: 11/06/2022]
Abstract
Building models of a biological system that are consistent with the myriad data available is one of the key challenges in biology. Modeling the structure and dynamics of macromolecular assemblies, for example, can give insights into how biological systems work, evolved, might be controlled, and even designed. Integrative structure modeling casts the building of structural models as a computational optimization problem, for which information about the assembly is encoded into a scoring function that evaluates candidate models. Here, we describe our open source software suite for integrative structure modeling, Integrative Modeling Platform (https://integrativemodeling.org), and demonstrate its use.
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Affiliation(s)
- Benjamin Webb
- California Institute for Quantitative Biosciences, University of California, San Francisco, California, 94158
| | - Shruthi Viswanath
- California Institute for Quantitative Biosciences, University of California, San Francisco, California, 94158
| | | | - Riccardo Pellarin
- Structural Bioinformatics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France
| | - Charles H Greenberg
- California Institute for Quantitative Biosciences, University of California, San Francisco, California, 94158
| | - Daniel Saltzberg
- California Institute for Quantitative Biosciences, University of California, San Francisco, California, 94158
| | - Andrej Sali
- California Institute for Quantitative Biosciences, University of California, San Francisco, California, 94158
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89
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Karagöz GE, Acosta-Alvear D, Nguyen HT, Lee CP, Chu F, Walter P. An unfolded protein-induced conformational switch activates mammalian IRE1. eLife 2017; 6:30700. [PMID: 28971800 PMCID: PMC5699868 DOI: 10.7554/elife.30700] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/02/2017] [Indexed: 12/17/2022] Open
Abstract
The unfolded protein response (UPR) adjusts the cell’s protein folding capacity in the endoplasmic reticulum (ER) according to need. IRE1 is the most conserved UPR sensor in eukaryotic cells. It has remained controversial, however, whether mammalian and yeast IRE1 use a common mechanism for ER stress sensing. Here, we show that similar to yeast, human IRE1α’s ER-lumenal domain (hIRE1α LD) binds peptides with a characteristic amino acid bias. Peptides and unfolded proteins bind to hIRE1α LD’s MHC-like groove and induce allosteric changes that lead to its oligomerization. Mutation of a hydrophobic patch at the oligomerization interface decoupled peptide binding to hIRE1α LD from its oligomerization, yet retained peptide-induced allosteric coupling within the domain. Importantly, impairing oligomerization of hIRE1α LD abolished IRE1’s activity in living cells. Our results provide evidence for a unifying mechanism of IRE1 activation that relies on unfolded protein binding-induced oligomerization. Proteins are long string-like molecules that fold into specific three-dimensional shapes. Most proteins that a cell uses to communicate with its environment are folded within a part of the cell called the endoplasmic reticulum. Dedicated sensor proteins in this cellular compartment track this process to make sure that it continues to meet the cell’s demand for protein folding. If it cannot meet the demand, unfolded or poorly folded proteins build up, which stresses the cell. IRE1 is a sensor protein that detects stress in the endoplasmic reticulum. It is found in a range of organisms from yeast to humans, where it spans the membrane that encloses the endoplasmic reticulum. When unfolded proteins accumulate, IRE1 proteins come together and form so-called oligomers. The IRE1 oligomers then become active and send signals outside of the endoplasmic reticulum. These signals adjust the cell’s protein-folding capacity according to its needs at that time. The yeast version of IRE1 directly recognizes unfolded proteins in the endoplasmic reticulum. Yet, its human counterpart was found to have a different three-dimensional structure, which suggested that it might use a different mechanism to detect the stress. Now, Karagöz et al. show that, as in yeast, the sensor part of human IRE1 does indeed bind to unfolded proteins directly. This binding causes this part of the protein to engage other copies of IRE1 and form the oligomers. To understand this interaction in more detail, Karagöz et al. used a technique called nuclear magnetic resonance spectroscopy to monitor changes in the shape of proteins. These observations revealed that binding to an unfolded protein causes other parts of IRE1 protein to change shape. In turn, these shape changes act as a switch that causes the oligomers to form. Stopping the sensor domains from forming oligomers inactivated the IRE1 protein in mammalian cells; this rendered IRE1 unresponsive to stress within the endoplasmic reticulum. The regulation of IRE1 affects many health disorders, including diabetes, cancer and neurodegenerative diseases. By showing that unfolded proteins switch IRE1 into its active, oligomeric state, these findings might lead to new approaches to manipulate IRE1’s activity with small molecules to help to treat these diseases.
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Affiliation(s)
- G Elif Karagöz
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Diego Acosta-Alvear
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Hieu T Nguyen
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, United States
| | - Crystal P Lee
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Feixia Chu
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, United States
| | - Peter Walter
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
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90
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Hage C, Falvo F, Schäfer M, Sinz A. Novel Concepts of MS-Cleavable Cross-linkers for Improved Peptide Structure Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2022-2038. [PMID: 28653243 DOI: 10.1007/s13361-017-1712-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/03/2017] [Accepted: 05/07/2017] [Indexed: 06/07/2023]
Abstract
The chemical cross-linking/mass spectrometry (MS) approach is gaining increasing importance as an alternative method for studying protein conformation and for deciphering protein interaction networks. This study is part of our ongoing efforts to develop innovative cross-linking principles for a facile and efficient assignment of cross-linked products. We evaluate two homobifunctional, amine-reactive, and MS-cleavable cross-linkers regarding their potential for automated analysis of cross-linked products. We introduce the bromine phenylurea (BrPU) linker that possesses a unique structure yielding a distinctive fragmentation pattern on collisional activation. Moreover, BrPU delivers the characteristic bromine isotope pattern and mass defect for all cross-linker-decorated fragments. We compare the fragmentation behavior of the BrPU linker with that of our previously described MS-cleavable TEMPO-Bz linker (which consists of a 2,2,6,6-tetramethylpiperidine-1-oxy moiety connected to a benzyl group) that was developed to perform free-radical-initiated peptide sequencing. Comparative collisional activation experiments (collision-induced dissociation and higher-energy collision-induced dissociation) with both cross-linkers were conducted in negative electrospray ionization mode with an Orbitrap Fusion mass spectrometer using five model peptides. As hypothesized in a previous study, the presence of a cross-linked N-terminal aspartic acid residue seems to be the prerequisite for the loss of an intact peptide from the cross-linked products. As the BrPU linker combines a characteristic mass shift with an isotope signature, it presents a more favorable combination for automated assignment of cross-linked products compared with the TEMPO-Bz linker. ᅟ.
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Affiliation(s)
- Christoph Hage
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany
| | - Francesco Falvo
- Department of Chemistry, University of Cologne, Greinstr. 4, 50939, Cologne, Germany
- Eurofins Umwelt West GmbH, Vorgebirgsstr. 20, 50389, Wesseling, Germany
| | - Mathias Schäfer
- Department of Chemistry, University of Cologne, Greinstr. 4, 50939, Cologne, Germany
| | - Andrea Sinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany.
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91
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Schmidt C, Urlaub H. Combining cryo-electron microscopy (cryo-EM) and cross-linking mass spectrometry (CX-MS) for structural elucidation of large protein assemblies. Curr Opin Struct Biol 2017; 46:157-168. [DOI: 10.1016/j.sbi.2017.10.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/21/2017] [Accepted: 10/05/2017] [Indexed: 01/11/2023]
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92
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Iacobucci C, Hage C, Schäfer M, Sinz A. A Novel MS-Cleavable Azo Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2039-2053. [PMID: 28717933 DOI: 10.1007/s13361-017-1744-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/13/2017] [Accepted: 06/15/2017] [Indexed: 06/07/2023]
Abstract
The chemical cross-linking/mass spectrometry (MS) approach is a growing research field in structural proteomics that allows gaining insights into protein conformations. It relies on creating distance constraints between cross-linked amino acid side chains that can further be used to derive protein structures. Currently, the most urgent task for designing novel cross-linking principles is an unambiguous and automated assignment of the created cross-linked products. Here, we introduce the homobifunctional, amine-reactive, and water soluble cross-linker azobisimidoester (ABI) as a prototype of a novel class of cross-linkers. The ABI-linker possesses an innovative modular scaffold combining the benefits of collisional activation lability with open shell chemistry. This MS-cleavable cross-linker can be efficiently operated via free radical initiated peptide sequencing (FRIPS) in positive ionization mode. Our proof-of-principle study challenges the gas phase behavior of the ABI-linker for the three amino acids, lysine, leucine, and isoleucine, as well as the model peptide thymopentin. The isomeric amino acids leucine and isoleucine could be discriminated by their characteristic side chain fragments. Collisional activation experiments were conducted via positive electrospray ionization (ESI) on two Orbitrap mass spectrometers. The ABI-mediated formation of odd electron product ions in MS/MS and MS3 experiments was evaluated and compared with a previously described azo-based cross-linker. All cross-linked products were amenable to automated analysis by the MeroX software, underlining the future potential of the ABI-linker for structural proteomics studies. Graphical Abstract ᅟ.
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Affiliation(s)
- Claudio Iacobucci
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle (Saale), Germany.
| | - Christoph Hage
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle (Saale), Germany
| | - Mathias Schäfer
- Department of Chemistry, Institute of Organic Chemistry, University of Cologne, Greinstr. 4, D-50939, Kӧln, Germany
| | - Andrea Sinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle (Saale), Germany.
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93
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Loquacious-PD facilitates Drosophila Dicer-2 cleavage through interactions with the helicase domain and dsRNA. Proc Natl Acad Sci U S A 2017; 114:E7939-E7948. [PMID: 28874570 DOI: 10.1073/pnas.1707063114] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Loquacious-PD (Loqs-PD) is required for biogenesis of many endogenous siRNAs in Drosophila In vitro, Loqs-PD enhances the rate of dsRNA cleavage by Dicer-2 and also enables processing of substrates normally refractory to cleavage. Using purified components, and Loqs-PD truncations, we provide a mechanistic basis for Loqs-PD functions. Our studies indicate that the 22 amino acids at the C terminus of Loqs-PD, including an FDF-like motif, directly interact with the Hel2 subdomain of Dicer-2's helicase domain. This interaction is RNA-independent, but we find that modulation of Dicer-2 cleavage also requires dsRNA binding by Loqs-PD. Furthermore, while the first dsRNA-binding motif of Loqs-PD is dispensable for enhancing cleavage of optimal substrates, it is essential for enhancing cleavage of suboptimal substrates. Finally, our studies define a previously unrecognized Dicer interaction interface and suggest that Loqs-PD is well positioned to recruit substrates into the helicase domain of Dicer-2.
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94
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Yu F, Li N, Yu W. Exhaustively Identifying Cross-Linked Peptides with a Linear Computational Complexity. J Proteome Res 2017; 16:3942-3952. [PMID: 28825304 DOI: 10.1021/acs.jproteome.7b00338] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Chemical cross-linking coupled to mass spectrometry is a powerful tool to study protein-protein interactions and protein conformations. Two linked peptides are ionized and fragmented to produce a tandem mass spectrum. In such an experiment, a tandem mass spectrum contains ions from two peptides. The peptide identification problem becomes a peptide-peptide pair identification problem. Currently, most tools do not search all possible pairs due to the quadratic time complexity. Consequently, missed findings are unavoidable. In our previous work, we developed a tool named ECL to search all pairs of peptides exhaustively. Unfortunately, it is very slow due to the quadratic computational complexity, especially when the database is large. Furthermore, ECL uses a score function without statistical calibration, while researchers1-3 have proposed that it is inappropriate to directly compare uncalibrated scores because different spectra have different random score distributions. Here we propose an advanced version of ECL, named ECL2. It achieves a linear time and space complexity by taking advantage of the additive property of a score function. It can search a data set containing tens of thousands of spectra against a database containing thousands of proteins in a few hours. Comparison with other five state-of-the-art tools shows that ECL2 is much faster than pLink, StavroX, ProteinProspector, and ECL. Kojak is the only one that is faster than ECL2, but Kojak does not exhaustively search all possible peptide pairs. The comparison shows that ECL2 has the highest sensitivity among the state-of-the-art tools. The experiment using a large-scale in vivo cross-linking data set demonstrates that ECL2 is the only tool that can find the peptide-spectrum matches (PSMs) passing the false discovery rate/q-value threshold. The result illustrates that the exhaustive search and a well-calibrated score function are useful to find PSMs from a huge search space.
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Affiliation(s)
- Fengchao Yu
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology , Hong Kong, China
| | - Ning Li
- Division of Life Science, The Hong Kong University of Science and Technology , Hong Kong, China.,Division of Biomedical Engineering, The Hong Kong University of Science and Technology , Hong Kong, China
| | - Weichuan Yu
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology , Hong Kong, China.,Division of Biomedical Engineering, The Hong Kong University of Science and Technology , Hong Kong, China
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95
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Maes E, Dyer JM, McKerchar HJ, Deb-Choudhury S, Clerens S. Protein-protein cross-linking and human health: the challenge of elucidating with mass spectrometry. Expert Rev Proteomics 2017; 14:917-929. [PMID: 28759730 DOI: 10.1080/14789450.2017.1362336] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
INTRODUCTION In several biomedical research fields, the cross-linking of peptides and proteins has an important impact on health and wellbeing. It is therefore of crucial importance to study this class of post-translational modifications in detail. The huge potential of mass spectrometric technologies in the mapping of these protein-protein cross-links is however overshadowed by the challenges that the field has to overcome. Areas covered: In this review, we summarize the different pitfalls and challenges that the protein-protein cross-linking field is confronted with when using mass spectrometry approaches. We additionally focus on native disulfide bridges as an example and provide some examples of cross-links that are important in the biomedical field. Expert commentary: The current flow of methodological improvements, mainly from the chemical cross-linking field, has delivered a significant contribution to deciphering native and insult-induced cross-links. Although an automated data analysis of proteome-wide peptide cross-linking is currently only possible in chemical cross-linking experiments, the field is well on the way towards a more automated analysis of native and insult-induced cross-links in raw mass spectrometry data that will boost its potential in biomedical applications.
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Affiliation(s)
- Evelyne Maes
- a Food & Bio-Based Products, AgResearch Ltd ., Lincoln , New Zealand
| | - Jolon M Dyer
- a Food & Bio-Based Products, AgResearch Ltd ., Lincoln , New Zealand.,b Biomolecular Interaction Centre , University of Canterbury , Christchurch , New Zealand.,c Riddet Institute, Massey University , Palmerston North , New Zealand.,d Wine, Food & Molecular Biosciences , Lincoln University , Lincoln , New Zealand
| | - Hannah J McKerchar
- a Food & Bio-Based Products, AgResearch Ltd ., Lincoln , New Zealand.,b Biomolecular Interaction Centre , University of Canterbury , Christchurch , New Zealand
| | | | - Stefan Clerens
- a Food & Bio-Based Products, AgResearch Ltd ., Lincoln , New Zealand.,b Biomolecular Interaction Centre , University of Canterbury , Christchurch , New Zealand
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96
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Larson AG, Elnatan D, Keenen MM, Trnka MJ, Johnston JB, Burlingame AL, Agard DA, Redding S, Narlikar GJ. Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin. Nature 2017; 547:236-240. [PMID: 28636604 PMCID: PMC5606208 DOI: 10.1038/nature22822] [Citation(s) in RCA: 1099] [Impact Index Per Article: 157.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 05/16/2017] [Indexed: 01/15/2023]
Abstract
Gene silencing by heterochromatin is proposed to occur in part as a result of the ability of heterochromatin protein 1 (HP1) proteins to spread across large regions of the genome, compact the underlying chromatin and recruit diverse ligands. Here we identify a new property of the human HP1α protein: the ability to form phase-separated droplets. While unmodified HP1α is soluble, either phosphorylation of its N-terminal extension or DNA binding promotes the formation of phase-separated droplets. Phosphorylation-driven phase separation can be promoted or reversed by specific HP1α ligands. Known components of heterochromatin such as nucleosomes and DNA preferentially partition into the HP1α droplets, but molecules such as the transcription factor TFIIB show no preference. Using a single-molecule DNA curtain assay, we find that both unmodified and phosphorylated HP1α induce rapid compaction of DNA strands into puncta, although with different characteristics. We show by direct protein delivery into mammalian cells that an HP1α mutant incapable of phase separation in vitro forms smaller and fewer nuclear puncta than phosphorylated HP1α. These findings suggest that heterochromatin-mediated gene silencing may occur in part through sequestration of compacted chromatin in phase-separated HP1 droplets, which are dissolved or formed by specific ligands on the basis of nuclear context.
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Affiliation(s)
- Adam G. Larson
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daniel Elnatan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Madeline M. Keenen
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael J. Trnka
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jonathan B. Johnston
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alma L. Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David A. Agard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sy Redding
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Geeta J. Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
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97
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Vizcaíno JA, Mayer G, Perkins S, Barsnes H, Vaudel M, Perez-Riverol Y, Ternent T, Uszkoreit J, Eisenacher M, Fischer L, Rappsilber J, Netz E, Walzer M, Kohlbacher O, Leitner A, Chalkley RJ, Ghali F, Martínez-Bartolomé S, Deutsch EW, Jones AR. The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics. Mol Cell Proteomics 2017; 16:1275-1285. [PMID: 28515314 PMCID: PMC5500760 DOI: 10.1074/mcp.m117.068429] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/15/2017] [Indexed: 12/31/2022] Open
Abstract
The first stable version of the Proteomics Standards Initiative mzIdentML open data standard (version 1.1) was published in 2012-capturing the outputs of peptide and protein identification software. In the intervening years, the standard has become well-supported in both commercial and open software, as well as a submission and download format for public repositories. Here we report a new release of mzIdentML (version 1.2) that is required to keep pace with emerging practice in proteome informatics. New features have been added to support: (1) scores associated with localization of modifications on peptides; (2) statistics performed at the level of peptides; (3) identification of cross-linked peptides; and (4) support for proteogenomics approaches. In addition, there is now improved support for the encoding of de novo sequencing of peptides, spectral library searches, and protein inference. As a key point, the underlying XML schema has only undergone very minor modifications to simplify as much as possible the transition from version 1.1 to version 1.2 for implementers, but there have been several notable updates to the format specification, implementation guidelines, controlled vocabularies and validation software. mzIdentML 1.2 can be described as backwards compatible, in that reading software designed for mzIdentML 1.1 should function in most cases without adaptation. We anticipate that these developments will provide a continued stable base for software teams working to implement the standard. All the related documentation is accessible at http://www.psidev.info/mzidentml.
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Affiliation(s)
- Juan Antonio Vizcaíno
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Gerhard Mayer
- §Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Simon Perkins
- ¶Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Harald Barsnes
- ‖Proteomics Unit, Department of Biomedicine, University of Bergen, Norway
- **Computational Biology Unit, Department of Informatics, University of Bergen, Norway
- ‡‡KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Norway
| | - Marc Vaudel
- ‖Proteomics Unit, Department of Biomedicine, University of Bergen, Norway
- ‡‡KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Norway
- §§Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Yasset Perez-Riverol
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Tobias Ternent
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Julian Uszkoreit
- §Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Martin Eisenacher
- §Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Lutz Fischer
- ¶¶Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Juri Rappsilber
- ¶¶Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- ‖‖Chair of Bioanalytics, Institute of Biotechnology Technische Universität Berlin, 13355 Berlin, Germany
| | - Eugen Netz
- Biomolecular Interactions group, Max Planck Institute for Developmental Biology, Tübingen D-72076, Germany
| | - Mathias Walzer
- Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany
| | - Oliver Kohlbacher
- Biomolecular Interactions group, Max Planck Institute for Developmental Biology, Tübingen D-72076, Germany
- Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany
- Dept. of Computer Science, University of Tübingen, Germany
- Quantitative Biology Center, University of Tübingen, Germany
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland
| | - Robert J Chalkley
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94143
| | - Fawaz Ghali
- ¶Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Salvador Martínez-Bartolomé
- Department of Chemical Physiology, The Scripps Research Institute, 10550, N. Torrey Pines Rd., La Jolla, California, 92037
| | | | - Andrew R Jones
- ¶Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK;
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98
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de Jong L, de Koning EA, Roseboom W, Buncherd H, Wanner MJ, Dapic I, Jansen PJ, van Maarseveen JH, Corthals GL, Lewis PJ, Hamoen LW, de Koster CG. In-Culture Cross-Linking of Bacterial Cells Reveals Large-Scale Dynamic Protein-Protein Interactions at the Peptide Level. J Proteome Res 2017; 16:2457-2471. [PMID: 28516784 PMCID: PMC5504490 DOI: 10.1021/acs.jproteome.7b00068] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Identification of
dynamic protein–protein interactions at
the peptide level on a proteomic scale is a challenging approach that
is still in its infancy. We have developed a system to cross-link
cells directly in culture with the special lysine cross-linker bis(succinimidyl)-3-azidomethyl-glutarate
(BAMG). We used the Gram-positive model bacterium Bacillus
subtilis as an exemplar system. Within 5 min extensive intracellular
cross-linking was detected, while intracellular cross-linking in a
Gram-negative species, Escherichia coli, was still
undetectable after 30 min, in agreement with the low permeability
in this organism for lipophilic compounds like BAMG. We were able
to identify 82 unique interprotein cross-linked peptides with <1%
false discovery rate by mass spectrometry and genome-wide database
searching. Nearly 60% of the interprotein cross-links occur in assemblies
involved in transcription and translation. Several of these interactions
are new, and we identified a binding site between the δ and
β′ subunit of RNA polymerase close to the downstream
DNA channel, providing a clue into how δ might regulate promoter
selectivity and promote RNA polymerase recycling. Our methodology
opens new avenues to investigate the functional dynamic organization
of complex protein assemblies involved in bacterial growth. Data are
available via ProteomeXchange with identifier PXD006287.
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Affiliation(s)
| | | | | | - Hansuk Buncherd
- Faculty of Medical Technology, Prince of Songkla University , Hatyai, Songkhla 90110, Thailand
| | | | | | | | | | | | - Peter J Lewis
- School of Environmental and Life Sciences, University of Newcastle , Callaghan, New South Wales 2308, Australia
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99
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Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification. Nat Commun 2017; 8:15473. [PMID: 28524877 PMCID: PMC5454533 DOI: 10.1038/ncomms15473] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/30/2017] [Indexed: 12/19/2022] Open
Abstract
We describe optimized fragmentation schemes and data analysis strategies substantially enhancing the depth and accuracy in identifying protein cross-links using non-restricted whole proteome databases. These include a novel hybrid data acquisition strategy to sequence cross-links at both MS2 and MS3 level and a new algorithmic design XlinkX v2.0 for data analysis. As proof-of-concept we investigated proteome-wide protein interactions in E. coli and HeLa cell lysates, respectively, identifying 1,158 and 3,301 unique cross-links at ∼1% false discovery rate. These protein interaction repositories provide meaningful structural information on many endogenous macromolecular assemblies, as we showcase on several protein complexes involved in translation, protein folding and carbohydrate metabolism. Chemical cross-linking combined with mass spectrometry (XL-MS) can provide information on protein conformations and interactions in highly complex samples. Here the authors describe an improved XL-MS workflow to increase the depth and fidelity of cross-link identification using whole proteome databases.
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100
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Barysz HM, Malmström J. Development of Large-scale Cross-linking Mass Spectrometry. Mol Cell Proteomics 2017; 17:1055-1066. [PMID: 28389583 DOI: 10.1074/mcp.r116.061663] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 03/26/2017] [Indexed: 11/06/2022] Open
Abstract
Cross-linking mass spectrometry (CLMS) provides distance constraints to study the structure of proteins, multiprotein complexes and protein-protein interactions which are critical for the understanding of protein function. CLMS is an attractive technology to bridge the gap between high-resolution structural biology techniques and proteomic-based interactome studies. However, as outlined in this review there are still several bottlenecks associated with CLMS which limit its application on a proteome-wide level. Specifically, there is an unmet need for comprehensive software that can reliably identify cross-linked peptides from large data sets. In this review we provide supporting information to reason that targeted proteomics of cross-links may provide the required sensitivity to reliably detect and quantify cross-linked peptides and that a reporter ion signature for cross-linked peptides may become a useful approach to increase confidence in the identification process of cross-linked peptides. In addition, the review summarizes the recent advances in CLMS workflows using the analysis of condensin complex in intact chromosomes as a model complex.
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Affiliation(s)
- Helena Maria Barysz
- From the ‡Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Johan Malmström
- From the ‡Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
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