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Degliesposti G. Probing Protein Complexes Composition, Stoichiometry, and Interactions by Peptide-Based Mass Spectrometry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:41-57. [PMID: 38507199 DOI: 10.1007/978-3-031-52193-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
The characterization of a protein complex by mass spectrometry can be conducted at different levels. Initial steps regard the qualitative composition of the complex and subunit identification. After that, quantitative information such as stoichiometric ratios and copy numbers for each subunit in a complex or super-complex is acquired. Peptide-based LC-MS/MS offers a wide number of methods and protocols for the characterization of protein complexes. This chapter concentrates on the applications of peptide-based LC-MS/MS for the qualitative, quantitative, and structural characterization of protein complexes focusing on subunit identification, determination of stoichiometric ratio and number of subunits per complex as well as on cross-linking mass spectrometry and hydrogen/deuterium exchange as methods for the structural investigation of the biological assemblies.
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2
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Grahn E, Kaufmann SV, Askarova M, Ninov M, Welp LM, Berger TK, Urlaub H, Kaupp UB. Control of intracellular pH and bicarbonate by CO 2 diffusion into human sperm. Nat Commun 2023; 14:5395. [PMID: 37669933 PMCID: PMC10480191 DOI: 10.1038/s41467-023-40855-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 08/14/2023] [Indexed: 09/07/2023] Open
Abstract
The reaction of CO2 with H2O to form bicarbonate (HCO3-) and H+ controls sperm motility and fertilization via HCO3--stimulated cAMP synthesis. A complex network of signaling proteins participates in this reaction. Here, we identify key players that regulate intracellular pH (pHi) and HCO3- in human sperm by quantitative mass spectrometry (MS) and kinetic patch-clamp fluorometry. The resting pHi is set by amiloride-sensitive Na+/H+ exchange. The sperm-specific putative Na+/H+ exchanger SLC9C1, unlike its sea urchin homologue, is not gated by voltage or cAMP. Transporters and channels implied in HCO3- transport are not detected, and may be present at copy numbers < 10 molecules/sperm cell. Instead, HCO3- is produced by diffusion of CO2 into cells and readjustment of the CO2/HCO3-/H+ equilibrium. The proton channel Hv1 may serve as a unidirectional valve that blunts the acidification ensuing from HCO3- synthesis. This work provides a new framework for the study of male infertility.
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Affiliation(s)
- Elena Grahn
- Max Planck Institute for Neurobiology of Behavior-caesar, Molecular Sensory Systems, Ludwig-Erhard-Allee 2, 53175, Bonn, Germany
| | - Svenja V Kaufmann
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Malika Askarova
- Max Planck Institute for Neurobiology of Behavior-caesar, Molecular Sensory Systems, Ludwig-Erhard-Allee 2, 53175, Bonn, Germany
| | - Momchil Ninov
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry, Am Fassberg 11, 37077, Göttingen, Germany
- University Medical Center Göttingen, Institute of Clinical Chemistry, Bioanalytics, Robert-Koch-Strasse 40, 37075, Göttingen, Germany
| | - Luisa M Welp
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry, Am Fassberg 11, 37077, Göttingen, Germany
- University Medical Center Göttingen, Institute of Clinical Chemistry, Bioanalytics, Robert-Koch-Strasse 40, 37075, Göttingen, Germany
| | - Thomas K Berger
- Max Planck Institute for Neurobiology of Behavior-caesar, Molecular Sensory Systems, Ludwig-Erhard-Allee 2, 53175, Bonn, Germany.
- Department of Neurophysiology, Institute of Physiology and Pathophysiology, Philipps-University Marburg, Deutschhausstrasse 1-2, 35037, Marburg, Germany.
| | - Henning Urlaub
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry, Am Fassberg 11, 37077, Göttingen, Germany.
- University Medical Center Göttingen, Institute of Clinical Chemistry, Bioanalytics, Robert-Koch-Strasse 40, 37075, Göttingen, Germany.
- Cluster of Excellence, Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC), University of Göttingen, Göttingen, Germany.
| | - U Benjamin Kaupp
- Max Planck Institute for Neurobiology of Behavior-caesar, Molecular Sensory Systems, Ludwig-Erhard-Allee 2, 53175, Bonn, Germany.
- Life & Medical Sciences Institute (LIMES), University Bonn, Carl-Troll-Strasse 31, 53115, Bonn, Germany.
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3
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Raghuraman BK, Bogdanova A, Moon H, Rzagalinski I, Geertsma ER, Hersemann L, Shevchenko A. Median-Based Absolute Quantification of Proteins Using Fully Unlabeled Generic Internal Standard (FUGIS). J Proteome Res 2021; 21:132-141. [PMID: 34807614 PMCID: PMC8749952 DOI: 10.1021/acs.jproteome.1c00596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
By reporting the
molar abundance of proteins, absolute quantification
determines their stoichiometry in complexes, pathways, or networks.
Typically, absolute quantification relies either on protein-specific
isotopically labeled peptide standards or on a semiempirical calibration
against the average abundance of peptides chosen from arbitrarily
selected proteins. In contrast, a generic protein standard FUGIS (fully
unlabeled generic internal standard) requires no isotopic labeling,
chemical synthesis, or external calibration and is applicable to quantifying
proteins of any organismal origin. The median intensity of the peptide
peaks produced by the tryptic digestion of FUGIS is used as a single-point
calibrant to determine the molar abundance of any codigested protein.
Powered by FUGIS, median-based absolute quantification (MBAQ) outperformed
other methods of untargeted proteome-wide absolute quantification.
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Affiliation(s)
- Bharath Kumar Raghuraman
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Aliona Bogdanova
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - HongKee Moon
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Ignacy Rzagalinski
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Eric R Geertsma
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Lena Hersemann
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
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4
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Low TY, Syafruddin SE, Mohtar MA, Vellaichamy A, A Rahman NS, Pung YF, Tan CSH. Recent progress in mass spectrometry-based strategies for elucidating protein-protein interactions. Cell Mol Life Sci 2021; 78:5325-5339. [PMID: 34046695 PMCID: PMC8159249 DOI: 10.1007/s00018-021-03856-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/03/2021] [Accepted: 05/14/2021] [Indexed: 02/07/2023]
Abstract
Protein-protein interactions are fundamental to various aspects of cell biology with many protein complexes participating in numerous fundamental biological processes such as transcription, translation and cell cycle. MS-based proteomics techniques are routinely applied for characterising the interactome, such as affinity purification coupled to mass spectrometry that has been used to selectively enrich and identify interacting partners of a bait protein. In recent years, many orthogonal MS-based techniques and approaches have surfaced including proximity-dependent labelling of neighbouring proteins, chemical cross-linking of two interacting proteins, as well as inferring PPIs from the co-behaviour of proteins such as the co-fractionating profiles and the thermal solubility profiles of proteins. This review discusses the underlying principles, advantages, limitations and experimental considerations of these emerging techniques. In addition, a brief account on how MS-based techniques are used to investigate the structural and functional properties of protein complexes, including their topology, stoichiometry, copy number and dynamics, are discussed.
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Affiliation(s)
- Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Jalan Yaacob Latiff, Bandar Tun Razak, 56000, Kuala Lumpur, Malaysia.
| | - Saiful Effendi Syafruddin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Jalan Yaacob Latiff, Bandar Tun Razak, 56000, Kuala Lumpur, Malaysia
| | - M Aiman Mohtar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Jalan Yaacob Latiff, Bandar Tun Razak, 56000, Kuala Lumpur, Malaysia
| | | | - Nisa Syakila A Rahman
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Jalan Yaacob Latiff, Bandar Tun Razak, 56000, Kuala Lumpur, Malaysia
| | - Yuh-Fen Pung
- Division of Biomedical Science, University of Nottingham Malaysia, 43500, Semenyih, Malaysia
| | - Chris Soon Heng Tan
- Department of Chemistry, College of Science , Southern University of Science and Technology, Shenzhen, 518055, China.
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5
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Kyrilis FL, Semchonok DA, Skalidis I, Tüting C, Hamdi F, O'Reilly FJ, Rappsilber J, Kastritis PL. Integrative structure of a 10-megadalton eukaryotic pyruvate dehydrogenase complex from native cell extracts. Cell Rep 2021; 34:108727. [PMID: 33567276 DOI: 10.1016/j.celrep.2021.108727] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 12/02/2020] [Accepted: 01/14/2021] [Indexed: 12/29/2022] Open
Abstract
The pyruvate dehydrogenase complex (PDHc) is a giant enzymatic assembly involved in pyruvate oxidation. PDHc components have been characterized in isolation, but the complex's quaternary structure has remained elusive due to sheer size, heterogeneity, and plasticity. Here, we identify fully assembled Chaetomium thermophilum α-keto acid dehydrogenase complexes in native cell extracts and characterize their domain arrangements utilizing mass spectrometry, activity assays, crosslinking, electron microscopy (EM), and computational modeling. We report the cryo-EM structure of the PDHc core and observe unique features of the previously unknown native state. The asymmetric reconstruction of the 10-MDa PDHc resolves spatial proximity of its components, agrees with stoichiometric data (60 E2p:12 E3BP:∼20 E1p: ≤ 12 E3), and proposes a minimum reaction path among component enzymes. The PDHc shows the presence of a dynamic pyruvate oxidation compartment, organized by core and peripheral protein species. Our data provide a framework for further understanding PDHc and α-keto acid dehydrogenase complex structure and function.
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Affiliation(s)
- Fotis L Kyrilis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany; Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
| | - Dmitry A Semchonok
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
| | - Ioannis Skalidis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany; Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
| | - Christian Tüting
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
| | - Farzad Hamdi
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
| | - Francis J O'Reilly
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, United Kingdom
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany; Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany; Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, Halle/Saale, Germany.
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6
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Yugandhar K, Gupta S, Yu H. 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] [Grants] [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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Affiliation(s)
- Kumar Yugandhar
- Department of Computational Biology, Cornell University, Ithaca, New York 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
| | - Shagun Gupta
- Department of Computational Biology, Cornell University, Ithaca, New York 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
| | - Haiyuan Yu
- Department of Computational Biology, Cornell University, Ithaca, New York 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
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7
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Will T, Helms V. Differential analysis of combinatorial protein complexes with CompleXChange. BMC Bioinformatics 2019; 20:300. [PMID: 31159772 PMCID: PMC6547514 DOI: 10.1186/s12859-019-2852-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 04/26/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although a considerable number of proteins operate as multiprotein complexes and not on their own, organism-wide studies so far are only able to quantify individual proteins or protein-coding genes in a condition-specific manner for a sizeable number of samples, but not their assemblies. Consequently, there exist large amounts of transcriptomic data and an increasing amount of data on proteome abundance, but quantitative knowledge on complexomes is missing. This deficiency impedes the applicability of the powerful tool of differential analysis in the realm of macromolecular complexes. Here, we present a pipeline for differential analysis of protein complexes based on predicted or manually assigned complexes and inferred complex abundances, which can be easily applied on a whole-genome scale. RESULTS We observed for simulated data that results obtained by our complex abundance estimation algorithm were in better agreement with the ground truth and physicochemically more reasonable compared to previous efforts that used linear programming while running in a fraction of the time. The practical usability of the method was assessed in the context of transcription factor complexes in human monocyte and lymphoblastoid samples. We demonstrated that our new method is robust against false-positive detection and reports deregulated complexomes that can only be partially explained by differential analysis of individual protein-coding genes. Furthermore we showed that deregulated complexes identified by the tool potentially harbor significant yet unused information content. CONCLUSIONS CompleXChange allows to analyze deregulation of the protein complexome on a whole-genome scale by integrating a plethora of input data that is already available. A platform-independent Java binary, a user guide with example data and the source code are freely available at https://sourceforge.net/projects/complexchange/ .
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Affiliation(s)
- Thorsten Will
- Center for Bioinformatics, Saarland University, Campus E2.1, Saarbrücken, 66123, Germany.,Graduate School of Computer Science, Saarland University, Campus E1.3, Saarbrücken, 66123, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Campus E2.1, Saarbrücken, 66123, Germany.
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8
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Menneteau T, Fabre B, Garrigues L, Stella A, Zivkovic D, Roux-Dalvai F, Mouton-Barbosa E, Beau M, Renoud ML, Amalric F, Sensébé L, Gonzalez-de-Peredo A, Ader I, Burlet-Schiltz O, Bousquet MP. Mass Spectrometry-based Absolute Quantification of 20S Proteasome Status for Controlled Ex-vivo Expansion of Human Adipose-derived Mesenchymal Stromal/Stem Cells. Mol Cell Proteomics 2019; 18:744-759. [PMID: 30700495 PMCID: PMC6442357 DOI: 10.1074/mcp.ra118.000958] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 01/21/2019] [Indexed: 01/18/2023] Open
Abstract
The proteasome controls a multitude of cellular processes through protein degradation and has been identified as a therapeutic target in oncology. However, our understanding of its function and the development of specific modulators are hampered by the lack of a straightforward method to determine the overall proteasome status in biological samples. Here, we present a method to determine the absolute quantity and stoichiometry of ubiquitous and tissue-specific human 20S proteasome subtypes based on a robust, absolute SILAC-based multiplexed LC-Selected Reaction Monitoring (SRM) quantitative mass spectrometry assay with high precision, accuracy, and sensitivity. The method was initially optimized and validated by comparison with a reference ELISA assay and by analyzing the dynamics of catalytic subunits in HeLa cells following IFNγ-treatment and in range of human tissues. It was then successfully applied to reveal IFNγ- and O2-dependent variations of proteasome status during primary culture of Adipose-derived-mesenchymal Stromal/Stem Cells (ADSCs). The results show the critical importance of controlling the culture conditions during cell expansion for future therapeutic use in humans. We hypothesize that a shift from the standard proteasome to the immunoproteasome could serve as a predictor of immunosuppressive and differentiation capacities of ADSCs and, consequently, that quality control should include proteasomal quantification in addition to examining other essential cell parameters. The method presented also provides a new powerful tool to conduct more individualized protocols in cancer or inflammatory diseases where selective inhibition of the immunoproteasome has been shown to reduce side effects.
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Affiliation(s)
- Thomas Menneteau
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France;; §STROMALab, Université de Toulouse, INSERM U1031, EFS, INP-ENVT, UPS, Toulouse, France
| | - Bertrand Fabre
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Luc Garrigues
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Alexandre Stella
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Dusan Zivkovic
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Florence Roux-Dalvai
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Emmanuelle Mouton-Barbosa
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Mathilde Beau
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Marie-Laure Renoud
- §STROMALab, Université de Toulouse, INSERM U1031, EFS, INP-ENVT, UPS, Toulouse, France
| | - François Amalric
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Luc Sensébé
- §STROMALab, Université de Toulouse, INSERM U1031, EFS, INP-ENVT, UPS, Toulouse, France
| | - Anne Gonzalez-de-Peredo
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Isabelle Ader
- §STROMALab, Université de Toulouse, INSERM U1031, EFS, INP-ENVT, UPS, Toulouse, France
| | - Odile Burlet-Schiltz
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France;.
| | - Marie-Pierre Bousquet
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France;.
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9
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Andjelković U, Josić D. Mass spectrometry based proteomics as foodomics tool in research and assurance of food quality and safety. Trends Food Sci Technol 2018. [DOI: 10.1016/j.tifs.2018.04.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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10
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Dörrbaum AR, Kochen L, Langer JD, Schuman EM. Local and global influences on protein turnover in neurons and glia. eLife 2018; 7:34202. [PMID: 29914620 PMCID: PMC6008053 DOI: 10.7554/elife.34202] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/19/2018] [Indexed: 12/31/2022] Open
Abstract
Regulation of protein turnover allows cells to react to their environment and maintain homeostasis. Proteins can show different turnover rates in different tissue, but little is known about protein turnover in different brain cell types. We used dynamic SILAC to determine half-lives of over 5100 proteins in rat primary hippocampal cultures as well as in neuron-enriched and glia-enriched cultures ranging from <1 to >20 days. In contrast to synaptic proteins, membrane proteins were relatively shorter-lived and mitochondrial proteins were longer-lived compared to the population. Half-lives also correlate with protein functions and the dynamics of the complexes they are incorporated in. Proteins in glia possessed shorter half-lives than the same proteins in neurons. The presence of glia sped up or slowed down the turnover of neuronal proteins. Our results demonstrate that both the cell-type of origin as well as the nature of the extracellular environment have potent influences on protein turnover.
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Affiliation(s)
- Aline R Dörrbaum
- Max Planck Institute for Brain Research, Frankfurt, Germany.,Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Lisa Kochen
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Julian D Langer
- Max Planck Institute for Brain Research, Frankfurt, Germany.,Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Frankfurt, Germany
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11
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Tassi M, De Vos J, Chatterjee S, Sobott F, Bones J, Eeltink S. Advances in native high-performance liquid chromatography and intact mass spectrometry for the characterization of biopharmaceutical products. J Sep Sci 2017; 41:125-144. [DOI: 10.1002/jssc.201700988] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 09/29/2017] [Accepted: 09/29/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Marco Tassi
- Department of Chemical Engineering; Vrije Universiteit Brussel (VUB); Brussels Belgium
| | - Jelle De Vos
- Department of Chemical Engineering; Vrije Universiteit Brussel (VUB); Brussels Belgium
| | - Sneha Chatterjee
- Biomolecular & Analytical Mass Spectrometry; Antwerp University; Antwerp Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry; Antwerp University; Antwerp Belgium
- Astbury Centre for Structural Molecular Biology; University of Leeds; Leeds UK
- School of Molecular and Cellular Biology; University of Leeds; Leeds UK
| | - Jonathan Bones
- The National Institute for Bioprocessing Research and Training (NIBRT); Dublin Ireland
| | - Sebastiaan Eeltink
- Department of Chemical Engineering; Vrije Universiteit Brussel (VUB); Brussels Belgium
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12
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Huang R, Chen Z, He L, He N, Xi Z, Li Z, Deng Y, Zeng X. Mass spectrometry-assisted gel-based proteomics in cancer biomarker discovery: approaches and application. Theranostics 2017; 7:3559-3572. [PMID: 28912895 PMCID: PMC5596443 DOI: 10.7150/thno.20797] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 07/12/2017] [Indexed: 12/13/2022] Open
Abstract
There is a critical need for the discovery of novel biomarkers for early detection and targeted therapy of cancer, a major cause of deaths worldwide. In this respect, proteomic technologies, such as mass spectrometry (MS), enable the identification of pathologically significant proteins in various types of samples. MS is capable of high-throughput profiling of complex biological samples including blood, tissues, urine, milk, and cells. MS-assisted proteomics has contributed to the development of cancer biomarkers that may form the foundation for new clinical tests. It can also aid in elucidating the molecular mechanisms underlying cancer. In this review, we discuss MS principles and instrumentation as well as approaches in MS-based proteomics, which have been employed in the development of potential biomarkers. Furthermore, the challenges in validation of MS biomarkers for their use in clinical practice are also reviewed.
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Affiliation(s)
- Rongrong Huang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhongsi Chen
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Lei He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology; Hunan University of Technology, Zhuzhou 412007, China
| | - Zhijiang Xi
- School of Medicine, Yangtze University, Jingzhou 434023, China
| | - Zhiyang Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- Department of Clinical Laboratory, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Yan Deng
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology; Hunan University of Technology, Zhuzhou 412007, China
| | - Xin Zeng
- Nanjing Maternity and Child Health Medical Institute, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing 210004, China
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13
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Zilkenat S, Grin I, Wagner S. Stoichiometry determination of macromolecular membrane protein complexes. Biol Chem 2017; 398:155-164. [PMID: 27664774 DOI: 10.1515/hsz-2016-0251] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/20/2016] [Indexed: 01/01/2023]
Abstract
Gaining knowledge of the structural makeup of protein complexes is critical to advance our understanding of their formation and functions. This task is particularly challenging for transmembrane protein complexes, and grows ever more imposing with increasing size of these large macromolecular structures. The last 10 years have seen a steep increase in solved high-resolution membrane protein structures due to both new and improved methods in the field, but still most structures of large transmembrane complexes remain elusive. An important first step towards the structure elucidation of these difficult complexes is the determination of their stoichiometry, which we discuss in this review. Knowing the stoichiometry of complex components not only answers unresolved structural questions and is relevant for understanding the molecular mechanisms of macromolecular machines but also supports further attempts to obtain high-resolution structures by providing constraints for structure calculations.
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14
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Holman SW, Hammond DE, Simpson DM, Waters J, Hurst JL, Beynon RJ. Protein turnover measurement using selected reaction monitoring-mass spectrometry (SRM-MS). PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0362. [PMID: 27644981 PMCID: PMC5031629 DOI: 10.1098/rsta.2015.0362] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/23/2016] [Indexed: 05/28/2023]
Abstract
Protein turnover represents an important mechanism in the functioning of cells, with deregulated synthesis and degradation of proteins implicated in many diseased states. Therefore, proteomics strategies to measure turnover rates with high confidence are of vital importance to understanding many biological processes. In this study, the more widely used approach of non-targeted precursor ion signal intensity (MS1) quantification is compared with selected reaction monitoring (SRM), a data acquisition strategy that records data for specific peptides, to determine if improved quantitative data would be obtained using a targeted quantification approach. Using mouse liver as a model system, turnover measurement of four tricarboxylic acid cycle proteins was performed using both MS1 and SRM quantification strategies. SRM outperformed MS1 in terms of sensitivity and selectivity of measurement, allowing more confident determination of protein turnover rates. SRM data are acquired using cheaper and more widely available tandem quadrupole mass spectrometers, making the approach accessible to a larger number of researchers than MS1 quantification, which is best performed on high mass resolution instruments. SRM acquisition is ideally suited to focused studies where the turnover of tens of proteins is measured, making it applicable in determining the dynamics of proteins complexes and complete metabolic pathways.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Stephen W Holman
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Dean E Hammond
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool L69 3BX, UK
| | - Deborah M Simpson
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - John Waters
- Mammalian Behaviour and Evolution Group, Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, University of Liverpool, Leahurst Campus, Neston CH64 7TE, UK
| | - Jane L Hurst
- Mammalian Behaviour and Evolution Group, Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, University of Liverpool, Leahurst Campus, Neston CH64 7TE, UK
| | - Robert J Beynon
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
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15
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Chait BT, Cadene M, Olinares PD, Rout MP, Shi Y. Revealing Higher Order Protein Structure Using Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:952-65. [PMID: 27080007 PMCID: PMC5125627 DOI: 10.1007/s13361-016-1385-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 03/14/2016] [Accepted: 03/15/2016] [Indexed: 05/24/2023]
Abstract
The development of rapid, sensitive, and accurate mass spectrometric methods for measuring peptides, proteins, and even intact protein assemblies has made mass spectrometry (MS) an extraordinarily enabling tool for structural biology. Here, we provide a personal perspective of the increasingly useful role that mass spectrometric techniques are exerting during the elucidation of higher order protein structures. Areas covered in this brief perspective include MS as an enabling tool for the high resolution structural biologist, for compositional analysis of endogenous protein complexes, for stoichiometry determination, as well as for integrated approaches for the structural elucidation of protein complexes. We conclude with a vision for the future role of MS-based techniques in the development of a multi-scale molecular microscope. Graphical Abstract ᅟ.
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Affiliation(s)
- Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, 10065, USA.
| | - Martine Cadene
- CBM, CNRS UPR4301, Rue Charles Sadron, CS 80054, 45071, Orleans Cedex 2, France
| | - Paul Dominic Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, 10065, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, 10065, USA
| | - Yi Shi
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, 10065, USA
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16
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Kito K, Okada M, Ishibashi Y, Okada S, Ito T. A strategy for absolute proteome quantification with mass spectrometry by hierarchical use of peptide-concatenated standards. Proteomics 2016; 16:1457-73. [DOI: 10.1002/pmic.201500414] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 02/18/2016] [Accepted: 03/24/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Keiji Kito
- Department of Life Sciences, School of Agriculture; Meiji University; Kawasaki Japan
| | - Mitsuhiro Okada
- Department of Life Sciences, School of Agriculture; Meiji University; Kawasaki Japan
| | - Yuko Ishibashi
- Department of Life Sciences, School of Agriculture; Meiji University; Kawasaki Japan
| | - Satoshi Okada
- Department of Biochemistry; Kyushu University Graduate School of Medical Science; Fukuoka Japan
| | - Takashi Ito
- Department of Biochemistry; Kyushu University Graduate School of Medical Science; Fukuoka Japan
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17
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Schmidt C, Beilsten-Edmands V, Robinson CV. Insights into Eukaryotic Translation Initiation from Mass Spectrometry of Macromolecular Protein Assemblies. J Mol Biol 2015; 428:344-356. [PMID: 26497764 DOI: 10.1016/j.jmb.2015.10.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 09/28/2015] [Accepted: 10/14/2015] [Indexed: 02/05/2023]
Abstract
Translation initiation in eukaryotes requires the interplay of at least 10 initiation factors that interact at the different steps of this phase of gene expression. The interactions of initiation factors and related proteins are in general controlled by phosphorylation, which serves as a regulatory switch to turn protein translation on or off. The structures of initiation factors and a complete description of their post-translational modification (PTM) status are therefore required in order to fully understand these processes. In recent years, mass spectrometry has contributed considerably to provide this information and nowadays is proving to be indispensable when studying dynamic heterogeneous protein complexes such as the eukaryotic initiation factors. Herein, we highlight mass spectrometric approaches commonly applied to identify interacting subunits and their PTMs and the structural techniques that allow the architecture of protein complexes to be assessed. We present recent structural investigations of initiation factors and their interactions with other factors and with ribosomes and we assess the models generated. These models allow us to locate PTMs within initiation factor complexes and to highlight possible roles for phosphorylation sites in regulating interaction interfaces.
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Affiliation(s)
- Carla Schmidt
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.
| | - Victoria Beilsten-Edmands
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.
| | - Carol V Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.
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