1
|
Escobar EE, Yang W, Lanzillotti MB, Juetten KJ, Shields S, Siegel D, Zhang YJ, Brodbelt JS. Tracking Inhibition of Human Small C-Terminal Domain Phosphatase 1 Using 193 nm Ultraviolet Photodissociation Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1330-1341. [PMID: 38662915 DOI: 10.1021/jasms.4c00098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Working in tandem with kinases via a dynamic interplay of phosphorylation and dephosphorylation of proteins, phosphatases regulate many cellular processes and thus represent compelling therapeutic targets. Here we leverage ultraviolet photodissociation to shed light on the binding characteristics of two covalent phosphatase inhibitors, T65 and rabeprazole, and their respective interactions with the human small C-terminal domain phosphatase 1 (SCP1) and its single-point mutant C181A, in which a nonreactive alanine replaces one key reactive cysteine. Top-down MS/MS analysis is used to localize the binding of T65 and rabeprazole on the two proteins and estimate the relative reactivities of each cysteine residue.
Collapse
Affiliation(s)
| | | | | | | | | | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive 0741, La Jolla, California 92093, United States
| | | | | |
Collapse
|
2
|
Paris T, Kiss A, Signor L, Lutfalla G, Blaise M, Boeri Erba E, Chaloin L, Yatime L. The IbeA protein from adherent invasive Escherichia coli is a flavoprotein sharing structural homology with FAD-dependent oxidoreductases. FEBS J 2024; 291:177-203. [PMID: 37786987 DOI: 10.1111/febs.16969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/22/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
Invasion of brain endothelium protein A (IbeA) is a virulence factor specific to pathogenic Escherichia coli. Originally identified in the K1 strain causing neonatal meningitis, it was more recently found in avian pathogenic Escherichia coli (APEC) and adherent invasive Escherichia coli (AIEC). In these bacteria, IbeA facilitates host cell invasion and intracellular survival, in particular, under harsh conditions like oxidative stress. Furthermore, IbeA from AIEC contributes to intramacrophage survival and replication, thus enhancing the inflammatory response within the intestine. Therefore, this factor is a promising drug target for anti-AIEC strategies in the context of Crohn's disease. Despite such an important role, the biological function of IbeA remains largely unknown. In particular, its exact nature and cellular localization, i.e., membrane-bound invasin versus cytosolic factor, are still of debate. Here, we developed an efficient protocol for recombinant expression of IbeA under native conditions and demonstrated that IbeA from AIEC is a soluble, homodimeric flavoprotein. Using mass spectrometry and tryptophan fluorescence measurements, we further showed that IbeA preferentially binds flavin adenine dinucleotide (FAD), with an affinity in the one-hundred nanomolar range and optimal binding under reducing conditions. 3D-modeling with AlphaFold revealed that IbeA shares strong structural homology with FAD-dependent oxidoreductases. Finally, we used ligand docking, mutational analyses, and molecular dynamics simulations to identify the FAD binding pocket within IbeA and characterize possible conformational changes occurring upon ligand binding. Overall, we suggest that the role of IbeA in the survival of AIEC within host cells, notably macrophages, is linked to modulation of redox processes.
Collapse
Affiliation(s)
- Théo Paris
- LPHI, Univ. Montpellier, CNRS, INSERM, France
| | - Agneta Kiss
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Luca Signor
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | | | | | | | | | | |
Collapse
|
3
|
Castel J, Delaux S, Hernandez-Alba O, Cianférani S. Recent advances in structural mass spectrometry methods in the context of biosimilarity assessment: from sequence heterogeneities to higher order structures. J Pharm Biomed Anal 2023; 236:115696. [PMID: 37713983 DOI: 10.1016/j.jpba.2023.115696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/17/2023]
Abstract
Biotherapeutics and their biosimilar versions have been flourishing in the biopharmaceutical market for several years. Structural and functional characterization is needed to achieve analytical biosimilarity through the assessment of critical quality attributes as required by regulatory authorities. The role of analytical strategies, particularly mass spectrometry-based methods, is pivotal to gathering valuable information for the in-depth characterization of biotherapeutics and biosimilarity assessment. Structural mass spectrometry methods (native MS, HDX-MS, top-down MS, etc.) provide information ranging from primary sequence assessment to higher order structure evaluation. This review focuses on recent developments and applications in structural mass spectrometry for biotherapeutic and biosimilar characterization.
Collapse
Affiliation(s)
- Jérôme Castel
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Delaux
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France.
| |
Collapse
|
4
|
Dowling P, Swandulla D, Ohlendieck K. Mass Spectrometry-Based Proteomic Technology and Its Application to Study Skeletal Muscle Cell Biology. Cells 2023; 12:2560. [PMID: 37947638 PMCID: PMC10649384 DOI: 10.3390/cells12212560] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Voluntary striated muscles are characterized by a highly complex and dynamic proteome that efficiently adapts to changed physiological demands or alters considerably during pathophysiological dysfunction. The skeletal muscle proteome has been extensively studied in relation to myogenesis, fiber type specification, muscle transitions, the effects of physical exercise, disuse atrophy, neuromuscular disorders, muscle co-morbidities and sarcopenia of old age. Since muscle tissue accounts for approximately 40% of body mass in humans, alterations in the skeletal muscle proteome have considerable influence on whole-body physiology. This review outlines the main bioanalytical avenues taken in the proteomic characterization of skeletal muscle tissues, including top-down proteomics focusing on the characterization of intact proteoforms and their post-translational modifications, bottom-up proteomics, which is a peptide-centric method concerned with the large-scale detection of proteins in complex mixtures, and subproteomics that examines the protein composition of distinct subcellular fractions. Mass spectrometric studies over the last two decades have decisively improved our general cell biological understanding of protein diversity and the heterogeneous composition of individual myofibers in skeletal muscles. This detailed proteomic knowledge can now be integrated with findings from other omics-type methodologies to establish a systems biological view of skeletal muscle function.
Collapse
Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany;
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| |
Collapse
|
5
|
Iuso D, Garcia-Saez I, Couté Y, Yamaryo-Botté Y, Boeri Erba E, Adrait A, Zeaiter N, Tokarska-Schlattner M, Jilkova ZM, Boussouar F, Barral S, Signor L, Couturier K, Hajmirza A, Chuffart F, Bourova-Flin E, Vitte AL, Bargier L, Puthier D, Decaens T, Rousseaux S, Botté C, Schlattner U, Petosa C, Khochbin S. Nucleoside diphosphate kinases 1 and 2 regulate a protective liver response to a high-fat diet. SCIENCE ADVANCES 2023; 9:eadh0140. [PMID: 37672589 PMCID: PMC10482350 DOI: 10.1126/sciadv.adh0140] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 08/02/2023] [Indexed: 09/08/2023]
Abstract
The synthesis of fatty acids from acetyl-coenzyme A (AcCoA) is deregulated in diverse pathologies, including cancer. Here, we report that fatty acid accumulation is negatively regulated by nucleoside diphosphate kinases 1 and 2 (NME1/2), housekeeping enzymes involved in nucleotide homeostasis that were recently found to bind CoA. We show that NME1 additionally binds AcCoA and that ligand recognition involves a unique binding mode dependent on the CoA/AcCoA 3' phosphate. We report that Nme2 knockout mice fed a high-fat diet (HFD) exhibit excessive triglyceride synthesis and liver steatosis. In liver cells, NME2 mediates a gene transcriptional response to HFD leading to the repression of fatty acid accumulation and activation of a protective gene expression program via targeted histone acetylation. Our findings implicate NME1/2 in the epigenetic regulation of a protective liver response to HFD and suggest a potential role in controlling AcCoA usage between the competing paths of histone acetylation and fatty acid synthesis.
Collapse
Affiliation(s)
- Domenico Iuso
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Isabel Garcia-Saez
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble 38000, France
| | - Yohann Couté
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, Grenoble 38000, France
| | - Yoshiki Yamaryo-Botté
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Elisabetta Boeri Erba
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble 38000, France
| | - Annie Adrait
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, Grenoble 38000, France
| | - Nour Zeaiter
- Univ. Grenoble Alpes, INSERM, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France
| | | | - Zuzana Macek Jilkova
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
- CHU Grenoble Alpes, Service d’hépato-gastroentérologie, Pôle Digidune, La Tronche 38700, France
| | - Fayçal Boussouar
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Sophie Barral
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Luca Signor
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble 38000, France
| | - Karine Couturier
- Univ. Grenoble Alpes, INSERM, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France
| | - Azadeh Hajmirza
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Florent Chuffart
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Ekaterina Bourova-Flin
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Anne-Laure Vitte
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Lisa Bargier
- Aix Marseille Université, INSERM, TAGC, TGML, Marseille 13288, France
| | - Denis Puthier
- Aix Marseille Université, INSERM, TAGC, TGML, Marseille 13288, France
| | - Thomas Decaens
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
- CHU Grenoble Alpes, Service d’hépato-gastroentérologie, Pôle Digidune, La Tronche 38700, France
| | - Sophie Rousseaux
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Cyrille Botté
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Uwe Schlattner
- Univ. Grenoble Alpes, INSERM, Institut Universitaire de France, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France
| | - Carlo Petosa
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble 38000, France
| | - Saadi Khochbin
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| |
Collapse
|
6
|
Rolland AD, Takata T, Donor MT, Lampi KJ, Prell JS. Eye lens β-crystallins are predicted by native ion mobility-mass spectrometry and computations to form compact higher-ordered heterooligomers. Structure 2023; 31:1052-1064.e3. [PMID: 37453416 PMCID: PMC10528727 DOI: 10.1016/j.str.2023.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 05/04/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023]
Abstract
Eye lens α- and β-/γ-crystallin proteins are not replaced after fiber cell denucleation and maintain lens transparency and refractive properties. The exceptionally high (∼400-500 mg/mL) concentration of crystallins in mature lens tissue and multiple other factors impede precise characterization of β-crystallin interactions, oligomer composition, size, and topology. Native ion mobility-mass spectrometry is used here to probe β-crystallin association and provide insight into homo- and heterooligomerization kinetics for these proteins. These experiments include separation and characterization of higher-order β-crystallin oligomers and illustrate the unique advantages of native IM-MS. Recombinantly expressed βB1, βB2, and βA3 isoforms are found to have different homodimerization propensities, and only βA3 forms larger homooligomers. Heterodimerization of βB2 with βA3 occurs ∼3 times as fast as that of βB1 with βA3, and βB1 and βB2 heterodimerize less readily. Ion mobility experiments, molecular dynamics simulations, and PISA analysis together reveal that observed oligomers are consistent with predominantly compact, ring-like topologies.
Collapse
Affiliation(s)
- Amber D Rolland
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR 97403-1253, USA
| | - Takumi Takata
- Kyoto University, Research Reactor Institute 2, Asashiro-Nishi, Kumatori-cho, Sennan-gun, Osaka 590-0494, Japan
| | - Micah T Donor
- Department of Biological & Molecular Sciences, George Fox University, 414 N Meridian St, Newberg, OR 97132, USA
| | - Kirsten J Lampi
- Integrative Biosciences, School of Dentistry, 3181 SW Sam Jackson Park Road, Oregon Health & Science University, Portland, OR 97239-3098, USA.
| | - James S Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR 97403-1253, USA; Materials Science Institute, 1252 University of Oregon, Eugene, OR 97403-1252, USA.
| |
Collapse
|
7
|
Laroussi H, Juarez‐Martinez AB, Le Roy A, Boeri Erba E, Gabel F, de Massy B, Kadlec J. Characterization of the REC114-MEI4-IHO1 complex regulating meiotic DNA double-strand break formation. EMBO J 2023; 42:e113866. [PMID: 37431931 PMCID: PMC10425845 DOI: 10.15252/embj.2023113866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023] Open
Abstract
Meiotic recombination is initiated by the formation of DNA double-strand breaks (DSBs), essential for fertility and genetic diversity. In the mouse, DSBs are formed by the catalytic TOPOVIL complex consisting of SPO11 and TOPOVIBL. To preserve genome integrity, the activity of the TOPOVIL complex is finely controlled by several meiotic factors including REC114, MEI4, and IHO1, but the underlying mechanism is poorly understood. Here, we report that mouse REC114 forms homodimers, that it associates with MEI4 as a 2:1 heterotrimer that further dimerizes, and that IHO1 forms coiled-coil-based tetramers. Using AlphaFold2 modeling combined with biochemical characterization, we uncovered the molecular details of these assemblies. Finally, we show that IHO1 directly interacts with the PH domain of REC114 by recognizing the same surface as TOPOVIBL and another meiotic factor ANKRD31. These results provide strong evidence for the existence of a ternary IHO1-REC114-MEI4 complex and suggest that REC114 could act as a potential regulatory platform mediating mutually exclusive interactions with several partners.
Collapse
Affiliation(s)
| | | | - Aline Le Roy
- Université Grenoble Alpes, CNRS, CEA, IBSGrenobleFrance
| | | | - Frank Gabel
- Université Grenoble Alpes, CNRS, CEA, IBSGrenobleFrance
| | - Bernard de Massy
- Institut de Génétique Humaine (IGH), Centre National de la Recherche ScientifiqueUniversity of MontpellierMontpellierFrance
| | - Jan Kadlec
- Université Grenoble Alpes, CNRS, CEA, IBSGrenobleFrance
| |
Collapse
|
8
|
Kreutzer AG, Guaglianone G, Yoo S, Parrocha CMT, Ruttenberg SM, Malonis RJ, Tong K, Lin YF, Nguyen JT, Howitz WJ, Diab MN, Hamza IL, Lai JR, Wysocki VH, Nowick JS. Probing differences among Aβ oligomers with two triangular trimers derived from Aβ. Proc Natl Acad Sci U S A 2023; 120:e2219216120. [PMID: 37216514 PMCID: PMC10235986 DOI: 10.1073/pnas.2219216120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/17/2023] [Indexed: 05/24/2023] Open
Abstract
The assembly of the β-amyloid peptide (Aβ) to form oligomers and fibrils is closely associated with the pathogenesis and progression of Alzheimer's disease. Aβ is a shape-shifting peptide capable of adopting many conformations and folds within the multitude of oligomers and fibrils the peptide forms. These properties have precluded detailed structural elucidation and biological characterization of homogeneous, well-defined Aβ oligomers. In this paper, we compare the structural, biophysical, and biological characteristics of two different covalently stabilized isomorphic trimers derived from the central and C-terminal regions Aβ. X-ray crystallography reveals the structures of the trimers and shows that each trimer forms a ball-shaped dodecamer. Solution-phase and cell-based studies demonstrate that the two trimers exhibit markedly different assembly and biological properties. One trimer forms small soluble oligomers that enter cells through endocytosis and activate capase-3/7-mediated apoptosis, while the other trimer forms large insoluble aggregates that accumulate on the outer plasma membrane and elicit cellular toxicity through an apoptosis-independent mechanism. The two trimers also exhibit different effects on the aggregation, toxicity, and cellular interaction of full-length Aβ, with one trimer showing a greater propensity to interact with Aβ than the other. The studies described in this paper indicate that the two trimers share structural, biophysical, and biological characteristics with oligomers of full-length Aβ. The varying structural, assembly, and biological characteristics of the two trimers provide a working model for how different Aβ trimers can assemble and lead to different biological effects, which may help shed light on the differences among Aβ oligomers.
Collapse
Affiliation(s)
- Adam G. Kreutzer
- Department of Chemistry, University of California Irvine, Irvine, CA92697
| | | | - Stan Yoo
- Department of Chemistry, University of California Irvine, Irvine, CA92697
| | | | | | - Ryan J. Malonis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY10461
| | - Karen Tong
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY10461
| | - Yu-Fu Lin
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH43210
| | - Jennifer T. Nguyen
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA92697
| | - William J. Howitz
- Department of Chemistry, University of California Irvine, Irvine, CA92697
| | - Michelle N. Diab
- Department of Chemistry, University of California Irvine, Irvine, CA92697
| | - Imane L. Hamza
- Department of Chemistry, University of California Irvine, Irvine, CA92697
| | - Jonathan R. Lai
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY10461
| | - Vicki H. Wysocki
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH43210
| | - James S. Nowick
- Department of Chemistry, University of California Irvine, Irvine, CA92697
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA92697
| |
Collapse
|
9
|
James VK, Sanders JD, Aizikov K, Fort KL, Grinfeld D, Makarov A, Brodbelt JS. Expanding Orbitrap Collision Cross-Section Measurements to Native Protein Applications Through Kinetic Energy and Signal Decay Analysis. Anal Chem 2023; 95:7656-7664. [PMID: 37133913 DOI: 10.1021/acs.analchem.3c00594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The measurement of collision cross sections (CCS, σ) offers supplemental information about sizes and conformations of ions beyond mass analysis alone. We have previously shown that CCSs can be determined directly from the time-domain transient decay of ions in an Orbitrap mass analyzer as ions oscillate around the central electrode and collide with neutral gas, thus removing them from the ion packet. Herein, we develop the modified hard collision model, thus deviating from the prior FT-MS hard sphere model, to determine CCSs as a function of center-of-mass collision energy in the Orbitrap analyzer. With this model, we aim to increase the upper mass limit of CCS measurement for native-like proteins, characterized by low charge states and presumed to be in more compact conformations. We also combine CCS measurements with collision induced unfolding and tandem mass spectrometry experiments to monitor protein unfolding and disassembly of protein complexes and measure CCSs of ejected monomers from protein complexes.
Collapse
Affiliation(s)
- Virginia K James
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - James D Sanders
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | | | - Kyle L Fort
- Thermo Fisher Scientific, Bremen 28199, Germany
| | | | - Alexander Makarov
- Thermo Fisher Scientific, Bremen 28199, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht 3584, The Netherlands
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
10
|
Fiorentino F, Rotili D, Mai A. Native mass spectrometry-directed drug discovery: Recent advances in investigating protein function and modulation. Drug Discov Today 2023; 28:103548. [PMID: 36871843 DOI: 10.1016/j.drudis.2023.103548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/15/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
Native mass spectrometry (nMS) is a biophysical method for studying protein complexes and can provide insights into subunit stoichiometry and composition, protein-ligand, and protein-protein interactions (PPIs). These analyses are made possible by preserving non-covalent interactions in the gas phase, thereby allowing the analysis of proteins in their native state. Consequently, nMS has been increasingly applied in early drug discovery campaigns for the characterization of protein-drug interactions and the evaluation of PPI modulators. Here, we discuss recent developments in nMS-directed drug discovery and provide a timely perspective on the possible applications of this technology in drug discovery.
Collapse
Affiliation(s)
- Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| |
Collapse
|
11
|
Dowling P, Gargan S, Swandulla D, Ohlendieck K. Fiber-Type Shifting in Sarcopenia of Old Age: Proteomic Profiling of the Contractile Apparatus of Skeletal Muscles. Int J Mol Sci 2023; 24:ijms24032415. [PMID: 36768735 PMCID: PMC9916839 DOI: 10.3390/ijms24032415] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
The progressive loss of skeletal muscle mass and concomitant reduction in contractile strength plays a central role in frailty syndrome. Age-related neuronal impairments are closely associated with sarcopenia in the elderly, which is characterized by severe muscular atrophy that can considerably lessen the overall quality of life at old age. Mass-spectrometry-based proteomic surveys of senescent human skeletal muscles, as well as animal models of sarcopenia, have decisively improved our understanding of the molecular and cellular consequences of muscular atrophy and associated fiber-type shifting during aging. This review outlines the mass spectrometric identification of proteome-wide changes in atrophying skeletal muscles, with a focus on contractile proteins as potential markers of changes in fiber-type distribution patterns. The observed trend of fast-to-slow transitions in individual human skeletal muscles during the aging process is most likely linked to a preferential susceptibility of fast-twitching muscle fibers to muscular atrophy. Studies with senescent animal models, including mostly aged rodent skeletal muscles, have confirmed fiber-type shifting. The proteomic analysis of fast versus slow isoforms of key contractile proteins, such as myosin heavy chains, myosin light chains, actins, troponins and tropomyosins, suggests them as suitable bioanalytical tools of fiber-type transitions during aging.
Collapse
Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, University of Bonn, D53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Correspondence: ; Tel.: +353-1-7083842
| |
Collapse
|
12
|
Kurisaki I, Suzuki M. Simulation toolkits at the molecular scale for trans-scale thermal signaling. Comput Struct Biotechnol J 2023; 21:2547-2557. [PMID: 37102156 PMCID: PMC10123322 DOI: 10.1016/j.csbj.2023.03.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 04/28/2023] Open
Abstract
Thermogenesis is a physiological activity of releasing heat that originates from intracellular biochemical reactions. Recent experimental studies discovered that externally applied heat changes intracellular signaling locally, resulting in global changes in cell morphology and signaling. Therefore, we hypothesize an inevitable contribution of thermogenesis in modulating biological system functions throughout the spatial scales from molecules to individual organisms. One key issue examining the hypothesis, namely, the "trans-scale thermal signaling," resides at the molecular scale on the amount of heat released via individual reactions and by which mechanism the heat is employed for cellular function operations. This review introduces atomistic simulation tool kits for studying the mechanisms of thermal signaling processes at the molecular scale that even state-of-the-art experimental methodologies of today are hardly accessible. We consider biological processes and biomolecules as potential heat sources in cells, such as ATP/GTP hydrolysis and multiple biopolymer complex formation and disassembly. Microscopic heat release could be related to mesoscopic processes via thermal conductivity and thermal conductance. Additionally, theoretical simulations to estimate these thermal properties in biological membranes and proteins are introduced. Finally, we envisage the future direction of this research field.
Collapse
Affiliation(s)
- Ikuo Kurisaki
- Waseda Research Institute for Science and Engineering, Waseda University, Bldg. No.55, S Tower, 4th Floor, 3–4-1 Okubo Shinjuku-ku, Tokyo 169–8555, Japan
- Corresponding authors.
| | - Madoka Suzuki
- Institute for Protein Research, Osaka University, 3–2 Yamadaoka, Suita, Osaka 565–0871, Japan
- Corresponding authors.
| |
Collapse
|
13
|
Abstract
The combination of large-scale protein separation techniques, sophisticated mass spectrometry, and systems bioinformatics has led to the establishment of proteomics as a distinct discipline within the wider field of protein biochemistry. Both discovery proteomics and targeted proteomics are widely used in biological and biomedical research, whereby the analytical approaches can be broadly divided into proteoform-centric top-down proteomics versus peptide-centric bottom-up proteomics. This chapter outlines the scientific value of top-down proteomics and describes how fluorescence two-dimensional difference gel electrophoresis can be combined with the systematic analysis of crucial post-translational modifications. The concept of on-membrane digestion following the electrophoretic transfer of proteins and the usefulness of comparative two-dimensional immunoblotting are discussed.
Collapse
Affiliation(s)
- Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
| |
Collapse
|
14
|
Drake ZC, Seffernick JT, Lindert S. Protein complex prediction using Rosetta, AlphaFold, and mass spectrometry covalent labeling. Nat Commun 2022; 13:7846. [PMID: 36543826 PMCID: PMC9772387 DOI: 10.1038/s41467-022-35593-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Covalent labeling (CL) in combination with mass spectrometry can be used as an analytical tool to study and determine structural properties of protein-protein complexes. However, data from these experiments is sparse and does not unambiguously elucidate protein structure. Thus, computational algorithms are needed to deduce structure from the CL data. In this work, we present a hybrid method that combines models of protein complex subunits generated with AlphaFold with differential CL data via a CL-guided protein-protein docking in Rosetta. In a benchmark set, the RMSD (root-mean-square deviation) of the best-scoring models was below 3.6 Å for 5/5 complexes with inclusion of CL data, whereas the same quality was only achieved for 1/5 complexes without CL data. This study suggests that our integrated approach can successfully use data obtained from CL experiments to distinguish between nativelike and non-nativelike models.
Collapse
Affiliation(s)
- Zachary C Drake
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, 43210, US
| | - Justin T Seffernick
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, 43210, US
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, 43210, US.
| |
Collapse
|
15
|
Marciano S, Dey D, Listov D, Fleishman SJ, Sonn-Segev A, Mertens H, Busch F, Kim Y, Harvey SR, Wysocki VH, Schreiber G. Protein quaternary structures in solution are a mixture of multiple forms. Chem Sci 2022; 13:11680-11695. [PMID: 36320402 PMCID: PMC9555727 DOI: 10.1039/d2sc02794a] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/21/2022] [Indexed: 11/21/2022] Open
Abstract
Over half the proteins in the E. coli cytoplasm form homo or hetero-oligomeric structures. Experimentally determined structures are often considered in determining a protein's oligomeric state, but static structures miss the dynamic equilibrium between different quaternary forms. The problem is exacerbated in homo-oligomers, where the oligomeric states are challenging to characterize. Here, we re-evaluated the oligomeric state of 17 different bacterial proteins across a broad range of protein concentrations and solutions by native mass spectrometry (MS), mass photometry (MP), size exclusion chromatography (SEC), and small-angle X-ray scattering (SAXS), finding that most exhibit several oligomeric states. Surprisingly, some proteins did not show mass-action driven equilibrium between the oligomeric states. For approximately half the proteins, the predicted oligomeric forms described in publicly available databases underestimated the complexity of protein quaternary structures in solution. Conversely, AlphaFold multimer provided an accurate description of the potential multimeric states for most proteins, suggesting that it could help resolve uncertainties on the solution state of many proteins.
Collapse
Affiliation(s)
- Shir Marciano
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot Israel
| | - Debabrata Dey
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot Israel
| | - Dina Listov
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot Israel
| | - Adar Sonn-Segev
- Refeyn Ltd 1 Electric Avenue, Ferry Hinksey Road Oxford OX2 0BY UK
| | - Haydyn Mertens
- Hamburg Outstation, European Molecular Biology Laboratory Notkestrasse 85 Hamburg 22607 Germany
| | - Florian Busch
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University Columbus OH 43210 USA
| | - Yongseok Kim
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University Columbus OH 43210 USA
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University Columbus OH 43210 USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University Columbus OH 43210 USA
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot Israel
| |
Collapse
|
16
|
Santambrogio C, Ponzini E, Grandori R. Native mass spectrometry for the investigation of protein structural (dis)order. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140828. [PMID: 35926718 DOI: 10.1016/j.bbapap.2022.140828] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/24/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
A central challenge in structural biology is represented by dynamic and heterogeneous systems, as typically represented by proteins in solution, with the extreme case of intrinsically disordered proteins (IDPs) [1-3]. These proteins lack a specific three-dimensional structure and have poorly organized secondary structure. For these reasons, they escape structural characterization by conventional biophysical methods. The investigation of these systems requires description of conformational ensembles, rather than of unique, defined structures or bundles of largely superimposable structures. Mass spectrometry (MS) has become a central tool in this field, offering a variety of complementary approaches to generate structural information on either folded or disordered proteins [4-6]. Two main categories of methods can be recognized. On one side, conformation-dependent reactions (such as cross-linking, covalent labeling, H/D exchange) are exploited to label molecules in solution, followed by the characterization of the labeling products by denaturing MS [7-11]. On the other side, non-denaturing ("native") MS can be used to directly explore the different conformational components in terms of geometry and structural compactness [12-16]. All these approaches have in common the capability to conjugate protein structure investigation with the peculiar analytical power of MS measurements, offering the possibility of assessing species distributions for folding and binding equilibria and the combination of both. These methods can be combined with characterization of noncovalent complexes [17, 18] and post-translational modifications [19-23]. This review focuses on the application of native MS to protein structure and dynamics investigation, with a general methodological section, followed by examples on specific proteins from our laboratory.
Collapse
Affiliation(s)
- Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
| | - Erika Ponzini
- Materials Science Department, University of Milano-Bicocca, Via R. Cozzi 55, 20125 Milan, Italy; COMiB Research Center, University of Milano-Bicocca, Via R. Cozzi 55, 20125 Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
| |
Collapse
|
17
|
Sipe SN, Lancaster EB, Butalewicz JP, Whitman CP, Brodbelt JS. Symmetry of 4-Oxalocrotonate Tautomerase Trimers Influences Unfolding and Fragmentation in the Gas Phase. J Am Chem Soc 2022; 144:12299-12309. [PMID: 35767842 DOI: 10.1021/jacs.2c03564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The recent discovery of asymmetric arrangements of trimers in the tautomerase superfamily (TSF) adds structural diversity to this already mechanistically diverse superfamily. Classification of asymmetric trimers has previously been determined using X-ray crystallography. Here, native mass spectrometry (MS) and ultraviolet photodissociation (UVPD) are employed as an integrated strategy for more rapid and sensitive differentiation of symmetric and asymmetric trimers. Specifically, the unfolding of symmetric and asymmetric trimers initiated by collisional heating was probed using UVPD, which revealed unique gas-phase unfolding pathways. Variations in UVPD patterns from native-like, compact trimeric structures to unfolded, extended conformations indicate a rearrangement of higher-order structure in the asymmetric trimers that are believed to be stabilized by salt-bridge triads, which are absent from the symmetric trimers. Consequently, the symmetric trimers were found to be less stable in the gas phase, resulting in enhanced UVPD fragmentation overall and a notable difference in higher-order re-structuring based on the extent of hydrogen migration of protein fragments. The increased stability of the asymmetric trimers may justify their evolution and concomitant diversification of the TSF. Facilitating the classification of TSF members as symmetric or asymmetric trimers assists in delineating the evolutionary history of the TSF.
Collapse
Affiliation(s)
- Sarah N Sipe
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Emily B Lancaster
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Jamie P Butalewicz
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Christian P Whitman
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States.,Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| |
Collapse
|
18
|
Snyder DT, Harvey SR, Wysocki VH. Surface-induced Dissociation Mass Spectrometry as a Structural Biology Tool. Chem Rev 2022; 122:7442-7487. [PMID: 34726898 PMCID: PMC9282826 DOI: 10.1021/acs.chemrev.1c00309] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Native mass spectrometry (nMS) is evolving into a workhorse for structural biology. The plethora of online and offline preparation, separation, and purification methods as well as numerous ionization techniques combined with powerful new hybrid ion mobility and mass spectrometry systems has illustrated the great potential of nMS for structural biology. Fundamental to the progression of nMS has been the development of novel activation methods for dissociating proteins and protein complexes to deduce primary, secondary, tertiary, and quaternary structure through the combined use of multiple MS/MS technologies. This review highlights the key features and advantages of surface collisions (surface-induced dissociation, SID) for probing the connectivity of subunits within protein and nucleoprotein complexes and, in particular, for solving protein structure in conjunction with complementary techniques such as cryo-EM and computational modeling. Several case studies highlight the significant role SID, and more generally nMS, will play in structural elucidation of biological assemblies in the future as the technology becomes more widely adopted. Cases are presented where SID agrees with solved crystal or cryoEM structures or provides connectivity maps that are otherwise inaccessible by "gold standard" structural biology techniques.
Collapse
Affiliation(s)
- Dalton T. Snyder
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210,Corresponding author:
| |
Collapse
|
19
|
Kurisaki I, Tanaka S. Remarked suppression of Aβ 42 protomer-protomer dissociation reaction elucidated by molecular dynamics simulation. Proteins 2022; 90:1367-1375. [PMID: 35137442 DOI: 10.1002/prot.26319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/24/2022] [Accepted: 02/02/2022] [Indexed: 01/27/2023]
Abstract
Multimeric protein complexes are molecular apparatuses to regulate biological systems and often determine their fate. Among proteins forming such molecular assemblies, amyloid proteins have drawn attention over a half-century since amyloid fibril formation of these proteins is supposed to be a common pathogenic cause for neurodegenerative diseases. This process is triggered by the accumulation of fibril-like aggregates, while the microscopic mechanisms are mostly elusive due to technical limitation of experimental methodologies in individually observing each of diverse aggregate species in the aqueous solution. We then addressed this problem by employing atomistic molecular dynamics simulations for the paradigmatic amyloid protein, amyloid-β (Aβ42 ). Seven different dimeric forms of oligomeric Aβ42 fibril-like aggregate in aqueous solution, ranging from tetramer to decamer, were considered. We found additive effects of the size of these fibril-like aggregates on their thermodynamic stability and have clarified kinetic suppression of protomer-protomer dissociation reactions at and beyond the point of pentamer dimer formation. This observation was obtained from the specific combination of the Aβ42 protomer structure and the physicochemical condition that we here examined, while it is worthwhile to recall that several amyloid fibrils take dimeric forms of their protomers. We could thus conclude that the stable formation of fibril-like protomer dimer should be involved in a turning point where rapid growth of amyloid fibrils is triggered.
Collapse
Affiliation(s)
- Ikuo Kurisaki
- Department of Computational Science, Graduate School of System Informatics, Kobe University, Kobe, Japan
| | - Shigenori Tanaka
- Department of Computational Science, Graduate School of System Informatics, Kobe University, Kobe, Japan
| |
Collapse
|
20
|
Characterization of a Salmonella transcription factor-DNA complex and identification of the inducer by native mass spectrometry. J Mol Biol 2022; 434:167480. [PMID: 35176290 PMCID: PMC8977229 DOI: 10.1016/j.jmb.2022.167480] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 11/21/2022]
Abstract
FraR, a transcriptional repressor, was postulated to regulate the metabolism of the Amadori compound fructose-asparagine (F-Asn) in the foodborne pathogen Salmonella enterica. Here, the DNA- and inducer-binding affinities and stoichiometries of FraR were determined and cross-validated by electrophoretic mobility-shift assays (EMSAs) and online buffer exchange coupled to native mass spectrometry (OBE-nMS). We demonstrate the utility of OBE-nMS to characterize protein and protein-DNA complexes that are not amenable to offline exchange into volatile buffers. OBE-nMS complemented EMSAs by revealing that FraR binds to the operator DNA as a dimer and by establishing 6-phosphofructose-aspartate as the inducer that weakens DNA binding by FraR. These results provide insights into how FraR regulates the expression of F-Asn-catabolizing enzymes and add to our understanding of the intricate bacterial circuitry that dictates utilization of diverse nutrients.
Collapse
|
21
|
Zhao F, Du Y, Zheng Z, Cui M, Liu Z. Native electrospray ionization mass spectrometry combined with molecular docking for the characterization of ginsenoside-myoglobin interactions. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e9203. [PMID: 34549468 DOI: 10.1002/rcm.9203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
RATIONALE The interactions between proteins and ligands are involved in many biological processes and early stages of drug development. Native electrospray ionization mass spectrometry (native ESI-MS) has played an important role in the characterization of protein-ligand interactions. Herein, native ESI-MS combined with molecular docking was used for the characterization of ginsenoside-myoglobin (Mb) interactions. METHODS The binding of ginsenosides (Rb3 , Rc, Rd, Re) to Mb was determined by native ESI-MS. Titration experiments were performed for the calculation of the dissociation constants (Kd ) of the complexes. Molecular docking was used to simulate the binding of ginsenosides with Mb by AutoDock. RESULTS The ginsenoside-Mb complex with stoichiometric ratio 1:1 was observed by native ESI-MS. The Kd values determined by the direct calculation method were matched with those obtained by the curve fitting method. However, the relative standard deviations (RSDs) obtained by direct calculation were larger than those obtained by curve fitting. From the molecular docking, it was inferred that hydrophobic interactions, hydrogen bonding and Van der Waals forces participate in the binding of ginsenosides to proteins. CONCLUSIONS The ginsenoside-Mb interactions can be characterized by ESI-MS combined with molecular docking. This approach can be helpful to investigate the interactions between natural drugs and proteins in various diseases.
Collapse
Affiliation(s)
- Fengjiao Zhao
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
- University of Science and Technology of China, Hefei, Anhui, China
| | - Yang Du
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
- University of Science and Technology of China, Hefei, Anhui, China
| | - Zhong Zheng
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
| | - Meng Cui
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
- University of Science and Technology of China, Hefei, Anhui, China
| | - Zhiqiang Liu
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
| |
Collapse
|
22
|
Priest L, Peters JS, Kukura P. Scattering-based Light Microscopy: From Metal Nanoparticles to Single Proteins. Chem Rev 2021; 121:11937-11970. [PMID: 34587448 PMCID: PMC8517954 DOI: 10.1021/acs.chemrev.1c00271] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Indexed: 02/02/2023]
Abstract
Our ability to detect, image, and quantify nanoscopic objects and molecules with visible light has undergone dramatic improvements over the past few decades. While fluorescence has historically been the go-to contrast mechanism for ultrasensitive light microscopy due to its superior background suppression and specificity, recent developments based on light scattering have reached single-molecule sensitivity. They also have the advantages of universal applicability and the ability to obtain information about the species of interest beyond its presence and location. Many of the recent advances are driven by novel approaches to illumination, detection, and background suppression, all aimed at isolating and maximizing the signal of interest. Here, we review these developments grouped according to the basic principles used, namely darkfield imaging, interferometric detection, and surface plasmon resonance microscopy.
Collapse
Affiliation(s)
| | | | - Philipp Kukura
- Physical and Theoretical
Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| |
Collapse
|
23
|
Abstract
Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.
Collapse
Affiliation(s)
- Amber D Rolland
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States.,Materials Science Institute, University of Oregon, Eugene, Oregon 97403-1252, United States
| |
Collapse
|
24
|
Bennett JL, Nguyen GTH, Donald WA. Protein-Small Molecule Interactions in Native Mass Spectrometry. Chem Rev 2021; 122:7327-7385. [PMID: 34449207 DOI: 10.1021/acs.chemrev.1c00293] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Small molecule drug discovery has been propelled by the continual development of novel scientific methodologies to occasion therapeutic advances. Although established biophysical methods can be used to obtain information regarding the molecular mechanisms underlying drug action, these approaches are often inefficient, low throughput, and ineffective in the analysis of heterogeneous systems including dynamic oligomeric assemblies and proteins that have undergone extensive post-translational modification. Native mass spectrometry can be used to probe protein-small molecule interactions with unprecedented speed and sensitivity, providing unique insights into polydisperse biomolecular systems that are commonly encountered during the drug discovery process. In this review, we describe potential and proven applications of native MS in the study of interactions between small, drug-like molecules and proteins, including large multiprotein complexes and membrane proteins. Approaches to quantify the thermodynamic and kinetic properties of ligand binding are discussed, alongside a summary of gas-phase ion activation techniques that have been used to interrogate the structure of protein-small molecule complexes. We additionally highlight some of the key areas in modern drug design for which native mass spectrometry has elicited significant advances. Future developments and applications of native mass spectrometry in drug discovery workflows are identified, including potential pathways toward studying protein-small molecule interactions on a whole-proteome scale.
Collapse
Affiliation(s)
- Jack L Bennett
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Giang T H Nguyen
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| |
Collapse
|
25
|
Sternicki LM, Nonomiya J, Liu M, Mulvihill MM, Quinn RJ. Native Mass Spectrometry for the Study of PROTAC GNE-987-Containing Ternary Complexes. ChemMedChem 2021; 16:2206-2210. [PMID: 33792163 PMCID: PMC8359942 DOI: 10.1002/cmdc.202100113] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Indexed: 12/14/2022]
Abstract
PROteolysis TArgeting Chimeras (PROTACs) promote the degradation, rather than inhibition, of a drug target as a mechanism for therapeutic treatment. Bifunctional PROTAC molecules allow simultaneous binding of both the target protein and an E3-Ubiquitin ligase, bringing the two proteins into close spatial proximity to allow ubiquitinylation and degradation of the target protein via the cell's endogenous protein degradation pathway. We utilized native mass spectrometry (MS) to study the ternary complexes promoted by the previously reported PROTAC GNE-987 between Brd4 bromodomains 1 and 2, and Von Hippel Lindeau E3-Ubiquitin Ligase. Native MS at high resolution allowed us to measure ternary complex formation as a function of PROTAC concentration to provide a measure of complex affinity and stability, whilst simultaneously measuring other intermediate protein species. Native MS provides a high-throughput, low sample consumption, direct screening method to measure ternary complexes for PROTAC development.
Collapse
Affiliation(s)
- Louise M. Sternicki
- Griffith Institute for Drug DiscoveryGriffith University46 Don Young RoadNathanQLD 4111Australia
| | - Jim Nonomiya
- Genentech Inc.1 DNA WaySouth San FranciscoCA 94080USA
| | - Miaomiao Liu
- Griffith Institute for Drug DiscoveryGriffith University46 Don Young RoadNathanQLD 4111Australia
| | | | - Ronald J. Quinn
- Griffith Institute for Drug DiscoveryGriffith University46 Don Young RoadNathanQLD 4111Australia
| |
Collapse
|
26
|
Chen S, Wu D, Robinson CV, Struwe WB. Native Mass Spectrometry Meets Glycomics: Resolving Structural Detail and Occupancy of Glycans on Intact Glycoproteins. Anal Chem 2021; 93:10435-10443. [PMID: 34279906 DOI: 10.1021/acs.analchem.1c01460] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Glycoproteins are inherently heterogeneous and therefore resolving structures in their entirety remains a major challenge in structural biology. Native mass spectrometry has transformed our ability to study glycoproteins, and despite advances in high-resolution instrumentation, there are comparatively a few studies demonstrating its potential with data largely limited to an overall measure of monosaccharide composition for all glycans across glycosylation sites for a given protein. Clearly, these readouts lack glycan topology information, namely, monosaccharide linkage and glycan branching. To address this deficiency, we developed a new approach that joins native mass spectrometry with glycan exoglycosidase sequencing, the combination of which provides remarkable glycoprotein structural details. We show how N-glycan branching, terminal fucosylation, LacNAc extensions, and N- and O-glycan occupancy (i.e., total number of glycans) can be directly characterized on intact glycoproteins with minimal sample preparation. Taken together, native exoglycosidase sequencing mass spectrometry (NES-MS) notably improves our ability to characterize protein glycosylation, addressing a significant need in structural biology that will enable new routes to understand glycoprotein function.
Collapse
Affiliation(s)
- Siyun Chen
- Physical and Theoretical Chemistry, Department of Chemistry, University of Oxford, OX1 3QZ Oxford, U.K
| | - Di Wu
- Physical and Theoretical Chemistry, Department of Chemistry, University of Oxford, OX1 3QZ Oxford, U.K
| | - Carol V Robinson
- Physical and Theoretical Chemistry, Department of Chemistry, University of Oxford, OX1 3QZ Oxford, U.K
| | - Weston B Struwe
- Physical and Theoretical Chemistry, Department of Chemistry, University of Oxford, OX1 3QZ Oxford, U.K
| |
Collapse
|
27
|
Collier MP, Moreira KB, Li KH, Chen YC, Itzhak D, Samant R, Leitner A, Burlingame A, Frydman J. Native mass spectrometry analyses of chaperonin complex TRiC/CCT reveal subunit N-terminal processing and re-association patterns. Sci Rep 2021; 11:13084. [PMID: 34158536 PMCID: PMC8219831 DOI: 10.1038/s41598-021-91086-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 05/05/2021] [Indexed: 11/14/2022] Open
Abstract
The eukaryotic chaperonin TRiC/CCT is a large ATP-dependent complex essential for cellular protein folding. Its subunit arrangement into two stacked eight-membered hetero-oligomeric rings is conserved from yeast to man. A recent breakthrough enables production of functional human TRiC (hTRiC) from insect cells. Here, we apply a suite of mass spectrometry techniques to characterize recombinant hTRiC. We find all subunits CCT1-8 are N-terminally processed by combinations of methionine excision and acetylation observed in native human TRiC. Dissociation by organic solvents yields primarily monomeric subunits with a small population of CCT dimers. Notably, some dimers feature non-canonical inter-subunit contacts absent in the initial hTRiC. This indicates individual CCT monomers can promiscuously re-assemble into dimers, and lack the information to assume the specific interface pairings in the holocomplex. CCT5 is consistently the most stable subunit and engages in the greatest number of non-canonical dimer pairings. These findings confirm physiologically relevant post-translational processing and function of recombinant hTRiC and offer quantitative insight into the relative stabilities of TRiC subunits and interfaces, a key step toward reconstructing its assembly mechanism. Our results also highlight the importance of assigning contacts identified by native mass spectrometry after solution dissociation as canonical or non-canonical when investigating multimeric assemblies.
Collapse
Affiliation(s)
| | | | - Kathy H Li
- Department of Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Yu-Chan Chen
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Rahul Samant
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, Zurich, Switzerland
| | - Alma Burlingame
- Department of Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, USA.
| |
Collapse
|
28
|
Song JH, Wagner ND, Yan J, Li J, Huang RYC, Balog AJ, Newitt JA, Chen G, Gross ML. Native mass spectrometry and gas-phase fragmentation provide rapid and in-depth topological characterization of a PROTAC ternary complex. Cell Chem Biol 2021; 28:1528-1538.e4. [PMID: 34081921 DOI: 10.1016/j.chembiol.2021.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/17/2021] [Accepted: 05/07/2021] [Indexed: 01/24/2023]
Abstract
Proteolysis-targeting chimeras (PROTACs) represent a new direction in small-molecule therapeutics whereby a heterobifunctional linker to a protein of interest (POI) induces its ubiquitination-based proteolysis by recruiting an E3 ligase. Here, we show that charge reduction, native mass spectrometry, and gas-phase activation methods combine for an in-depth analysis of a PROTAC-linked ternary complex. Electron capture dissociation (ECD) of the intact POI-PROTAC-VCB complex (a trimeric subunit of an E3 ubiquitin ligase) promotes POI dissociation. Collision-induced dissociation (CID) causes elimination of the nonperipheral PROTAC, producing an intact VCB-POI complex not seen in solution but consistent with PROTAC-induced protein-protein interactions. In addition, we used ion mobility spectrometry (IMS) and collisional activation to identify the source of this unexpected dissociation. Together, the evidence shows that this integrated approach can be used to screen for ternary complex formation and PROTAC-protein contacts and may report on PROTAC-induced protein-protein interactions, a characteristic correlated with PROTAC selectivity and efficacy.
Collapse
Affiliation(s)
- Jong Hee Song
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nicole D Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Jing Yan
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Jing Li
- Bristol Myers Squibb Company, Research and Early Development, Princeton, NJ 08543, USA
| | - Richard Y-C Huang
- Bristol Myers Squibb Company, Research and Early Development, Princeton, NJ 08543, USA
| | - Aaron J Balog
- Bristol Myers Squibb Company, Research and Early Development, Princeton, NJ 08543, USA
| | - John A Newitt
- Bristol Myers Squibb Company, Research and Early Development, Princeton, NJ 08543, USA
| | - Guodong Chen
- Bristol Myers Squibb Company, Research and Early Development, Princeton, NJ 08543, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA.
| |
Collapse
|
29
|
Krichel B, Bylapudi G, Schmidt C, Blanchet C, Schubert R, Brings L, Koehler M, Zenobi R, Svergun D, Lorenzen K, Madhugiri R, Ziebuhr J, Uetrecht C. Hallmarks of Alpha- and Betacoronavirus non-structural protein 7+8 complexes. SCIENCE ADVANCES 2021; 7:7/10/eabf1004. [PMID: 33658206 PMCID: PMC7929516 DOI: 10.1126/sciadv.abf1004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 01/19/2021] [Indexed: 05/02/2023]
Abstract
Coronaviruses infect many different species including humans. The last two decades have seen three zoonotic coronaviruses, with SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) causing a pandemic in 2020. Coronaviral non-structural proteins (nsps) form the replication-transcription complex (RTC). Nsp7 and nsp8 interact with and regulate the RNA-dependent RNA-polymerase and other enzymes in the RTC. However, the structural plasticity of nsp7+8 complexes has been under debate. Here, we present the framework of nsp7+8 complex stoichiometry and topology based on native mass spectrometry and complementary biophysical techniques of nsp7+8 complexes from seven coronaviruses in the genera Alpha- and Betacoronavirus including SARS-CoV-2. Their complexes cluster into three groups, which systematically form either heterotrimers or heterotetramers or both, exhibiting distinct topologies. Moreover, even at high protein concentrations, SARS-CoV-2 nsp7+8 consists primarily of heterotetramers. From these results, the different assembly paths can be pinpointed to specific residues and an assembly model proposed.
Collapse
Affiliation(s)
- Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Ganesh Bylapudi
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | | | | | | | | | - Martin Koehler
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zürich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zürich, Switzerland
| | - Dmitri Svergun
- EMBL Hamburg c/o DESY, Notkestraße 85, 22607 Hamburg, Germany
| | | | - Ramakanth Madhugiri
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.
- European XFEL GmbH, Schenefeld, Germany
| |
Collapse
|
30
|
Affiliation(s)
- James E. Keener
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Guozhi Zhang
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Michael T. Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
| |
Collapse
|
31
|
Sever AIM, Yin V, Konermann L. Interrogating the Quaternary Structure of Noncanonical Hemoglobin Complexes by Electrospray Mass Spectrometry and Collision-Induced Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:270-280. [PMID: 33124417 DOI: 10.1021/jasms.0c00320] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Various activation methods are available for the fragmentation of gaseous protein complexes produced by electrospray ionization (ESI). Such experiments can potentially yield insights into quaternary structure. Collision-induced dissociation (CID) is the most widely used fragmentation technique. Unfortunately, CID of protein complexes is dominated by the ejection of highly charged monomers, a process that does not yield any structural insights. Using hemoglobin (Hb) as a model system, this work examines under what conditions CID generates structurally informative subcomplexes. Native ESI mainly produced tetrameric Hb ions. In addition, "noncanonical" hexameric and octameric complexes were observed. CID of all these species [(αβ)2, (αβ)3, and (αβ)4] predominantly generated highly charged monomers. In addition, we observed hexamer → tetramer + dimer dissociation, implying that hexamers have a tetramer··dimer architecture. Similarly, the observation of octamer → two tetramer dissociation revealed that octamers have a tetramer··tetramer composition. Gas-phase candidate structures of Hb assemblies were produced by molecular dynamics (MD) simulations. Ion mobility spectrometry was used to identify the most likely candidates. Our data reveal that the capability of CID to produce structurally informative subcomplexes depends on the fate of protein-protein interfaces after transfer into the gas phase. Collapse of low affinity interfaces conjoins the corresponding subunits and favors CID via monomer ejection. Structurally informative subcomplexes are formed only if low affinity interfaces do not undergo a major collapse. However, even in these favorable cases CID is still dominated by monomer ejection, requiring careful analysis of the experimental data for the identification of structurally informative subcomplexes.
Collapse
Affiliation(s)
- Alexander I M Sever
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Victor Yin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| |
Collapse
|
32
|
Favier A, Gans P, Boeri Erba E, Signor L, Muthukumar SS, Pfannschmidt T, Blanvillain R, Cobessi D. The Plastid-Encoded RNA Polymerase-Associated Protein PAP9 Is a Superoxide Dismutase With Unusual Structural Features. FRONTIERS IN PLANT SCIENCE 2021; 12:668897. [PMID: 34276730 PMCID: PMC8278866 DOI: 10.3389/fpls.2021.668897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/28/2021] [Indexed: 05/09/2023]
Abstract
In Angiosperms, the plastid-encoded RNA polymerase (PEP) is a multimeric enzyme, essential for the proper expression of the plastid genome during chloroplast biogenesis. It is especially required for the light initiated expression of photosynthesis genes and the subsequent build-up of the photosynthetic apparatus. The PEP complex is composed of a prokaryotic-type core of four plastid-encoded subunits and 12 nuclear-encoded PEP-associated proteins (PAPs). Among them, there are two iron superoxide dismutases, FSD2/PAP9 and FSD3/PAP4. Superoxide dismutases usually are soluble enzymes not bound into larger protein complexes. To investigate this unusual feature, we characterized PAP9 using molecular genetics, fluorescence microscopy, mass spectrometry, X-ray diffraction, and solution-state NMR. Despite the presence of a predicted nuclear localization signal within the sequence of the predicted chloroplast transit peptide, PAP9 was mainly observed within plastids. Mass spectrometry experiments with the recombinant Arabidopsis PAP9 suggested that monomers and dimers of PAP9 could be associated to the PEP complex. In crystals, PAP9 occurred as a dimeric enzyme that displayed a similar fold to that of the FeSODs or manganese SOD (MnSODs). A zinc ion, instead of the expected iron, was found to be penta-coordinated with a trigonal-bipyramidal geometry in the catalytic center of the recombinant protein. The metal coordination involves a water molecule and highly conserved residues in FeSODs. Solution-state NMR and DOSY experiments revealed an unfolded C-terminal 34 amino-acid stretch in the stand-alone protein and few internal residues interacting with the rest of the protein. We hypothesize that this C-terminal extension had appeared during evolution as a distinct feature of the FSD2/PAP9 targeting it to the PEP complex. Close vicinity to the transcriptional apparatus may allow for the protection against the strongly oxidizing aerial environment during plant conquering of terrestrial habitats.
Collapse
Affiliation(s)
- Adrien Favier
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Pierre Gans
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | | | - Luca Signor
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | | | | | - Robert Blanvillain
- Université Grenoble-Alpes, CNRS, CEA, INRA, IRIG-LPCV, Grenoble, France
- *Correspondence: Robert Blanvillain,
| | - David Cobessi
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
- David Cobessi,
| |
Collapse
|
33
|
Divalent cations influence the dimerization mode of murine S100A9 protein by modulating its disulfide bond pattern. J Struct Biol 2020; 213:107689. [PMID: 33359632 DOI: 10.1016/j.jsb.2020.107689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 12/19/2022]
Abstract
S100A9, with its congener S100A8, belongs to the S100 family of calcium-binding proteins found exclusively in vertebrates. These two proteins are major constituents of neutrophils. In response to a pathological condition, they can be released extracellularly and become alarmins that induce both pro- and anti-inflammatory signals, through specific cell surface receptors. They also act as antimicrobial agents, mainly as a S100A8/A9 heterocomplex, through metal sequestration. The mechanisms whereby divalent cations modulate the extracellular functions of S100A8 and S100A9 are still unclear. Importantly, it has been proposed that these ions may affect both the ternary and quaternary structure of these proteins, thereby influencing their physiological properties. In the present study, we report the crystal structures of WT and C80A murine S100A9 (mS100A9), determined at 1.45 and 2.35 Å resolution, respectively, in the presence of calcium and zinc. These structures reveal a canonical homodimeric form for the protein. They also unravel an intramolecular disulfide bridge that stabilizes the C-terminal tail in a rigid conformation, thus shaping a second Zn-binding site per S100A9 protomer. In solution, mS100A9 apparently binds only two zinc ions per homodimer, with an affinity in the micromolar range, and aggregates in the presence of excess zinc. Using mass spectrometry, we demonstrate that mS100A9 can form both non-covalent and covalent homodimers with distinct disulfide bond patterns. Interestingly, calcium and zinc seem to affect differentially the relative proportion of these forms. We discuss how the metal-dependent interconversion between mS100A9 homodimers may explain the versatility of physiological functions attributed to the protein.
Collapse
|
34
|
Giampà M, Sgobba E. Insight to Functional Conformation and Noncovalent Interactions of Protein-Protein Assembly Using MALDI Mass Spectrometry. Molecules 2020; 25:E4979. [PMID: 33126406 PMCID: PMC7662314 DOI: 10.3390/molecules25214979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 11/16/2022] Open
Abstract
Noncovalent interactions are the keys to the structural organization of biomolecule e.g., proteins, glycans, lipids in the process of molecular recognition processes e.g., enzyme-substrate, antigen-antibody. Protein interactions lead to conformational changes, which dictate the functionality of that protein-protein complex. Besides biophysics techniques, noncovalent interaction and conformational dynamics, can be studied via mass spectrometry (MS), which represents a powerful tool, due to its low sample consumption, high sensitivity, and label-free sample. In this review, the focus will be placed on Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) and its role in the analysis of protein-protein noncovalent assemblies exploring the relationship within noncovalent interaction, conformation, and biological function.
Collapse
Affiliation(s)
- Marco Giampà
- MR Cancer Group, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Olav Kyrres Gate 9, 7030 Trondheim, Norway
| | - Elvira Sgobba
- Genetics and Plant Physiology, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden;
| |
Collapse
|
35
|
Krichel B, Bylapudi G, Schmidt C, Blanchet C, Schubert R, Brings L, Koehler M, Zenobi R, Svergun D, Lorenzen K, Madhugiri R, Ziebuhr J, Uetrecht C. Hallmarks of Alpha- and Betacoronavirus non-structural protein 7+8 complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.09.30.320762. [PMID: 33024972 PMCID: PMC7536876 DOI: 10.1101/2020.09.30.320762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Coronaviruses infect many different species including humans. The last two decades have seen three zoonotic coronaviruses with SARS-CoV-2 causing a pandemic in 2020. Coronaviral non-structural proteins (nsp) built up the replication-transcription complex (RTC). Nsp7 and nsp8 interact with and regulate the RNA-dependent RNA-polymerase and other enzymes in the RTC. However, the structural plasticity of nsp7+8 complex has been under debate. Here, we present the framework of nsp7+8 complex stoichiometry and topology based on a native mass spectrometry and complementary biophysical techniques of nsp7+8 complexes from seven coronaviruses in the genera Alpha- and Betacoronavirus including SARS-CoV-2. Their complexes cluster into three groups, which systematically form either heterotrimers or heterotetramers or both, exhibiting distinct topologies. Moreover, even at high protein concentrations mainly heterotetramers are observed for SARS-CoV-2 nsp7+8. From these results, the different assembly paths can be pinpointed to specific residues and an assembly model is proposed.
Collapse
Affiliation(s)
- Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Ganesh Bylapudi
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | | | | | | | | | - Martin Koehler
- ETH Zurich D-CHAB Lab of Organic Chemistry, Zürich, Switzerland
| | - Renato Zenobi
- ETH Zurich D-CHAB Lab of Organic Chemistry, Zürich, Switzerland
| | - Dmitri Svergun
- EMBL Hamburg c/o DESY, Notkestraße 85, 22607 Hamburg, Germany
| | | | - Ramakanth Madhugiri
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- European XFEL GmbH, Schenefeld, Germany
| |
Collapse
|