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Fernandes TM, Silva MA, Morgado L, Salgueiro CA. Hemes on a string: insights on the functional mechanisms of PgcA from Geobacter sulfurreducens. J Biol Chem 2023; 299:105167. [PMID: 37595873 PMCID: PMC10570954 DOI: 10.1016/j.jbc.2023.105167] [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: 05/24/2023] [Revised: 08/05/2023] [Accepted: 08/10/2023] [Indexed: 08/20/2023] Open
Abstract
Microbial extracellular reduction of insoluble compounds requires soluble electron shuttles that diffuse in the environment, freely diffusing cytochromes, or direct contact with cellular conductive appendages that release or harvest electrons to assure a continuous balance between cellular requirements and environmental conditions. In this work, we produced and characterized the three cytochrome domains of PgcA, an extracellular triheme cytochrome that contributes to Fe(III) and Mn(IV) oxides reduction in Geobacter sulfurreducens. The three monoheme domains are structurally homologous, but their heme groups show variable axial coordination and reduction potential values. Electron transfer experiments monitored by NMR and visible spectroscopy show the variable extent to which the domains promiscuously exchange electrons while reducing different electron acceptors. The results suggest that PgcA is part of a new class of cytochromes - microbial heme-tethered redox strings - that use low-complexity protein stretches to bind metals and promote intra- and intermolecular electron transfer events through its cytochrome domains.
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Affiliation(s)
- Tomás M Fernandes
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Marta A Silva
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Leonor Morgado
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
| | - Carlos A Salgueiro
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
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2
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Ghosh R, Thomas DS, Arcot J. Molecular Recognition Patterns between Vitamin B12 and Proteins Explored through STD-NMR and In Silico Studies. Foods 2023; 12:foods12030575. [PMID: 36766105 PMCID: PMC9914923 DOI: 10.3390/foods12030575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 02/03/2023] Open
Abstract
Ligand-receptor molecular recognition is the basis of biological processes. The Saturation Transfer Difference-NMR (STD-NMR) technique has been recently used to gain qualitative and quantitative information about physiological interactions at an atomic resolution. The molecular recognition patterns between the cyanocobalamin (CNBL)/aqua cobalamin (OHBL) and different plant and animal proteins were investigated via STD-NMR supplemented by molecular docking. This study demonstrates that myoglobin has the highest binding affinity and that gluten has the lowest affinity. Casein also shows a higher binding affinity for cyanocobalamin when compared with that of plant-based proteins. STD-NMR results showed the moderate binding capability of casein with both CNBL and OHBL. Computer simulation confirmed the recognition mode in theory and was compared with the experiments. This work is beneficial for understanding the binding affinity and biological action of cyanocobalamin and will attract researchers to use NMR technology to link the chemical and physiological properties of nutrients.
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Affiliation(s)
- Ruchira Ghosh
- Food and Health, School of Chemical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
| | | | - Jayashree Arcot
- Food and Health, School of Chemical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
- Correspondence: ; Tel.: +61-293855360
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3
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Almeida FCL, Sanches K, Caruso IP, Melo FA. NMR Relaxation Dispersion Experiments to Study Phosphopeptide Recognition by SH2 Domains: The Grb2-SH2-Phosphopeptide Encounter Complex. Methods Mol Biol 2023; 2705:135-151. [PMID: 37668973 DOI: 10.1007/978-1-0716-3393-9_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Protein interactions are at the essence of life. Proteins evolved not to have stable structures, but rather to be specialized in participating in a network of interactions. Every interaction involving proteins comprises the formation of an encounter complex, which may have two outcomes: (i) the dissociation or (ii) the formation of the final specific complex. Here, we present a methodology to characterize the encounter complex of the Grb2-SH2 domain with a phosphopeptide. This method can be generalized to other protein partners. It consists of the measurement of 15N CPMG relaxation dispersion (RD) profiles of the protein in the free state, which describes the residues that are in conformational exchange. We then acquire the dispersion profiles of the protein at a semisaturated concentration of the ligand. At this condition, the chemical exchange between the free and bound state leads to the observation of dispersion profiles in residues that are not in conformational exchange in the free state. This is due to fuzzy interactions that are typical of the encounter complexes. The transient "touching" of the ligand in the protein partner generates these new relaxation dispersion profiles. For the Grb2-SH2 domain, we observed a wider surface at SH2 for the encounter complex than the phosphopeptide (pY) binding site, which might explain the molecular recognition of remote phosphotyrosine. The Grb2-SH2-pY encounter complex is dominated by electrostatic interactions, which contribute to the fuzziness of the complex, but also have contribution of hydrophobic interactions.
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Affiliation(s)
- Fabio C L Almeida
- National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
- Institute of Medical Biochemistry - IBqM, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Karoline Sanches
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
- ARC Centre for Fragment-Based Design, Monash University, Parkville, VIC, Australia
| | - Icaro P Caruso
- National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), Sao Jose do Rio Preto, Sao Paulo, Brazil
| | - Fernando A Melo
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), Sao Jose do Rio Preto, Sao Paulo, Brazil
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4
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Casado-Combreras MÁ, Rivero-Rodríguez F, Elena-Real CA, Molodenskiy D, Díaz-Quintana A, Martinho M, Gerbaud G, González-Arzola K, Velázquez-Campoy A, Svergun D, Belle V, De la Rosa MA, Díaz-Moreno I. PP2A is activated by cytochrome c upon formation of a diffuse encounter complex with SET/TAF-Iβ. Comput Struct Biotechnol J 2022; 20:3695-3707. [PMID: 35891793 PMCID: PMC9293736 DOI: 10.1016/j.csbj.2022.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/25/2022] Open
Abstract
Intrinsic protein flexibility is of overwhelming relevance for intermolecular recognition and adaptability of highly dynamic ensemble of complexes, and the phenomenon is essential for the understanding of numerous biological processes. These conformational ensembles-encounter complexes-lack a unique organization, which prevents the determination of well-defined high resolution structures. This is the case for complexes involving the oncoprotein SET/template-activating factor-Iβ (SET/TAF-Iβ), a histone chaperone whose functions and interactions are significantly affected by its intrinsic structural plasticity. Besides its role in chromatin remodeling, SET/TAF-Iβ is an inhibitor of protein phosphatase 2A (PP2A), which is a key phosphatase counteracting transcription and signaling events controlling the activity of DNA damage response (DDR) mediators. During DDR, SET/TAF-Iβ is sequestered by cytochrome c (Cc) upon migration of the hemeprotein from mitochondria to the cell nucleus. Here, we report that the nuclear SET/TAF-Iβ:Cc polyconformational ensemble is able to activate PP2A. In particular, the N-end folded, globular region of SET/TAF-Iβ (a.k.a. SET/TAF-Iβ ΔC)-which exhibits an unexpected, intrinsically highly dynamic behavior-is sufficient to be recognized by Cc in a diffuse encounter manner. Cc-mediated blocking of PP2A inhibition is deciphered using an integrated structural and computational approach, combining small-angle X-ray scattering, electron paramagnetic resonance, nuclear magnetic resonance, calorimetry and molecular dynamics simulations.
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Key Words
- ANP32B, Acidic leucine-rich nuclear phosphoprotein family member B
- BTFA, 3-bromo-1,1,1-trifluoroacetone
- CD, Circular dichroism
- CDK9, Cyclin-dependent kinase 9
- CW, Continuous wave
- Cc, Cytochrome c
- Cytochrome c
- DDR, DNA damage response
- DEER, Double electron–electron resonance
- DLS, Dynamic light scattering
- DMEM, Dulbecco’s modified Eagle’s medium
- DNA, Deoxyribonucleic acid
- DTT, Dithiotreitol
- Dmax, Maximum dimension
- EDTA, Ethylenediamine tetraacetic acid
- EGTA, Ethyleneglycol tetraacetic acid
- EPR, Electron paramagnetic resonance
- Encounter complex
- FBS, Fetal bovine serum
- GUI, Graphical user interface
- HEK, Human embryonic kidney cells
- HRP, Horseradish peroxidase
- I2PP2A, Inhibitor 2 of the protein phosphatase 2A
- I3PP2A, Inhibitor 3 of the protein phosphatase 2A
- INTAC, Integrator-PP2A complex
- IPTG, Isopropyl-β-D-1-thiogalactopyranoside
- ITC, Isothermal titration calorimetry
- Ip/Id, Intensity ratio of NMR resonances between paramagnetic and diamagnetic samples
- LB, Luria-Bertani
- MD, Molecular dynamics
- MTS, (1-acetoxy-2,2,5,5-tetramethyl-δ-3-pyrroline-3-methyl) methanethiosulfonate
- MTSL, (1-oxyl-2,2,5,5-tetramethyl- δ −3-pyrroline-3-methyl) methanethiosulfonate
- MW, Molecular weight
- Molecular dynamics
- NAP1, Nucleosome assembly protein 1
- NAPL, Nucleosome assembly protein L
- NMA, Normal mode analysis
- NMR, Nuclear magnetic resonance
- NPT, Constant number, pressure and temperature
- NVT, Constant number, volume and temperature
- Nuclear magnetic resonance
- OD600, Optical density measured at 600 nm
- OPC, Optimal 3-charge, 4-point rigid water model
- PCR, Polymerase chain reaction
- PME, Particle mesh Ewald
- PMSF, Phenylmethylsulfonyl fluoride
- PP2A, Protein phosphatase 2A
- PRE, Paramagnetic relaxation enhancement
- PVDF, Polyvinylidene fluoride
- Protein phosphatase 2A
- RNA, Ribonucleic acid
- RNApol II, RNA polymerase II
- Rg, Radius of gyration
- SAXS, Small-angle X-ray scattering
- SC, Sample changer
- SDS-PAGE, Sodium dodecylsulfate-polyacrylamide gel electrophoresis
- SDSL, Site-directed spin labeling
- SEC, Size-exclusion chromatography
- SET/TAF-Iβ
- SET/TAF-Iβ ΔC, SET/template-activating factor-Iβ construct lacking its C-terminal domain
- SET/TAF-Iβ, SET/template-activating factor-Iβ
- SPRi, Surface plasmon resonance imaging
- TAF-Iα, Template-activating factor-Iα
- TPBS, Tween 20-phosphate buffered saline
- VPS75, Vacuolar protein sorting-associated protein 75
- WT, Wild type
- XRD, X-ray diffraction
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Affiliation(s)
- Miguel Á. Casado-Combreras
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Francisco Rivero-Rodríguez
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Carlos A. Elena-Real
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
- Centre de Biologie Structurale (CBS), INSERM, Centre National de la Recherche Scientifique (CNRS) and Université de Montpellier. 29 rue de Navacelles, 34090 Montpellier, France
| | - Dmitry Molodenskiy
- European Molecular Biology Laboratory, Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestr. 85, 22607 Hamburg, Germany
| | - Antonio Díaz-Quintana
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Marlène Martinho
- Aix Marseille Univ. Centre National de la Recherche Scientifique (CNRS), BIP UMR7281, Bioénergétique et Ingénierie des protéines, 13402 Marseille, France
| | - Guillaume Gerbaud
- Aix Marseille Univ. Centre National de la Recherche Scientifique (CNRS), BIP UMR7281, Bioénergétique et Ingénierie des protéines, 13402 Marseille, France
| | - Katiuska González-Arzola
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Adrián Velázquez-Campoy
- Institute of Biocomputation and Physic of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza. C. de Mariano Esquillor Gómez, Edificio I+D, 50018 Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, C. Pedro Cerbuna, 12, 50009 Zaragoza, Spain
- Instituto de Investigación Sanitaria de Aragón (IIS Aragon), Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), C. de Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestr. 85, 22607 Hamburg, Germany
| | - Valérie Belle
- Aix Marseille Univ. Centre National de la Recherche Scientifique (CNRS), BIP UMR7281, Bioénergétique et Ingénierie des protéines, 13402 Marseille, France
| | - Miguel A. De la Rosa
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
| | - Irene Díaz-Moreno
- Institute for Chemical Research (IIQ), Scientific Research Centre “Isla de la Cartuja” (cicCartuja), University of Seville and CSIC, Avda. Américo Vespucio, 49, 41092 Seville, Spain
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5
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Obi CD, Bhuiyan T, Dailey HA, Medlock AE. Ferrochelatase: Mapping the Intersection of Iron and Porphyrin Metabolism in the Mitochondria. Front Cell Dev Biol 2022; 10:894591. [PMID: 35646904 PMCID: PMC9133952 DOI: 10.3389/fcell.2022.894591] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/14/2022] [Indexed: 12/29/2022] Open
Abstract
Porphyrin and iron are ubiquitous and essential for sustaining life in virtually all living organisms. Unlike iron, which exists in many forms, porphyrin macrocycles are mostly functional as metal complexes. The iron-containing porphyrin, heme, serves as a prosthetic group in a wide array of metabolic pathways; including respiratory cytochromes, hemoglobin, cytochrome P450s, catalases, and other hemoproteins. Despite playing crucial roles in many biological processes, heme, iron, and porphyrin intermediates are potentially cytotoxic. Thus, the intersection of porphyrin and iron metabolism at heme synthesis, and intracellular trafficking of heme and its porphyrin precursors are tightly regulated processes. In this review, we discuss recent advances in understanding the physiological dynamics of eukaryotic ferrochelatase, a mitochondrially localized metalloenzyme. Ferrochelatase catalyzes the terminal step of heme biosynthesis, the insertion of ferrous iron into protoporphyrin IX to produce heme. In most eukaryotes, except plants, ferrochelatase is localized to the mitochondrial matrix, where substrates are delivered and heme is synthesized for trafficking to multiple cellular locales. Herein, we delve into the structural and functional features of ferrochelatase, as well as its metabolic regulation in the mitochondria. We discuss the regulation of ferrochelatase via post-translational modifications, transportation of substrates and product across the mitochondrial membrane, protein-protein interactions, inhibition by small-molecule inhibitors, and ferrochelatase in protozoal parasites. Overall, this review presents insight on mitochondrial heme homeostasis from the perspective of ferrochelatase.
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Affiliation(s)
- Chibuike David Obi
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Tawhid Bhuiyan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Harry A. Dailey
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- Department of Microbiology, University of Georgia, Athens, GA, United States
| | - Amy E. Medlock
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- Augusta University/University of Georgia Medical Partnership, University of Georgia, Athens, GA, United States
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6
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Echeverria I, Braberg H, Krogan NJ, Sali A. Integrative structure determination of histones H3 and H4 using genetic interactions. FEBS J 2022; 290:2565-2575. [PMID: 35298864 PMCID: PMC9481981 DOI: 10.1111/febs.16435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 02/11/2022] [Accepted: 03/15/2022] [Indexed: 11/28/2022]
Abstract
Integrative structure modeling is increasingly used for determining the architectures of biological assemblies, especially those that are structurally heterogeneous. Recently, we reported on how to convert in vivo genetic interaction measurements into spatial restraints for structural modeling: first, phenotypic profiles are generated for each point mutation and thousands of gene deletions or environmental perturbations. Following, the phenotypic profile similarities are converted into distance restraints on the pairs of mutated residues. We illustrate the approach by determining the structure of the histone H3-H4 complex. The method is implemented in our open-source IMP program, expanding the structural biology toolbox by allowing structural characterization based on in vivo data without the need to purify the target system. We compare genetic interaction measurements to other sources of structural information, such as residue coevolution and deep-learning structure prediction of complex subunits. We also suggest that determining genetic interactions could benefit from new technologies, such as CRISPR-Cas9 approaches to gene editing, especially for mammalian cells. Finally, we highlight the opportunity for using genetic interactions to determine recalcitrant biomolecular structures, such as those of disordered proteins, transient protein assemblies, and host-pathogen protein complexes.
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Affiliation(s)
- Ignacia Echeverria
- Department of Cellular and Molecular Pharmacology University of California, San Francisco CA USA
- Quantitative Biosciences Institute University of California, San Francisco CA USA
- Department of Bioengineering and Therapeutic Sciences University of California, San Francisco CA USA
| | - Hannes Braberg
- Department of Cellular and Molecular Pharmacology University of California, San Francisco CA USA
- Quantitative Biosciences Institute University of California, San Francisco CA USA
| | - Nevan J. Krogan
- Department of Cellular and Molecular Pharmacology University of California, San Francisco CA USA
- Quantitative Biosciences Institute University of California, San Francisco CA USA
- Gladstone Institute of Data Science and Biotechnology J. David Gladstone Institutes San Francisco CA USA
| | - Andrej Sali
- Quantitative Biosciences Institute University of California, San Francisco CA USA
- Department of Bioengineering and Therapeutic Sciences University of California, San Francisco CA USA
- Department of Pharmaceutical Chemistry University of California, San Francisco CA USA
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7
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Greco TM, Secker C, Ramos ES, Federspiel JD, Liu JP, Perez AM, Al-Ramahi I, Cantle JP, Carroll JB, Botas J, Zeitlin SO, Wanker EE, Cristea IM. Dynamics of huntingtin protein interactions in the striatum identifies candidate modifiers of Huntington disease. Cell Syst 2022; 13:304-320.e5. [PMID: 35148841 PMCID: PMC9317655 DOI: 10.1016/j.cels.2022.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/18/2021] [Accepted: 01/24/2022] [Indexed: 12/13/2022]
Abstract
Huntington disease (HD) is a monogenic neurodegenerative disorder with one causative gene, huntingtin (HTT). Yet, HD pathobiology is multifactorial, suggesting that cellular factors influence disease progression. Here, we define HTT protein-protein interactions (PPIs) perturbed by the mutant protein with expanded polyglutamine in the mouse striatum, a brain region with selective HD vulnerability. Using metabolically labeled tissues and immunoaffinity purification-mass spectrometry, we establish that polyglutamine-dependent modulation of HTT PPI abundances and relative stability starts at an early stage of pathogenesis in a Q140 HD mouse model. We identify direct and indirect PPIs that are also genetic disease modifiers using in-cell two-hybrid and behavioral assays in HD human cell and Drosophila models, respectively. Validated, disease-relevant mHTT-dependent interactions encompass mediators of synaptic neurotransmission (SNAREs and glutamate receptors) and lysosomal acidification (V-ATPase). Our study provides a resource for understanding mHTT-dependent dysfunction in cortico-striatal cellular networks, partly through impaired synaptic communication and endosomal-lysosomal system. A record of this paper's Transparent Peer Review process is included in the supplemental information.
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Affiliation(s)
- Todd M Greco
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ, USA
| | - Christopher Secker
- Neuroproteomics, Max Delbrück Centre for Molecular Medicine, Berlin, Germany
| | - Eduardo Silva Ramos
- Neuroproteomics, Max Delbrück Centre for Molecular Medicine, Berlin, Germany
| | - Joel D Federspiel
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ, USA
| | - Jeh-Ping Liu
- Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Alma M Perez
- Jan and Dan Duncan Neurological Research Institute, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ismael Al-Ramahi
- Jan and Dan Duncan Neurological Research Institute, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey P Cantle
- Department of Psychology, Western Washington University, Bellingham, WA, USA
| | - Jeffrey B Carroll
- Department of Psychology, Western Washington University, Bellingham, WA, USA
| | - Juan Botas
- Jan and Dan Duncan Neurological Research Institute, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Scott O Zeitlin
- Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Erich E Wanker
- Neuroproteomics, Max Delbrück Centre for Molecular Medicine, Berlin, Germany
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ, USA.
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8
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Dong X, Qin LY, Gong Z, Qin S, Zhou HX, Tang C. Preferential Interactions of a Crowder Protein with the Specific Binding Site of a Native Protein Complex. J Phys Chem Lett 2022; 13:792-800. [PMID: 35044179 PMCID: PMC8852806 DOI: 10.1021/acs.jpclett.1c03794] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nonspecific binding of crowder proteins with functional proteins is likely prevalent in vivo, yet direct quantitative evidence, let alone residue-specific information, is scarce. Here we present nuclear magnetic resonance (NMR) characterization showing that bovine serum albumin weakly but preferentially interacts with the histidine carrier protein (HPr). Notably, the binding interface overlaps with that for HPr's specific partner protein, EIN, leading to competition. The crowder protein thus decreases the EIN-HPr binding affinity and accelerates the dissociation of the native complex. In contrast, Ficoll-70 stabilizes the native complex and slows its dissociation, as one would expect from excluded-volume and microviscosity effects. Our atomistic modeling of macromolecular crowding rationalizes the experimental data and provides quantitative insights into the energetics of protein-crowder interactions. The integrated NMR and modeling study yields benchmarks for the effects of crowded cellular environments on protein-protein specific interactions, with implications for evolution regarding how nonspecific binding can be minimized or exploited.
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Affiliation(s)
- Xu Dong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Ling-Yun Qin
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Sanbo Qin
- Department of Chemistry and Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, United States
| | - Huan-Xiang Zhou
- Department of Chemistry and Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Chun Tang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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9
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Czaplewski C, Gong Z, Lubecka EA, Xue K, Tang C, Liwo A. Recent Developments in Data-Assisted Modeling of Flexible Proteins. Front Mol Biosci 2022; 8:765562. [PMID: 35004845 PMCID: PMC8740120 DOI: 10.3389/fmolb.2021.765562] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
Many proteins can fold into well-defined conformations. However, intrinsically-disordered proteins (IDPs) do not possess a defined structure. Moreover, folded multi-domain proteins often digress into alternative conformations. Collectively, the conformational dynamics enables these proteins to fulfill specific functions. Thus, most experimental observables are averaged over the conformations that constitute an ensemble. In this article, we review the recent developments in the concept and methods for the determination of the dynamic structures of flexible peptides and proteins. In particular, we describe ways to extract information from nuclear magnetic resonance small-angle X-ray scattering (SAXS), and chemical cross-linking coupled with mass spectroscopy (XL-MS) measurements. All these techniques can be used to obtain ensemble-averaged restraints or to re-weight the simulated conformational ensembles.
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Affiliation(s)
| | - Zhou Gong
- Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Emilia A Lubecka
- Faculty of Electronics, Telecommunications and Informatics, Gdańsk University of Technology, Gdańsk, Poland
| | - Kai Xue
- PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Chun Tang
- PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
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10
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Prieto VA, Namitz KEW, Showalter SA. Transient Electrostatic Interactions between Fcp1 and Rap74 Bias the Conformational Ensemble of the Complex with Minimal Impact on Binding Affinity. J Phys Chem B 2021; 125:10917-10927. [PMID: 34550709 DOI: 10.1021/acs.jpcb.1c05131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Intrinsically disordered protein (IDP) sequences often contain a high proportion of charged residues in conjunction with their high degree of hydrophilicity and solvation. For high net charge IDPs, long-range electrostatic interactions are thought to play a role in modulating the strength or kinetics of protein-protein interactions. In this work, we examined intramolecular interactions mediated by charged regions of a model IDP, the C-terminal tail of the phosphatase Fcp1. Specifically, this work focuses on intermolecular interactions between acidic and basic patches in the primary structure of Fcp1 and their contributions to binding its predominantly basic partner, the winged helix domain of Rap74. We observe both intramolecular and intermolecular interactions through paramagnetic relaxation enhancement (PRE) consistent with oppositely charged regions associating with one another, both in unbound Fcp1 and in the Fcp1-Rap74 complex. Formation of this complex is strongly driven by hydrophobic interactions in the minimal binding motif. Here, we test the hypothesis that charged residues in Fcp1 that flank the binding helix also contribute to the strength of binding. Charge inversion mutations in Fcp1 generally support this hypothesis, while PRE data suggest substitution of observed transient interactions in the unbound ensemble for similarly transient interactions with Rap74 in the complex.
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Affiliation(s)
- Victor A Prieto
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Kevin E W Namitz
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Scott A Showalter
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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11
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Han SJ, Noh M, Jang J, Lee JB, Kim KS. Electric fields regulate cellular elasticity through intracellular Ca 2+ concentrations. J Cell Physiol 2021; 236:7450-7463. [PMID: 33993476 DOI: 10.1002/jcp.30417] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 04/25/2021] [Accepted: 04/28/2021] [Indexed: 11/06/2022]
Abstract
Cellular elasticity is a key factor related to a broad range of physiological and pathological processes. The elasticity of a single cell has thus emerged as a potential biomarker to characterize the cellular state. Both internal and external stimuli affect cellular elasticity, and changes in elasticity can cause alterations in cellular characteristics or function. The application of electric fields (EFs) is a promising method that can be used to change cellular elasticity; however, the mechanisms underlying its effect remain unknown. Here, we demonstrate EFs-induced elasticity changes in human dermal fibroblasts and discuss the underlying mechanism related to actin polymerization. Cellular elasticity increases after EF (50 mV/mm) stimulation, reaching a maximum at 30 min before decreasing between 30 and 120 min. The cellular elasticity under EF stimulation, regardless of stimulation time, is higher than that of the control. F-actin regulates the elasticity of cells through gelsolin activation. We show changes in intracellular Ca2+ caused by EFs, which induced gelsolin activation and F-actin content changes. This result demonstrates a series of processes in which external electrical stimulation conditions regulate cellular elasticity.
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Affiliation(s)
- Se Jik Han
- Department of Biomedical Engineering, Graduate School, Kyung Hee University, Seoul, Korea.,Department of Biomedical Engineering, Kyung Hee University, Seoul, Korea
| | - Minjoo Noh
- Innovation Lab, Department of Innovation, Cosmax R&I Center, Gyeonggi do, Korea
| | - Jihui Jang
- Innovation Lab, Department of Innovation, Cosmax R&I Center, Gyeonggi do, Korea
| | - Jun Bae Lee
- Innovation Lab, Department of Innovation, Cosmax R&I Center, Gyeonggi do, Korea
| | - Kyung Sook Kim
- Department of Biomedical Engineering, Kyung Hee University, Seoul, Korea
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12
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Gong Z, Ye SX, Nie ZF, Tang C. The Conformational Preference of Chemical Cross-linkers Determines the Cross-linking Probability of Reactive Protein Residues. J Phys Chem B 2020; 124:4446-4453. [PMID: 32369371 DOI: 10.1021/acs.jpcb.0c02522] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemical cross-linking mass spectrometry (XLMS) is an emerging technique in structural biology. Providing the cross-linked peptides are identified by mass spectrometry with high confidence, a distance restraint can be applied between the two reactive protein residues, with the upper bound corresponding to the maximal span of the cross-linker. However, as the upper bound is typically over 20 Å, cross-link distance restraints are unrestrictive and provide a marginal improvement in protein structural refinement. Here we analyze the experimental cross-links for lysine or acidic residues and show that the distribution of Cβ-Cβ' distances can be described with two overlapping Gaussian species. In addition to the pairwise occurrence probability of the reactive protein residues, we show that the distribution profile of the cross-link distances is determined by the intrinsic conformational propensity of the cross-linker. The cross-linker prefers either a compact or extended conformation and, once attached to a reactive protein residue, predominantly an extended conformation. Consequently, the long-distance Gaussian species occurs at a much higher probability than the short-distance species in the observed cross-links. Together, the probabilistic distribution of the cross-link distance allows the construction of a more restrictive restraint for structural modeling and better use of the XLMS data.
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Affiliation(s)
- Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China
| | - Shang-Xiang Ye
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China
| | - Ze-Feng Nie
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China
| | - Chun Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China
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13
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Ubiquitin is double-phosphorylated by PINK1 for enhanced pH-sensitivity of conformational switch. Protein Cell 2020; 10:908-913. [PMID: 31278634 PMCID: PMC6881470 DOI: 10.1007/s13238-019-0644-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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14
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Arter WE, Levin A, Krainer G, Knowles TPJ. Microfluidic approaches for the analysis of protein-protein interactions in solution. Biophys Rev 2020; 12:575-585. [PMID: 32266673 PMCID: PMC7242286 DOI: 10.1007/s12551-020-00679-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/02/2020] [Indexed: 12/15/2022] Open
Abstract
Exploration and characterisation of the human proteome is a key objective enabling a heightened understanding of biological function, malfunction and pharmaceutical design. Since proteins typically exhibit their behaviour by binding to other proteins, the challenge of probing protein-protein interactions has been the focus of new and improved experimental approaches. Here, we review recently developed microfluidic techniques for the study and quantification of protein-protein interactions. We focus on methodologies that utilise the inherent strength of microfluidics for the control of mass transport on the micron scale, to facilitate surface and membrane-free interrogation and quantification of interacting proteins. Thus, the microfluidic tools described here provide the capability to yield insights on protein-protein interactions under physiological conditions. We first discuss the defining principles of microfluidics, and methods for the analysis of protein-protein interactions that utilise the diffusion-controlled mixing characteristic of fluids at the microscale. We then describe techniques that employ electrophoretic forces to manipulate and fractionate interacting protein systems for their biophysical characterisation, before discussing strategies that use microdroplet compartmentalisation for the analysis of protein interactions. We conclude by highlighting future directions for the field, such as the integration of microfluidic experiments into high-throughput workflows for the investigation of protein interaction networks.
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Affiliation(s)
- William E Arter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Aviad Levin
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Georg Krainer
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK.
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15
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Abstract
Functions of intrinsically disordered proteins do not require structure. Such structure-independent functionality has melted away the classic rigid "lock and key" representation of structure-function relationships in proteins, opening a new page in protein science, where molten keys operate on melted locks and where conformational flexibility and intrinsic disorder, structural plasticity and extreme malleability, multifunctionality and binding promiscuity represent a new-fangled reality. Analysis and understanding of this new reality require novel tools, and some of the techniques elaborated for the examination of intrinsically disordered protein functions are outlined in this review.
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Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33620, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Russian Federation
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16
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Yang QF, Tang C. On the necessity of an integrative approach to understand protein structural dynamics. J Zhejiang Univ Sci B 2019; 20:496-502. [PMID: 31090275 DOI: 10.1631/jzus.b1900135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Proteins are dynamic, fluctuating between multiple conformational states. Protein dynamics, spanning orders of magnitude in time and space, allow proteins to perform specific functions. Moreover, under certain conditions, proteins can morph into a different set of conformations. Thus, a complete understanding of protein structural dynamics can provide mechanistic insights into protein function. Here, we review the latest developments in methods used to determine protein ensemble structures and to characterize protein dynamics. Techniques including X-ray crystallography, cryogenic electron microscopy, and small angle scattering can provide structural information on specific conformational states or on the averaged shape of the protein, whereas techniques including nuclear magnetic resonance, fluorescence resonance energy transfer (FRET), and chemical cross-linking coupled with mass spectrometry provide information on the fluctuation of the distances between protein domains, residues, and atoms for the multiple conformational states of the protein. In particular, FRET measurements at the single-molecule level allow rapid resolution of protein conformational states, where information is otherwise obscured in bulk measurements. Taken together, the different techniques complement each other and their integrated use can offer a clear picture of protein structure and dynamics.
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Affiliation(s)
- Qing-Fen Yang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Chun Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan 430071, China
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17
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Yagi-Utsumi M. NMR Characterization of Conformational Dynamics and Molecular Assemblies of Proteins. Biol Pharm Bull 2019; 42:867-872. [PMID: 31155585 DOI: 10.1248/bpb.b19-00115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Dynamic conformational transitions and molecular assemblies are essential properties of proteins, and relevant to their biological and pathological functions. Neurodegenerative diseases are known to be caused by abnormal, toxic assemblies of related proteins, e.g., amyloid β (Aβ) in Alzheimer's disease. Growing evidence indicates that the aggregation of various amyloidogenic proteins, including Aβ, can be highly enhanced at glycolipid membranes, suggesting that dynamic glycolipid-dependent conformational changes of proteins constitute crucial steps for their subsequent pathogenic amyloid fibril formation. It has also been proposed that several proteins, including molecular chaperones, can capture amyloidogenic proteins and thereby suppress their fibrillization. NMR spectroscopy provides a powerful tool for characterizing the conformational dynamics and intermolecular interactions of proteins, as well as for exploring transiently formed weak interactions among proteins in solution with various biomolecules, such as glycolipids. Our research group therefore attempted to elucidate the structural basis of protein-glycolipid and protein-protein interactions that either promote or suppress molecular assemblies of amyloidogenic proteins, using both solution and solid-state NMR methods in conjunction with other biophysical techniques. Our findings provide structural views of molecular processes involving amyloidogenic proteins of clinical and pathological interest and offer clues for the development of drugs to prevent and treat neurodegenerative diseases.
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Affiliation(s)
- Maho Yagi-Utsumi
- Institute for Molecular Science, National Institutes of National Sciences.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of National Sciences.,Graduate School of Pharmaceutical Sciences, Nagoya City University
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18
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Refining RNA solution structures with the integrative use of label-free paramagnetic relaxation enhancement NMR. BIOPHYSICS REPORTS 2019. [DOI: 10.1007/s41048-019-00099-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
AbstractNMR structure calculation is inherently integrative, and can incorporate new experimental data as restraints. As RNAs have lower proton densities and are more conformational heterogenous than proteins, the refinement of RNA structures can benefit from additional types of restraints. Paramagnetic relaxation enhancement (PRE) provides distance information between a paramagnetic probe and protein or RNA nuclei. However, covalent conjugation of a paramagnetic probe is difficult for RNAs, thus limiting the use of PRE NMR for RNA structure characterization. Here, we show that the solvent PRE can be accurately measured for RNA labile imino protons, simply with the addition of an inert paramagnetic cosolute. Demonstrated on three RNAs that have increasingly complex topologies, we show that the incorporation of the solvent PRE restraints can significantly improve the precision and accuracy of RNA structures. Importantly, the solvent PRE data can be collected for RNAs without isotope enrichment. Thus, the solvent PRE method can work integratively with other biophysical techniques for better characterization of RNA structures.
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19
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Arthanari H, Takeuchi K, Dubey A, Wagner G. Emerging solution NMR methods to illuminate the structural and dynamic properties of proteins. Curr Opin Struct Biol 2019; 58:294-304. [PMID: 31327528 PMCID: PMC6778509 DOI: 10.1016/j.sbi.2019.06.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 06/03/2019] [Accepted: 06/10/2019] [Indexed: 12/20/2022]
Abstract
The first recognition of protein breathing was more than 50 years ago. Today, we are able to detect the multitude of interaction modes, structural polymorphisms, and binding-induced changes in protein structure that direct function. Solution-state NMR spectroscopy has proved to be a powerful technique, not only to obtain high-resolution structures of proteins, but also to provide unique insights into the functional dynamics of proteins. Here, we summarize recent technical landmarks in solution NMR that have enabled characterization of key biological macromolecular systems. These methods have been fundamental to atomic resolution structure determination and quantitative analysis of dynamics over a wide range of time scales by NMR. The ability of NMR to detect lowly populated protein conformations and transiently formed complexes plays a critical role in its ability to elucidate functionally important structural features of proteins and their dynamics.
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Affiliation(s)
- Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States.
| | - Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 135-0064 Tokyo, Japan.
| | - Abhinav Dubey
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States.
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20
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Liu Z, Dong X, Yi HW, Yang J, Gong Z, Wang Y, Liu K, Zhang WP, Tang C. Structural basis for the recognition of K48-linked Ub chain by proteasomal receptor Rpn13. Cell Discov 2019; 5:19. [PMID: 30962947 PMCID: PMC6443662 DOI: 10.1038/s41421-019-0089-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 01/18/2023] Open
Abstract
The interaction between K48-linked ubiquitin (Ub) chain and Rpn13 is important for proteasomal degradation of ubiquitinated substrate proteins. Only the complex structure between the N-terminal domain of Rpn13 (Rpn13NTD) and Ub monomer has been characterized, while it remains unclear how Rpn13 specifically recognizes K48-linked Ub chain. Using single-molecule FRET, here we show that K48-linked diubiquitin (K48-diUb) fluctuates among distinct conformational states, and a preexisting compact state is selectively enriched by Rpn13NTD. The same binding mode is observed for full-length Rpn13 and longer K48-linked Ub chain. Using solution NMR spectroscopy, we have determined the complex structure between Rpn13NTD and K48-diUb. In this structure, Rpn13NTD simultaneously interacts with proximal and distal Ub subunits of K48-diUb that remain associated in the complex, thus corroborating smFRET findings. The proximal Ub interacts with Rpn13NTD similarly as the Ub monomer in the known Rpn13NTD:Ub structure, while the distal Ub binds to a largely electrostatic surface of Rpn13NTD. Thus, a charge-reversal mutation in Rpn13NTD weakens the interaction between Rpn13 and K48-linked Ub chain, causing accumulation of ubiquitinated proteins. Moreover, physical blockage of the access of the distal Ub to Rpn13NTD with a proximity-attached Ub monomer can disrupt the interaction between Rpn13 and K48-diUb. Taken together, the bivalent interaction of K48-linked Ub chain with Rpn13 provides the structural basis for Rpn13 linkage selectivity, which opens a new window for modulating proteasomal function.
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Affiliation(s)
- Zhu Liu
- 1CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071 China.,2National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xu Dong
- 1CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071 China
| | - Hua-Wei Yi
- 1CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071 China.,3University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ju Yang
- 1CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071 China.,3University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhou Gong
- 1CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071 China
| | - Yi Wang
- 4Department of Pharmacology, Institute of Neuroscience, Key Laboratory of Medical Neurobiology of Ministry of Health of China, and Zhejiang Province Key Laboratory of Mental Disorder's Management, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310027 China
| | - Kan Liu
- 1CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071 China
| | - Wei-Ping Zhang
- 4Department of Pharmacology, Institute of Neuroscience, Key Laboratory of Medical Neurobiology of Ministry of Health of China, and Zhejiang Province Key Laboratory of Mental Disorder's Management, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310027 China
| | - Chun Tang
- 1CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071 China.,3University of Chinese Academy of Sciences, Beijing, 100049 China.,5Wuhan National Laboratory for Optoelectronics, Wuhan, Hubei Province 430074 China
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21
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Young D, Pedre B, Ezeriņa D, De Smet B, Lewandowska A, Tossounian MA, Bodra N, Huang J, Astolfi Rosado L, Van Breusegem F, Messens J. Protein Promiscuity in H 2O 2 Signaling. Antioxid Redox Signal 2019; 30:1285-1324. [PMID: 29635930 DOI: 10.1089/ars.2017.7013] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SIGNIFICANCE Decrypting the cellular response to oxidative stress relies on a comprehensive understanding of the redox signaling pathways stimulated under oxidizing conditions. Redox signaling events can be divided into upstream sensing of oxidants, midstream redox signaling of protein function, and downstream transcriptional redox regulation. Recent Advances: A more and more accepted theory of hydrogen peroxide (H2O2) signaling is that of a thiol peroxidase redox relay, whereby protein thiols with low reactivity toward H2O2 are instead oxidized through an oxidative relay with thiol peroxidases. CRITICAL ISSUES These ultrareactive thiol peroxidases are the upstream redox sensors, which form the first cellular port of call for H2O2. Not all redox-regulated interactions between thiol peroxidases and cellular proteins involve a transfer of oxidative equivalents, and the nature of redox signaling is further complicated through promiscuous functions of redox-regulated "moonlighting" proteins, of which the precise cellular role under oxidative stress can frequently be obscured by "polygamous" interactions. An ultimate goal of redox signaling is to initiate a rapid response, and in contrast to prokaryotic oxidant-responsive transcription factors, mammalian systems have developed redox signaling pathways, which intersect both with kinase-dependent activation of transcription factors, as well as direct oxidative regulation of transcription factors through peroxiredoxin (Prx) redox relays. FUTURE DIRECTIONS We highlight that both transcriptional regulation and cell fate can be modulated either through oxidative regulation of kinase pathways, or through distinct redox-dependent associations involving either Prxs or redox-responsive moonlighting proteins with functional promiscuity. These protein associations form systems of crossregulatory networks with multiple nodes of potential oxidative regulation for H2O2-mediated signaling.
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Affiliation(s)
- David Young
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Brandan Pedre
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Daria Ezeriņa
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Barbara De Smet
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Aleksandra Lewandowska
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Maria-Armineh Tossounian
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Nandita Bodra
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Jingjing Huang
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Leonardo Astolfi Rosado
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Frank Van Breusegem
- 2 Brussels Center for Redox Biology, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Joris Messens
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
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22
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Endutkin AV, Yudkina AV, Sidorenko VS, Zharkov DO. Transient protein-protein complexes in base excision repair. J Biomol Struct Dyn 2018; 37:4407-4418. [PMID: 30488779 DOI: 10.1080/07391102.2018.1553741] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Transient protein-protein complexes are of great importance for organizing multiple enzymatic reactions into productive reaction pathways. Base excision repair (BER), a process of critical importance for maintaining genome stability against a plethora of DNA-damaging factors, involves several enzymes, including DNA glycosylases, AP endonucleases, DNA polymerases, DNA ligases and accessory proteins acting sequentially on the same damaged site in DNA. Rather than being assembled into one stable multisubunit complex, these enzymes pass the repair intermediates between them in a highly coordinated manner. In this review, we discuss the nature and the role of transient complexes arising during BER as deduced from structural and kinetic data. Almost all of the transient complexes are DNA-mediated, although some may also exist in solution and strengthen under specific conditions. The best-studied example, the interactions between DNA glycosylases and AP endonucleases, is discussed in more detail to provide a framework for distinguishing between stable and transient complexes based on the kinetic data. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anton V Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine , Novosibirsk , Russia.,Novosibirsk State University , Novosibirsk , Russia.,Podalirius Ltd. , Novosibirsk , Russia
| | - Anna V Yudkina
- SB RAS Institute of Chemical Biology and Fundamental Medicine , Novosibirsk , Russia.,Novosibirsk State University , Novosibirsk , Russia
| | - Viktoriya S Sidorenko
- Department of Pharmacological Sciences, Stony Brook University , Stony Brook , NY , USA
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine , Novosibirsk , Russia.,Novosibirsk State University , Novosibirsk , Russia
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23
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Chen PC, Hennig J. The role of small-angle scattering in structure-based screening applications. Biophys Rev 2018; 10:1295-1310. [PMID: 30306530 PMCID: PMC6233350 DOI: 10.1007/s12551-018-0464-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/04/2018] [Indexed: 12/16/2022] Open
Abstract
In many biomolecular interactions, changes in the assembly states and structural conformations of participants can act as a complementary reporter of binding to functional and thermodynamic assays. This structural information is captured by a number of structural biology and biophysical techniques that are viable either as primary screens in small-scale applications or as secondary screens to complement higher throughput methods. In particular, small-angle X-ray scattering (SAXS) reports the average distance distribution between all atoms after orientational averaging. Such information is important when for example investigating conformational changes involved in inhibitory and regulatory mechanisms where binding events do not necessarily cause functional changes. Thus, we summarise here the current and prospective capabilities of SAXS-based screening in the context of other methods that yield structural information. Broad guidelines are also provided to assist readers in preparing screening protocols that are tailored to available X-ray sources.
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Affiliation(s)
- Po-Chia Chen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69126, Heidelberg, Germany.
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69126, Heidelberg, Germany.
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24
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Goretzki B, Glogowski NA, Diehl E, Duchardt-Ferner E, Hacker C, Gaudet R, Hellmich UA. Structural Basis of TRPV4 N Terminus Interaction with Syndapin/PACSIN1-3 and PIP 2. Structure 2018; 26:1583-1593.e5. [PMID: 30244966 DOI: 10.1016/j.str.2018.08.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/13/2018] [Accepted: 08/01/2018] [Indexed: 12/15/2022]
Abstract
Transient receptor potential (TRP) channels are polymodally regulated ion channels. TRPV4 (vanilloid 4) is sensitized by PIP2 and desensitized by Syndapin3/PACSIN3, which bind to the structurally uncharacterized TRPV4 N terminus. We determined the nuclear magnetic resonance structure of the Syndapin3/PACSIN3 SH3 domain in complex with the TRPV4 N-terminal proline-rich region (PRR), which binds as a class I polyproline II (PPII) helix. This PPII conformation is broken by a conserved proline in a cis conformation. Beyond the PPII, we find that the proximal TRPV4 N terminus is unstructured, a feature conserved across species thus explaining the difficulties in resolving it in previous structural studies. Syndapin/PACSIN SH3 domain binding leads to rigidification of both the PRR and the adjacent PIP2 binding site. We determined the affinities of the TRPV4 N terminus for PACSIN1, 2, and 3 SH3 domains and PIP2 and deduce a hierarchical interaction network where Syndapin/PACSIN binding influences the PIP2 binding site but not vice versa.
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Affiliation(s)
- Benedikt Goretzki
- Institute for Pharmacy and Biochemistry, Johannes Gutenberg-Universität Mainz, 55128 Mainz, Germany; Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität, 60438 Frankfurt am Main, Germany
| | - Nina A Glogowski
- Institute for Pharmacy and Biochemistry, Johannes Gutenberg-Universität Mainz, 55128 Mainz, Germany; Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität, 60438 Frankfurt am Main, Germany
| | - Erika Diehl
- Institute for Pharmacy and Biochemistry, Johannes Gutenberg-Universität Mainz, 55128 Mainz, Germany; Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität, 60438 Frankfurt am Main, Germany
| | - Elke Duchardt-Ferner
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität, 60438 Frankfurt am Main, Germany; Institute for Molecular Biosciences, Goethe-Universität, 60438 Frankfurt am Main, Germany
| | - Carolin Hacker
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität, 60438 Frankfurt am Main, Germany; Institute for Molecular Biosciences, Goethe-Universität, 60438 Frankfurt am Main, Germany
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ute A Hellmich
- Institute for Pharmacy and Biochemistry, Johannes Gutenberg-Universität Mainz, 55128 Mainz, Germany; Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität, 60438 Frankfurt am Main, Germany.
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25
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Blaffert J, Haeri HH, Blech M, Hinderberger D, Garidel P. Spectroscopic methods for assessing the molecular origins of macroscopic solution properties of highly concentrated liquid protein solutions. Anal Biochem 2018; 561-562:70-88. [PMID: 30243977 DOI: 10.1016/j.ab.2018.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/08/2018] [Accepted: 09/17/2018] [Indexed: 01/14/2023]
Abstract
In cases of subcutaneous injection of therapeutic monoclonal antibodies, high protein concentrations (>50 mg/ml) are often required. During the development of these high concentration liquid formulations (HCLF), challenges such as aggregation, gelation, opalescence, phase separation, and high solution viscosities are more prone compared to low concentrated protein formulations. These properties can impair manufacturing processes, as well as protein stability and shelf life. To avoid such unfavourable solution properties, a detailed understanding about the nature of these properties and their driving forces are required. However, the fundamental mechanisms that lead to macroscopic solution properties, as above mentioned, are complex and not fully understood, yet. Established analytical methods for assessing the colloidal stability, i.e. the ability of a native protein to remain dispersed in solution, are restricted to dilute conditions and provide parameters such as the second osmotic virial coefficient, B22, and the diffusion interaction coefficient, kD. These parameters are routinely applied for qualitative estimations and identifications of proteins with challenging solution behaviours, such as high viscosities and aggregation, although the assays are prepared for low protein concentration conditions, typically between 0.1 and 20 mg/ml ("ideal" solution conditions). Quantitative analysis of samples of high protein concentration is difficult and it is hard to obtain information about the driving forces of such solution properties and corresponding protein-protein self-interactions. An advantage of using specific spectroscopic methods is the potential of directly analysing highly concentrated protein solutions at different solution conditions. This allows for collecting/gaining valuable information about the fundamental mechanisms of solution properties of the high protein concentration regime. In addition, the derived parameters might be more predictive as compared to the parameters originating from assays which are optimized for the low protein concentration range. The provided information includes structural data, molecular dynamics at various timescales and protein-solvent interactions, which can be obtained at molecular resolution. Herein, we provide an overview about spectroscopic techniques for analysing the origins of macroscopic solution behaviours in general, with a specific focus on pharmaceutically relevant high protein concentration and formulation conditions.
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Affiliation(s)
- Jacob Blaffert
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Haleh Hashemi Haeri
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Michaela Blech
- Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany
| | - Dariush Hinderberger
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Patrick Garidel
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany; Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany.
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26
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Dantas JM, Ferreira MR, Catarino T, Kokhan O, Pokkuluri PR, Salgueiro CA. Molecular interactions between Geobacter sulfurreducens triheme cytochromes and the redox active analogue for humic substances. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:619-630. [PMID: 29777686 DOI: 10.1016/j.bbabio.2018.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 05/09/2018] [Accepted: 05/15/2018] [Indexed: 01/17/2023]
Abstract
The bacterium Geobacter sulfurreducens can transfer electrons to quinone moieties of humic substances or to anthraquinone-2,6-disulfonate (AQDS), a model for the humic acids. The reduced form of AQDS (AH2QDS) can also be used as energy source by G. sulfurreducens. Such bidirectional utilization of humic substances confers competitive advantages to these bacteria in Fe(III) enriched environments. Previous studies have shown that the triheme cytochrome PpcA from G. sulfurreducens has a bifunctional behavior toward the humic substance analogue. It can reduce AQDS but the protein can also be reduced by AH2QDS. Using stopped-flow kinetic measurements we were able to demonstrate that other periplasmic members of the PpcA-family in G. sulfurreducens (PpcB, PpcD and PpcE) also showed the same behavior. The extent of the electron transfer is thermodynamically controlled favoring the reduction of the cytochromes. NMR spectra recorded for 13C,15N-enriched samples in the presence increasing amounts of AQDS showed perturbations in the chemical shift signals of the cytochromes. The chemical shift perturbations on cytochromes backbone NH and 1H heme methyl signals were used to map their interaction regions with AQDS, showing that each protein forms a low-affinity binding complex through well-defined positive surface regions in the vicinity of heme IV (PpcB, PpcD and PpcE) and I (PpcE). Docking calculations performed using NMR chemical shift perturbations allowed modeling the interactions between AQDS and each cytochrome at a molecular level. Overall, the results obtained provided important structural-functional relationships to rationalize the microbial respiration of humic substances in G. sulfurreducens.
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Affiliation(s)
- Joana M Dantas
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Marisa R Ferreira
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Teresa Catarino
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal; Departamento de Química, Faculdade de Ciências e Tecnologia, FCT, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Oleksandr Kokhan
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA
| | - P Raj Pokkuluri
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Carlos A Salgueiro
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal.
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27
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Gong Z, Schwieters CD, Tang C. Theory and practice of using solvent paramagnetic relaxation enhancement to characterize protein conformational dynamics. Methods 2018; 148:48-56. [PMID: 29656079 DOI: 10.1016/j.ymeth.2018.04.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/19/2018] [Accepted: 04/06/2018] [Indexed: 01/01/2023] Open
Abstract
Paramagnetic relaxation enhancement (PRE) has been established as a powerful tool in NMR for investigating protein structure and dynamics. The PRE is usually measured with a paramagnetic probe covalently attached at a specific site of an otherwise diamagnetic protein. The present work provides the numerical formulation for probing protein structure and conformational dynamics based on the solvent PRE (sPRE) measurement, using two alternative approaches. An inert paramagnetic cosolute randomly collides with the protein, and the resulting sPRE manifests the relative solvent exposure of protein nuclei. To make the back-calculated sPRE values most consistent with the observed values, the protein structure is either refined against the sPRE, or an ensemble of conformers is selected from a pre-generated library using a Monte Carlo algorithm. The ensemble structure comprises either N conformers of equal occupancy, or two conformers with different relative populations. We demonstrate the sPRE method using GB1, a structurally rigid protein, and calmodulin, a protein comprising two domains and existing in open and closed states. The sPRE can be computed with a stand-alone program for rapid evaluation, or with the invocation of a module in the latest release of the structure calculation software Xplor-NIH. As a label-free method, the sPRE measurement can be readily integrated with other biophysical techniques. The current limitations of the sPRE method are also discussed, regarding accurate measurement and theoretical calculation, model selection and suitable timescale.
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Affiliation(s)
- Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China
| | - Charles D Schwieters
- Office of Intramural Research, Center for Information Technology, National Institutes of Health, Building 12A, Bethesda, MD 20892, United States
| | - Chun Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China.
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28
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Abstract
N6-methyladenosine (m6A), a ubiquitous RNA modification, is installed by METTL3-METTL14 complex. The structure of the heterodimeric complex between the methyltransferase domains (MTDs) of METTL3 and METTL14 has been previously determined. However, the MTDs alone possess no enzymatic activity. Here we present the solution structure for the zinc finger domain (ZFD) of METTL3, the inclusion of which fulfills the methyltransferase activity of METTL3-METTL14. We show that the ZFD specifically binds to an RNA containing 5′-GGACU-3′ consensus sequence, but does not to one without. The ZFD thus serves as the target recognition domain, a structural feature previously shown for DNA methyltransferases, and cooperates with the MTDs of METTL3-METTL14 for catalysis. However, the interaction between the ZFD and the specific RNA is extremely weak, with the binding affinity at several hundred micromolar under physiological conditions. The ZFD contains two CCCH-type zinc fingers connected by an anti-parallel β-sheet. Mutational analysis and NMR titrations have mapped the functional interface to a contiguous surface. As a division of labor, the RNA-binding interface comprises basic residues from zinc finger 1 and hydrophobic residues from β-sheet and zinc finger 2. Further we show that the linker between the ZFD and MTD of METTL3 is flexible but partially folded, which may permit the cooperation between the two domains during catalysis. Together, the structural characterization of METTL3 ZFD paves the way to elucidate the atomic details of the entire process of RNA m6A modification.
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29
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Dal Cortivo G, Wagner GE, Cortelletti P, Padmanabha Das KM, Zangger K, Speghini A, Dell'Orco D, Meyer NH. Luminescent and paramagnetic properties of nanoparticles shed light on their interactions with proteins. Sci Rep 2018; 8:3420. [PMID: 29467422 PMCID: PMC5821874 DOI: 10.1038/s41598-018-21571-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/06/2018] [Indexed: 12/14/2022] Open
Abstract
Nanoparticles have been recognized as promising tools for targeted drug-delivery and protein therapeutics. However, the mechanisms of protein-nanoparticle interaction and the dynamics underlying the binding process are poorly understood. Here, we present a general methodology for the characterization of protein-nanoparticle interaction on a molecular level. To this end we combined biophysical techniques including nuclear magnetic resonance (NMR), circular dichroism (CD), resonance energy transfer (RET) and surface plasmon resonance (SPR). Particularly, we analyzed molecular mechanisms and dynamics of the interaction of CaF2 nanoparticles with the prototypical calcium sensor calmodulin (CaM). We observed the transient formation of an intermediate encounter complex involving the structural region linking the two domains. Specific interaction of CaM with CaF2 NPs is driven by the N-terminal EF-hands, which seem to recognize Ca2+ on the surface of the nanoparticle. We conclude that CaF2 NP-CaM interaction is fully compatible with potential applications in nanomedicine. Overall, the methods presented in this work can be extended to other systems and may be useful to quantitatively characterize structural and dynamic features of protein-NP interactions with important implications for nanomedicine and nano-biotechnology.
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Affiliation(s)
- Giuditta Dal Cortivo
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, Strada le Grazie 8, Verona, Italy
| | - Gabriel E Wagner
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
| | - Paolo Cortelletti
- Nanomaterials Research Group, Department of Biotechnology, University of Verona and INSTM, UdR Verona, Strada Le Grazie 15, Verona, Italy
| | | | - Klaus Zangger
- Institute of Chemistry, University of Graz, Heinrichstr. 28, 8010, Graz, Austria
| | - Adolfo Speghini
- Nanomaterials Research Group, Department of Biotechnology, University of Verona and INSTM, UdR Verona, Strada Le Grazie 15, Verona, Italy
| | - Daniele Dell'Orco
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, Strada le Grazie 8, Verona, Italy.
| | - N Helge Meyer
- Department of Human Medicine and Department of Neuroscience, University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26131, Oldenburg, Germany.
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30
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Abstract
Virus-like particle (VLP) technologies are based on virus-inspired artificial structures and the intrinsic ability of viral proteins to self-assemble at controlled conditions. Therefore, the basic knowledge about the mechanisms of viral particle formation is highly important for designing of industrial applications. As an alternative to genetic and chemical processes, different physical methods are frequently used for VLP construction, including well characterized protein complexes for introduction of foreign molecules in VLP structures.This chapter shortly discusses the mechanisms how the viruses form their perfectly ordered structures as well as the principles and most interesting application examples, how to exploit the structural and assembly/disassembly properties of viral structures for creation of new nanomaterials.
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Affiliation(s)
- Andris Zeltins
- Latvian Biomedical Research and Study Centre, Riga, Latvia.
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31
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Manning MC, Liu J, Li T, Holcomb RE. Rational Design of Liquid Formulations of Proteins. THERAPEUTIC PROTEINS AND PEPTIDES 2018; 112:1-59. [DOI: 10.1016/bs.apcsb.2018.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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32
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Miura K. An Overview of Current Methods to Confirm Protein-Protein Interactions. Protein Pept Lett 2018; 25:728-733. [PMID: 30129399 PMCID: PMC6204658 DOI: 10.2174/0929866525666180821122240] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 08/11/2018] [Accepted: 08/11/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND The research field of protein-protein interactions is interdisciplinary and specialized field that spans all aspects of biology, physics and chemistry. Therefore, in order to discuss the protein-protein interaction in detail and rigorously, it is desirable to integrate knowledge and methods of many related fields including boundary areas such as biochemistry, biophysics and physical chemistry in addition to biology, physics and chemistry. OBJECTIVE The purpose of this review is to overview current methods to confirm protein-protein interactions. Furthermore, I discuss future prospects of methodology based on current status. RESULTS It is often necessary to integrate, combine and validate multiple results from various methods to understand protein-protein interactions in detail. CONCLUSION It might be desirable for the addition of tags, labeling, and immobilization to solid phases to be unnecessary, and to obtain information on affinity, kinetics, and structure via the analytical method for protein-protein interactions. Therefore, I argue that novel methods based on principles that have already been sufficiently studied in physics or chemistry, but insufficiently applied to the life sciences, should be established to further develop the study of protein-protein interactions.
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Affiliation(s)
- Kenji Miura
- Address correspondence to this author at the Department of Developmental Anatomy and Regenerative Biology, National Defense Medical College, Tokorozawa, Saitama, Japan; Tel: +81 4 2995 1754; E-mail:
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33
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Fex Svenningsen Å, Löring S, Sørensen AL, Huynh HUB, Hjæresen S, Martin N, Moeller JB, Elkjær ML, Holmskov U, Illes Z, Andersson M, Nielsen SB, Benedikz E. Macrophage migration inhibitory factor (MIF) modulates trophic signaling through interaction with serine protease HTRA1. Cell Mol Life Sci 2017; 74:4561-4572. [PMID: 28726057 PMCID: PMC5663815 DOI: 10.1007/s00018-017-2592-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 07/05/2017] [Accepted: 07/11/2017] [Indexed: 02/07/2023]
Abstract
Macrophage migration inhibitory factor (MIF), a small conserved protein, is abundant in the immune- and central nervous system (CNS). MIF has several receptors and binding partners that can modulate its action on a cellular level. It is upregulated in neurodegenerative diseases and cancer although its function is far from clear. Here, we report the finding of a new binding partner to MIF, the serine protease HTRA1. This enzyme cleaves several growth factors, extracellular matrix molecules and is implicated in some of the same diseases as MIF. We show that the function of the binding between MIF and HTRA1 is to inhibit the proteolytic activity of HTRA1, modulating the availability of molecules that can change cell growth and differentiation. MIF is therefore the first endogenous inhibitor ever found for HTRA1. It was found that both molecules were present in astrocytes and that the functional binding has the ability to modulate astrocytic activities important in development and disease of the CNS.
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Affiliation(s)
- Åsa Fex Svenningsen
- Department of Molecular Medicine-Neurobiology Research, University of Southern Denmark, J.B. Winslows Vej 21.1, 5000, Odense, Denmark.
| | - Svenja Löring
- Department of Molecular Medicine-Neurobiology Research, University of Southern Denmark, J.B. Winslows Vej 21.1, 5000, Odense, Denmark
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, Meibergdreef 69-71, 1105 BK, Amsterdam, The Netherlands
| | - Anna Lahn Sørensen
- Department of Molecular Medicine-Neurobiology Research, University of Southern Denmark, J.B. Winslows Vej 21.1, 5000, Odense, Denmark
| | - Ha Uyen Buu Huynh
- Department of Molecular Medicine-Neurobiology Research, University of Southern Denmark, J.B. Winslows Vej 21.1, 5000, Odense, Denmark
| | - Simone Hjæresen
- Department of Molecular Medicine-Neurobiology Research, University of Southern Denmark, J.B. Winslows Vej 21.1, 5000, Odense, Denmark
| | - Nellie Martin
- Department of Neurology, Odense University Hospital, University of Southern Denmark, Sdr. Boulevard 29, 5000, Odense C, Denmark
| | - Jesper Bonnet Moeller
- Department of Molecular Medicine-Cancer and Inflammation, University of Southern Denmark, J.B. Winslows Vej 21.1, 5000, Odense, Denmark
- Weill Cornell Medicine, Cornell University, 413 East 69th Street, New York, 10021, USA
| | - Maria Louise Elkjær
- Department of Neurology, Odense University Hospital, University of Southern Denmark, Sdr. Boulevard 29, 5000, Odense C, Denmark
| | - Uffe Holmskov
- Department of Molecular Medicine-Cancer and Inflammation, University of Southern Denmark, J.B. Winslows Vej 21.1, 5000, Odense, Denmark
| | - Zsolt Illes
- Department of Neurology, Odense University Hospital, University of Southern Denmark, Sdr. Boulevard 29, 5000, Odense C, Denmark
| | - Malin Andersson
- Department of Pharmaceutical Biosciences, Uppsala University, Box 59, 751 24, Uppsala, Sweden
| | - Solveig Beck Nielsen
- Department of Molecular Medicine-Neurobiology Research, University of Southern Denmark, J.B. Winslows Vej 21.1, 5000, Odense, Denmark
| | - Eirikur Benedikz
- Department of Molecular Medicine-Neurobiology Research, University of Southern Denmark, J.B. Winslows Vej 21.1, 5000, Odense, Denmark
- Faculty of Health, University College Zealand, Parkvej 190, 4700, Næstved, Denmark
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Frye SA, Beyene GT, Namouchi A, Gómez-Muñoz M, Homberset H, Kalayou S, Riaz T, Tønjum T, Balasingham SV. The helicase DinG responds to stress due to DNA double strand breaks. PLoS One 2017; 12:e0187900. [PMID: 29121674 PMCID: PMC5679670 DOI: 10.1371/journal.pone.0187900] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 10/27/2017] [Indexed: 12/20/2022] Open
Abstract
Neisseria meningitidis (Nm) is a Gram-negative nasopharyngeal commensal that can cause septicaemia and meningitis. The neisserial DNA damage-inducible protein DinG is a helicase related to the mammalian helicases XPD and FANCJ. These helicases belong to superfamily 2, are ATP dependent and exert 5′ → 3′ directionality. To better understand the role of DinG in neisserial genome maintenance, the Nm DinG (DinGNm) enzymatic activities were assessed in vitro and phenotypical characterization of a dinG null mutant (NmΔdinG) was performed. Like its homologues, DinGNm possesses 5′ → 3′ directionality and prefers DNA substrates containing a 5′-overhang. ATPase activity of DinGNm is strictly DNA-dependent and DNA unwinding activity requires nucleoside triphosphate and divalent metal cations. DinGNm directly binds SSBNm with a Kd of 313 nM. Genotoxic stress analysis demonstrated that NmΔdinG was more sensitive to double-strand DNA breaks (DSB) induced by mitomycin C (MMC) than the Nm wildtype, defining the role of neisserial DinG in DSB repair. Notably, when NmΔdinG cells grown under MMC stress assessed by quantitative mass spectrometry, 134 proteins were shown to be differentially abundant (DA) compared to unstressed NmΔdinG cells. Among the DNA replication, repair and recombination proteins affected, polymerase III subunits and recombinational repair proteins RuvA, RuvB, RecB and RecD were significantly down regulated while TopA and SSB were upregulated under stress condition. Most of the other DA proteins detected are involved in metabolic functions. The present study shows that the helicase DinG is probably involved in regulating metabolic pathways as well as in genome maintenance.
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Affiliation(s)
- Stephan A. Frye
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- * E-mail: (SVB); (SAF)
| | | | - Amine Namouchi
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | | | | | - Shewit Kalayou
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Tahira Riaz
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- Department of Microbiology, University of Oslo, Oslo, Norway
| | - Seetha V. Balasingham
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- * E-mail: (SVB); (SAF)
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35
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Liu Z, Gong Z, Cao Y, Ding YH, Dong MQ, Lu YB, Zhang WP, Tang C. Characterizing Protein Dynamics with Integrative Use of Bulk and Single-Molecule Techniques. Biochemistry 2017; 57:305-313. [PMID: 28945353 DOI: 10.1021/acs.biochem.7b00817] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A protein dynamically samples multiple conformations, and the conformational dynamics enables protein function. Most biophysical measurements are ensemble-based, with the observables averaged over all members of the ensemble. Though attainable, the decomposition of the observables to the constituent conformational states can be computationally expensive and ambiguous. Here we show that the incorporation of single-molecule fluorescence resonance energy transfer (smFRET) data resolves the ambiguity and affords protein ensemble structures that are more precise and accurate. Using K63-linked diubiquitin, we characterize the dynamic domain arrangements of the model system, with the use of chemical cross-linking coupled with mass spectrometry (CXMS), small-angle X-ray scattering (SAXS), and smFRET techniques. CXMS allows the modeling of protein conformational states that are alternatives to the crystal structure. SAXS provides ensemble-averaged low-resolution shape information. Importantly, smFRET affords state-specific populations, and the FRET distances validate the ensemble structures obtained by refining against CXMS and SAXS restraints. Together, the integrative use of bulk and single-molecule techniques affords better insight into protein dynamics and shall be widely implemented in structural biology.
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Affiliation(s)
- Zhu Liu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences , Wuhan, Hubei 430071, China.,Department of Pharmacology, Institute of Neuroscience, Key Laboratory of Medical Neurobiology of Ministry of Health of China, and Zhejiang Province Key Laboratory of Mental Disorder's Management, Zhejiang University School of Medicine , Hangzhou, Zhejiang 310058, China
| | - Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences , Wuhan, Hubei 430071, China
| | - Yong Cao
- National Institute of Biological Sciences , Beijing 102206, China
| | - Yue-He Ding
- National Institute of Biological Sciences , Beijing 102206, China.,RNA Therapeutics Institute, University of Massachusetts Medical School , 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Meng-Qiu Dong
- National Institute of Biological Sciences , Beijing 102206, China
| | - Yun-Bi Lu
- Department of Pharmacology, Institute of Neuroscience, Key Laboratory of Medical Neurobiology of Ministry of Health of China, and Zhejiang Province Key Laboratory of Mental Disorder's Management, Zhejiang University School of Medicine , Hangzhou, Zhejiang 310058, China
| | - Wei-Ping Zhang
- Department of Pharmacology, Institute of Neuroscience, Key Laboratory of Medical Neurobiology of Ministry of Health of China, and Zhejiang Province Key Laboratory of Mental Disorder's Management, Zhejiang University School of Medicine , Hangzhou, Zhejiang 310058, China
| | - Chun Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences , Wuhan, Hubei 430071, China
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Sugiki T, Kobayashi N, Fujiwara T. Modern Technologies of Solution Nuclear Magnetic Resonance Spectroscopy for Three-dimensional Structure Determination of Proteins Open Avenues for Life Scientists. Comput Struct Biotechnol J 2017; 15:328-339. [PMID: 28487762 PMCID: PMC5408130 DOI: 10.1016/j.csbj.2017.04.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/31/2017] [Accepted: 04/03/2017] [Indexed: 02/07/2023] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for structural studies of chemical compounds and biomolecules such as DNA and proteins. Since the NMR signal sensitively reflects the chemical environment and the dynamics of a nuclear spin, NMR experiments provide a wealth of structural and dynamic information about the molecule of interest at atomic resolution. In general, structural biology studies using NMR spectroscopy still require a reasonable understanding of the theory behind the technique and experience on how to recorded NMR data. Owing to the remarkable progress in the past decade, we can easily access suitable and popular analytical resources for NMR structure determination of proteins with high accuracy. Here, we describe the practical aspects, workflow and key points of modern NMR techniques used for solution structure determination of proteins. This review should aid NMR specialists aiming to develop new methods that accelerate the structure determination process, and open avenues for non-specialist and life scientists interested in using NMR spectroscopy to solve protein structures.
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Affiliation(s)
- Toshihiko Sugiki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Naohiro Kobayashi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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Teilum K, Kunze MBA, Erlendsson S, Kragelund BB. (S)Pinning down protein interactions by NMR. Protein Sci 2017; 26:436-451. [PMID: 28019676 PMCID: PMC5326574 DOI: 10.1002/pro.3105] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 12/14/2016] [Accepted: 12/14/2016] [Indexed: 11/29/2022]
Abstract
Protein molecules are highly diverse communication platforms and their interaction repertoire stretches from atoms over small molecules such as sugars and lipids to macromolecules. An important route to understanding molecular communication is to quantitatively describe their interactions. These types of analyses determine the amounts and proportions of individual constituents that participate in a reaction as well as their rates of reactions and their thermodynamics. Although many different methods are available, there is currently no single method able to quantitatively capture and describe all types of protein reactions, which can span orders of magnitudes in affinities, reaction rates, and lifetimes of states. As the more versatile technique, solution NMR spectroscopy offers a remarkable catalogue of methods that can be successfully applied to the quantitative as well as qualitative descriptions of protein interactions. In this review we provide an easy-access approach to NMR for the non-NMR specialist and describe how and when solution state NMR spectroscopy is the method of choice for addressing protein ligand interaction. We describe very briefly the theoretical background and illustrate simple protein-ligand interactions as well as typical strategies for measuring binding constants using NMR spectroscopy. Finally, this review provides examples of caveats of the method as well as the options to improve the outcome of an NMR analysis of a protein interaction reaction.
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Affiliation(s)
- Kaare Teilum
- Structural Biology and NMR LaboratoryThe Linderstrøm‐Lang Centre for Protein Science, Department of Biology, University of CopenhagenOle Maaløes Vej 5, DK‐2200Copenhagen NDenmark
| | - Micha Ben Achim Kunze
- Structural Biology and NMR LaboratoryThe Linderstrøm‐Lang Centre for Protein Science, Department of Biology, University of CopenhagenOle Maaløes Vej 5, DK‐2200Copenhagen NDenmark
| | - Simon Erlendsson
- Structural Biology and NMR LaboratoryThe Linderstrøm‐Lang Centre for Protein Science, Department of Biology, University of CopenhagenOle Maaløes Vej 5, DK‐2200Copenhagen NDenmark
| | - Birthe B. Kragelund
- Structural Biology and NMR LaboratoryThe Linderstrøm‐Lang Centre for Protein Science, Department of Biology, University of CopenhagenOle Maaløes Vej 5, DK‐2200Copenhagen NDenmark
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38
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Interaction studies between periplasmic cytochromes provide insights into extracellular electron transfer pathways of Geobacter sulfurreducens. Biochem J 2017; 474:797-808. [DOI: 10.1042/bcj20161022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/13/2017] [Accepted: 01/16/2017] [Indexed: 11/17/2022]
Abstract
Geobacter bacteria usually prevail among other microorganisms in soils and sediments where Fe(III) reduction has a central role. This reduction is achieved by extracellular electron transfer (EET), where the electrons are exported from the interior of the cell to the surrounding environment. Periplasmic cytochromes play an important role in establishing an interface between inner and outer membrane electron transfer components. In addition, periplasmic cytochromes, in particular nanowire cytochromes that contain at least 12 haem groups, have been proposed to play a role in electron storage in conditions of an environmental lack of electron acceptors. Up to date, no redox partners have been identified in Geobacter sulfurreducens, and concomitantly, the EET and electron storage mechanisms remain unclear. In this work, NMR chemical shift perturbation measurements were used to probe for an interaction between the most abundant periplasmic cytochrome PpcA and the dodecahaem cytochrome GSU1996, one of the proposed nanowire cytochromes in G. sulfurreducens. The perturbations on the haem methyl signals of GSU1996 and PpcA showed that the proteins form a transient redox complex in an interface that involves haem groups from two different domains located at the C-terminal of GSU1996. Overall, the present study provides for the first time a clear evidence for an interaction between periplasmic cytochromes that might be relevant for the EET and electron storage pathways in G. sulfurreducens.
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Gong Z, Gu XH, Guo DC, Wang J, Tang C. Protein Structural Ensembles Visualized by Solvent Paramagnetic Relaxation Enhancement. Angew Chem Int Ed Engl 2016; 56:1002-1006. [DOI: 10.1002/anie.201609830] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/09/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences; Wuhan Hubei Province 430071 China
| | - Xin-Hua Gu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences; Wuhan Hubei Province 430071 China
| | - Da-Chuan Guo
- CAS Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences; Wuhan Hubei Province 430071 China
| | - Jin Wang
- Department of Physics and Astronomy and Department of Chemistry; State University of New York at Stony Brook; Stony Brook New York 11794 USA
| | - Chun Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences; Wuhan Hubei Province 430071 China
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40
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Gong Z, Gu XH, Guo DC, Wang J, Tang C. Protein Structural Ensembles Visualized by Solvent Paramagnetic Relaxation Enhancement. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609830] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences; Wuhan Hubei Province 430071 China
| | - Xin-Hua Gu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences; Wuhan Hubei Province 430071 China
| | - Da-Chuan Guo
- CAS Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences; Wuhan Hubei Province 430071 China
| | - Jin Wang
- Department of Physics and Astronomy and Department of Chemistry; State University of New York at Stony Brook; Stony Brook New York 11794 USA
| | - Chun Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences; Wuhan Hubei Province 430071 China
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Bugge K, Lindorff-Larsen K, Kragelund BB. Understanding single-pass transmembrane receptor signaling from a structural viewpoint-what are we missing? FEBS J 2016; 283:4424-4451. [PMID: 27350538 DOI: 10.1111/febs.13793] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 06/10/2016] [Accepted: 06/27/2016] [Indexed: 11/30/2022]
Abstract
Single-pass transmembrane receptors are involved in essential processes of both physiological and pathological nature and represent more than 1300 proteins in the human genome. Despite the high biological relevance of these receptors, the mechanisms of the signal transductions they facilitate are incompletely understood. One major obstacle is the lack of structures of the transmembrane domains that connect the extracellular ligand-binding domains to the intracellular signaling platforms. Over a period of almost 20 years since the first structure was reported, only 21 of these receptors have become represented by a transmembrane domain structure. This scarceness stands in strong contrast to the significance of these transmembrane α-helices for receptor functionality. In this review, we explore the properties and qualities of the current set of structures, as well as the methodological difficulties associated with their characterization and the challenges left to be overcome. Without an increased and focused effort to bring this class of proteins on par with the remaining membrane protein field, a serious lag in their biological understanding looms. Design of pharmaceutical agents, prediction of mutational affects in relation to disease, and deciphering of functional mechanisms require high-resolution structural information, especially when dealing with a domain carrying so much functionality in so few residues.
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Affiliation(s)
- Katrine Bugge
- Department of Biology, Structural Biology and NMR Laboratory, University of Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, Structural Biology and NMR Laboratory, University of Copenhagen, Denmark
| | - Birthe B Kragelund
- Department of Biology, Structural Biology and NMR Laboratory, University of Copenhagen, Denmark
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Visualizing the Ensemble Structures of Protein Complexes Using Chemical Cross-Linking Coupled with Mass Spectrometry. BIOPHYSICS REPORTS 2015; 1:127-138. [PMID: 27340691 PMCID: PMC4871902 DOI: 10.1007/s41048-015-0015-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 11/11/2015] [Indexed: 11/30/2022] Open
Abstract
Graphical Abstract ![]()
Abstract Chemical cross-linking coupled with mass spectrometry (CXMS) identifies protein residues that are close in space, and has been increasingly used for modeling the structures of protein complexes. Here we show that a single structure is usually sufficient to account for the intermolecular cross-links identified for a stable complex with sub-µmol/L binding affinity. In contrast, we show that the distance between two cross-linked residues in the different subunits of a transient or fleeting complex may exceed the maximum length of the cross-linker used, and the cross-links cannot be fully accounted for with a unique complex structure. We further show that the seemingly incompatible cross-links identified with high confidence arise from alternative modes of protein-protein interactions. By converting the intermolecular cross-links to ambiguous distance restraints, we established a rigid-body simulated annealing refinement protocol to seek the minimum set of conformers collectively satisfying the CXMS data. Hence we demonstrate that CXMS allows the depiction of the ensemble structures of protein complexes and elucidates the interaction dynamics for transient and fleeting complexes. Electronic supplementary material The online version of this article (doi:10.1007/s41048-015-0015-y) contains supplementary material, which is available to authorized users.
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