51
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Baldus M. High-resolution NMR in the native state. IUCRJ 2017; 4:102-103. [PMID: 28250946 PMCID: PMC5330518 DOI: 10.1107/s2052252517002846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
High-resolution NMR provides increasing possibilities to probe biomolecular structure in the native state. In this issue, Luchinat and Banci [IUCrJ (2017), 4, 108-118] discuss progress on using in-cell NMR in prokaryotic and eukaryotic cell preparations.
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Affiliation(s)
- Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
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52
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Kaplan M, Narasimhan S, de Heus C, Mance D, van Doorn S, Houben K, Popov-Čeleketić D, Damman R, Katrukha EA, Jain P, Geerts WJC, Heck AJR, Folkers GE, Kapitein LC, Lemeer S, van Bergen En Henegouwen PMP, Baldus M. EGFR Dynamics Change during Activation in Native Membranes as Revealed by NMR. Cell 2016; 167:1241-1251.e11. [PMID: 27839865 DOI: 10.1016/j.cell.2016.10.038] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 08/08/2016] [Accepted: 10/20/2016] [Indexed: 10/20/2022]
Abstract
The epidermal growth factor receptor (EGFR) represents one of the most common target proteins in anti-cancer therapy. To directly examine the structural and dynamical properties of EGFR activation by the epidermal growth factor (EGF) in native membranes, we have developed a solid-state nuclear magnetic resonance (ssNMR)-based approach supported by dynamic nuclear polarization (DNP). In contrast to previous crystallographic results, our experiments show that the ligand-free state of the extracellular domain (ECD) is highly dynamic, while the intracellular kinase domain (KD) is rigid. Ligand binding restricts the overall and local motion of EGFR domains, including the ECD and the C-terminal region. We propose that the reduction in conformational entropy of the ECD by ligand binding favors the cooperative binding required for receptor dimerization, causing allosteric activation of the intracellular tyrosine kinase.
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Affiliation(s)
- Mohammed Kaplan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Siddarth Narasimhan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Cecilia de Heus
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Deni Mance
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Sander van Doorn
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Klaartje Houben
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Dušan Popov-Čeleketić
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Reinier Damman
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Eugene A Katrukha
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Purvi Jain
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Willie J C Geerts
- Biomolecular Imaging, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Lukas C Kapitein
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, the Netherlands
| | | | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands.
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53
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Wong WCV, Narkevicius A, Chow WY, Reid DG, Rajan R, Brooks RA, Green M, Duer MJ. Solid state NMR of isotope labelled murine fur: a powerful tool to study atomic level keratin structure and treatment effects. JOURNAL OF BIOMOLECULAR NMR 2016; 66:93-98. [PMID: 27699524 PMCID: PMC5095156 DOI: 10.1007/s10858-016-0056-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/23/2016] [Indexed: 06/06/2023]
Abstract
We have prepared mouse fur extensively 13C,15N-labelled in all amino acid types enabling application of 2D solid state NMR techniques which establish covalent and spatial proximities within, and in favorable cases between, residues. 13C double quantum-single quantum correlation and proton driven spin diffusion techniques are particularly useful for resolving certain amino acid types. Unlike 1D experiments on isotopically normal material, the 2D methods allow the chemical shifts of entire spin systems of numerous residue types to be determined, particularly those with one or more distinctively shifted atoms such as Gly, Ser, Thr, Tyr, Phe, Val, Leu, Ile and Pro. Also the partial resolution of the amide signals into two signal envelopes comprising of α-helical, and β-sheet/random coil components, enables resolution of otherwise overlapped α-carbon signals into two distinct cross peak families corresponding to these respective secondary structural regions. The increase in resolution conferred by extensive labelling offers new opportunities to study the chemical fate and structural environments of specific atom and amino acid types under the influence of commercial processes, and therapeutic or cosmetic treatments.
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Affiliation(s)
| | - Aurimas Narkevicius
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Wing Ying Chow
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - David G Reid
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Rakesh Rajan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Roger A Brooks
- Department of Trauma and Orthopaedic Surgery, Addenbrooke's Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Maggie Green
- Central Biomedical Resources, School of Clinical Medicine, University of Cambridge, West Forvie Building, Forvie Site, Robinson Way, Cambridge, CB2 0SZ, UK
| | - Melinda J Duer
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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54
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Palazzo L, Daniels CM, Nettleship JE, Rahman N, McPherson RL, Ong S, Kato K, Nureki O, Leung AKL, Ahel I. ENPP1 processes protein ADP-ribosylation in vitro. FEBS J 2016; 283:3371-88. [PMID: 27406238 PMCID: PMC5030157 DOI: 10.1111/febs.13811] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 06/27/2016] [Accepted: 07/11/2016] [Indexed: 12/30/2022]
Abstract
ADP-ribosylation is a conserved post-translational protein modification that plays a role in all major cellular processes, particularly DNA repair, transcription, translation, stress response and cell death. Hence, dysregulation of ADP-ribosylation is linked to the physiopathology of several human diseases including cancers, diabetes and neurodegenerative disorders. Protein ADP-ribosylation can be reversed by the macrodomain-containing proteins PARG, TARG1, MacroD1 and MacroD2, which hydrolyse the ester bond known to link proteins to ADP-ribose as well as consecutive ADP-ribose subunits; targeting this bond can thus result in the complete removal of the protein modification or the conversion of poly(ADP-ribose) to mono(ADP-ribose). Recently, proteins containing the NUDIX domain - namely human NUDT16 and bacterial RppH - have been shown to process in vitro protein ADP-ribosylation through an alternative mechanism, converting it into protein-conjugated ribose-5'-phosphate (R5P, also known as pR). Though this protein modification was recently identified in mammalian tissues, its physiological relevance and the mechanism of generating protein phosphoribosylation are currently unknown. Here, we identified ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) as the first known mammalian enzyme lacking a NUDIX domain to generate pR from ADP-ribose on modified proteins in vitro. Thus, our data show that at least two enzyme families - Nudix and ENPP/NPP - are able to metabolize protein-conjugated ADP-ribose to pR in vitro, suggesting that pR exists and may be conserved from bacteria to mammals. We also demonstrate the utility of ENPP1 for converting protein-conjugated mono(ADP-ribose) and poly(ADP-ribose) into mass spectrometry-friendly pR tags, thus facilitating the identification of ADP-ribosylation sites.
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Affiliation(s)
- Luca Palazzo
- Sir William Dunn School of PathologyUniversity of OxfordUK
| | - Casey M. Daniels
- Department of Biochemistry and Molecular BiologyBloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMDUSA,Present address: Laboratory of Systems BiologyNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD20892USA
| | - Joanne E. Nettleship
- OPPF‐UKThe Research Complex at HarwellRutherford Appleton LaboratoryHarwell OxfordUK,Division of Structural BiologyHenry Wellcome Building for Genomic MedicineUniversity of OxfordUK
| | - Nahid Rahman
- OPPF‐UKThe Research Complex at HarwellRutherford Appleton LaboratoryHarwell OxfordUK,Division of Structural BiologyHenry Wellcome Building for Genomic MedicineUniversity of OxfordUK
| | - Robert Lyle McPherson
- Department of Biochemistry and Molecular BiologyBloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMDUSA
| | - Shao‐En Ong
- Department of PharmacologyUniversity of WashingtonSeattleWAUSA
| | - Kazuki Kato
- Department of Biophysics and BiochemistryGraduate School of ScienceThe University of TokyoJapan
| | - Osamu Nureki
- Department of Biophysics and BiochemistryGraduate School of ScienceThe University of TokyoJapan
| | - Anthony K. L. Leung
- Department of Biochemistry and Molecular BiologyBloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMDUSA,Department of OncologyJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Ivan Ahel
- Sir William Dunn School of PathologyUniversity of OxfordUK
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55
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Structure of fully protonated proteins by proton-detected magic-angle spinning NMR. Proc Natl Acad Sci U S A 2016; 113:9187-92. [PMID: 27489348 DOI: 10.1073/pnas.1602248113] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Protein structure determination by proton-detected magic-angle spinning (MAS) NMR has focused on highly deuterated samples, in which only a small number of protons are introduced and observation of signals from side chains is extremely limited. Here, we show in two fully protonated proteins that, at 100-kHz MAS and above, spectral resolution is high enough to detect resolved correlations from amide and side-chain protons of all residue types, and to reliably measure a dense network of (1)H-(1)H proximities that define a protein structure. The high data quality allowed the correct identification of internuclear distance restraints encoded in 3D spectra with automated data analysis, resulting in accurate, unbiased, and fast structure determination. Additionally, we find that narrower proton resonance lines, longer coherence lifetimes, and improved magnetization transfer offset the reduced sample size at 100-kHz spinning and above. Less than 2 weeks of experiment time and a single 0.5-mg sample was sufficient for the acquisition of all data necessary for backbone and side-chain resonance assignment and unsupervised structure determination. We expect the technique to pave the way for atomic-resolution structure analysis applicable to a wide range of proteins.
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56
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Mroue KH, Xu J, Zhu P, Morris MD, Ramamoorthy A. Selective detection and complete identification of triglycerides in cortical bone by high-resolution (1)H MAS NMR spectroscopy. Phys Chem Chem Phys 2016; 18:18687-91. [PMID: 27374353 DOI: 10.1039/c6cp03506j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using (1)H-based magic angle spinning solid-state NMR spectroscopy, we report an atomistic-level characterization of triglycerides in compact cortical bone. By suppressing contributions from immobile molecules present in bone, we show that a (1)H-based constant-time uniform-sign cross-peak (CTUC) two-dimensional COSY-type experiment that correlates the chemical shifts of protons can selectively detect a mobile triglyceride layer as the main component of small lipid droplets embedded on the surface of collagen fibrils. High sensitivity and resolution afforded by this NMR approach could be potentially utilized to investigate the origin of triglycerides and their pathological roles associated with bone fractures, diseases, and aging.
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Affiliation(s)
- Kamal H Mroue
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, USA.
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57
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Ito K, Tsutsumi Y, Date Y, Kikuchi J. Fragment Assembly Approach Based on Graph/Network Theory with Quantum Chemistry Verifications for Assigning Multidimensional NMR Signals in Metabolite Mixtures. ACS Chem Biol 2016; 11:1030-8. [PMID: 26789380 DOI: 10.1021/acschembio.5b00894] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The abundant observation of chemical fragment information for molecular complexities is a major advantage of biological NMR analysis. Thus, the development of a novel technique for NMR signal assignment and metabolite identification may offer new possibilities for exploring molecular complexities. We propose a new signal assignment approach for metabolite mixtures by assembling H-H, H-C, C-C, and Q-C fragmental information obtained by multidimensional NMR, followed by the application of graph and network theory. High-speed experiments and complete automatic signal assignments were achieved for 12 combined mixtures of (13)C-labeled standards. Application to a (13)C-labeled seaweed extract showed 66 H-C, 60 H-H, 326 C-C, and 28 Q-C correlations, which were successfully assembled to 18 metabolites by the automatic assignment. The validity of automatic assignment was supported by quantum chemical calculations. This new approach can predict entire metabolite structures from peak networks of biological extracts.
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Affiliation(s)
- Kengo Ito
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 235-0045, Japan
| | - Yu Tsutsumi
- Bruker BioSpin K.K., 3-9 Moriya-cho, Kanagawa-ku, Yokohama 221-0022, Japan
| | - Yasuhiro Date
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 235-0045, Japan
| | - Jun Kikuchi
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 235-0045, Japan
- Graduate
School of Bioagricultural Sciences and School of Agricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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58
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Lenton S, Nylander T, Holt C, Sawyer L, Härtlein M, Müller H, Teixeira SCM. Structural studies of hydrated samples of amorphous calcium phosphate and phosphoprotein nanoclusters. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 45:405-12. [PMID: 26780236 DOI: 10.1007/s00249-015-1109-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 11/25/2015] [Accepted: 12/17/2015] [Indexed: 11/28/2022]
Abstract
There are abundant examples of nanoclusters and inorganic microcrystals in biology. Their study under physiologically relevant conditions remains challenging due to their heterogeneity, instability, and the requirements of sample preparation. Advantages of using neutron diffraction and contrast matching to characterize biomaterials are highlighted in this article. We have applied these and complementary techniques to search for nanocrystals within clusters of calcium phosphate sequestered by bovine phosphopeptides, derived from osteopontin or casein. The neutron diffraction patterns show broad features that could be consistent with hexagonal hydroxyapatite crystallites smaller than 18.9 Å. Such nanocrystallites are, however, undetected by the complementary X-ray and FTIR data, collected on the same samples. The absence of a distinct diffraction pattern from the nanoclusters supports the generally accepted amorphous calcium phosphate structure of the mineral core.
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Affiliation(s)
- Samuel Lenton
- EPSAM, Keele University, Staffordshire, ST5 5BG, UK.,Institut Laue-Langevin, 71 Avenue des Martyrs, 38042, Grenoble Cedex 9, France.,School of Physics and Astronomy, Astbury Center for Structural Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK
| | - Tommy Nylander
- Division of Physical Chemistry, Department of Chemistry, Lund University, 124, Lund, S221 00, Sweden
| | - Carl Holt
- Institute of Molecular, Cell, and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Lindsay Sawyer
- Structural Biochemistry Group, University of Edinburgh, Roger Land Building, The King's Buildings, Mayfield Road, EH9 3JR, Edinburgh, UK
| | - Michael Härtlein
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042, Grenoble Cedex 9, France
| | - Harrald Müller
- European Synchrotron Radiation Facility, CS 40220, 38043, Grenoble, France
| | - Susana C M Teixeira
- EPSAM, Keele University, Staffordshire, ST5 5BG, UK. .,Institut Laue-Langevin, 71 Avenue des Martyrs, 38042, Grenoble Cedex 9, France.
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59
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Wong VWC, Reid DG, Chow WY, Rajan R, Green M, Brooks RA, Duer MJ. Preparation of highly and generally enriched mammalian tissues for solid state NMR. JOURNAL OF BIOMOLECULAR NMR 2015; 63:119-123. [PMID: 26407607 DOI: 10.1007/s10858-015-9977-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/08/2015] [Indexed: 06/05/2023]
Abstract
An appreciable level of isotope labelling is essential for future NMR structure elucidation of mammalian biomaterials, which are either poorly expressed, or unexpressable, using micro-organisms. We present a detailed protocol for high level (13)C enrichment even in slow turnover murine biomaterials (fur keratin), using a customized diet supplemented with commercial labelled algal hydrolysate and formulated as a gel to minimize wastage, which female mice consumed during pregnancy and lactation. This procedure produced approximately eightfold higher fur keratin labelling in pups, exposed in utero and throughout life to label, than in adults exposed for the same period, showing both the effectiveness, and necessity, of this approach.
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Affiliation(s)
| | - David G Reid
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Wing Ying Chow
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Rakesh Rajan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Maggie Green
- Central Biomedical Resources, School of Clinical Medicine, University of Cambridge, West Forvie Building, Forvie Site, Robinson Way, Cambridge, CB2 0SZ, UK
| | - Roger A Brooks
- Department of Trauma and Orthopaedic Surgery, Addenbrooke's Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Melinda J Duer
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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60
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61
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Hegedűs C, Robaszkiewicz A, Lakatos P, Szabó É, Virág L. Poly(ADP-ribose) in the bone: from oxidative stress signal to structural element. Free Radic Biol Med 2015; 82:179-86. [PMID: 25660995 DOI: 10.1016/j.freeradbiomed.2015.01.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 01/20/2015] [Accepted: 01/26/2015] [Indexed: 01/16/2023]
Abstract
Contrary to common perception bone is a dynamic organ flexibly adapting to changes in mechanical loading by shifting the delicate balance between bone formation and bone resorption carried out by osteoblasts and osteoclasts, respectively. In the past decades numerous studies demonstrating production of reactive oxygen or nitrogen intermediates, effects of different antioxidants, and involvement of prototypical redox control mechanisms (Nrf2-Keap1, Steap4, FoxO, PAMM, caspase-2) have proven the central role of redox regulation in the bone. Poly(ADP-ribosyl)ation (PARylation), a NAD-dependent protein modification carried out by poly(ADP-ribose) polymerase (PARP) enzymes recently emerged as a new regulatory mechanism fine-tuning osteoblast differentiation and mineralization. Interestingly PARylation does not simply serve as a signaling mechanism during osteoblast differentiation but also couples it to osteoblast death. Even more strikingly, the poly(ADP-ribose) polymer likely released from succumbed cells at the terminal stage of differentiation is incorporated into the bone matrix representing the first structural role of this versatile biopolymer. Moreover, this new paradigm explains why and how osteodifferentiation and death of cells entering this pathway are closely coupled to each other. Here we review the role of reactive oxygen and nitrogen intermediates as well as PARylation in osteoblast and osteoclast differentiation, function, and cell death.
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Affiliation(s)
- Csaba Hegedűs
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Agnieszka Robaszkiewicz
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Department of Environmental Pollution Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Poland
| | - Petra Lakatos
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Éva Szabó
- Division of Dermatology, Faculty of Medicine, University of Debrecen, Nagyerdei krt 98, H-4032 Debrecen, Hungary.
| | - László Virág
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; MTA-DE Cell Biology and Signaling Research Group, Debrecen, Hungary.
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62
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Duer MJ. The contribution of solid-state NMR spectroscopy to understanding biomineralization: atomic and molecular structure of bone. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:98-110. [PMID: 25797009 DOI: 10.1016/j.jmr.2014.12.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/15/2014] [Accepted: 12/23/2014] [Indexed: 05/06/2023]
Abstract
Solid-state NMR spectroscopy has had a major impact on our understanding of the structure of mineralized tissues, in particular bone. Bone exemplifies the organic-inorganic composite structure inherent in mineralized tissues. The organic component of the extracellular matrix in bone is primarily composed of ordered fibrils of collagen triple-helical molecules, in which the inorganic component, calcium phosphate particles, composed of stacks of mineral platelets, are arranged around the fibrils. This perspective argues that key factors in our current structural model of bone mineral have come about through NMR spectroscopy and have yielded the primary information on how the mineral particles interface and bind with the underlying organic matrix. The structure of collagen within the organic matrix of bone or any other structural tissue has yet to be determined, but here too, this perspective shows there has been real progress made through application of solid-state NMR spectroscopy in conjunction with other techniques. In particular, NMR spectroscopy has highlighted the fact that even within these structural proteins, there is considerable dynamics, which suggests that one should be cautious when using inherently static structural models, such as those arising from X-ray diffraction analyses, to gain insight into molecular roles. It is clear that the NMR approach is still in its infancy in this area, and that we can expect many more developments in the future, particularly in understanding the molecular mechanisms of bone diseases and ageing.
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Affiliation(s)
- Melinda J Duer
- Dept. of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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63
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Kistemaker HAV, Lameijer LN, Meeuwenoord NJ, Overkleeft HS, van der Marel GA, Filippov DV. Synthesis of Well-Defined Adenosine Diphosphate Ribose Oligomers. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412283] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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64
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Kistemaker HAV, Lameijer LN, Meeuwenoord NJ, Overkleeft HS, van der Marel GA, Filippov DV. Synthesis of well-defined adenosine diphosphate ribose oligomers. Angew Chem Int Ed Engl 2015; 54:4915-8. [PMID: 25704172 DOI: 10.1002/anie.201412283] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Indexed: 11/10/2022]
Abstract
The post-translational modification of proteins that is known as adenosine diphosphate ribosylation (ADPr) regulates a wide variety of important biological processes, such as DNA-damage repair and cellular metabolism. This modification is also involved in carcinogenesis and the process of aging. Therefore, a better understanding of the function of ADP-ribosylation is crucial for the development of novel therapeutics. To facilitate the elucidation of the biology of ADPr, the availability of well-defined fragments of poly(ADP-ribose) is essential. Herein we report a solid-phase synthetic approach for the preparation of ADP-ribose oligomers of exactly defined length. The methodology is exemplified by the first reported synthesis of an ADP-ribose dimer and trimer.
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Affiliation(s)
- Hans A V Kistemaker
- Leiden Institute of Chemistry, Department of Bio-organic Synthesis, Leiden University, Einsteinweg 55, 2333 CC Leiden (The Netherlands) http://biosyn.lic.leidenuniv.nl/
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65
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Amgarten B, Rajan R, Martínez-Sáez N, Oliveira BL, Albuquerque IS, Brooks RA, Reid DG, Duer MJ, Bernardes GJL. Collagen labelling with an azide-proline chemical reporter in live cells. Chem Commun (Camb) 2015; 51:5250-2. [DOI: 10.1039/c4cc07974d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Biosynthetic incorporation of an azide-proline chemical reporter into collagen allows selective imaging in live foetal ovine osteoblasts using a strain-promoted [3+2] azide–alkyne cycloaddition reaction.
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Affiliation(s)
| | - Rakesh Rajan
- Division of Trauma & Orthopaedic Surgery
- University of Cambridge
- Addenbrooke's Hospital
- Cambridge CB2 0QQ
- UK
| | | | - Bruno L. Oliveira
- Athinoula A. Martinos Center for Biomedical Imaging
- Department of Radiology
- Massachusetts General Hospital
- Harvard Medical School
- Charlestown
| | - Inês S. Albuquerque
- Instituto de Medicina Molecular
- Faculdade de Medicina da Universidade de Lisboa
- Av. Prof. Egas Moniz
- 1649-028 Lisboa
- Portugal
| | - Roger A. Brooks
- Division of Trauma & Orthopaedic Surgery
- University of Cambridge
- Addenbrooke's Hospital
- Cambridge CB2 0QQ
- UK
| | - David G. Reid
- Department of Chemistry
- University of Cambridge
- CB2 1EW Cambridge
- UK
| | - Melinda J. Duer
- Department of Chemistry
- University of Cambridge
- CB2 1EW Cambridge
- UK
| | - Gonçalo J. L. Bernardes
- Department of Chemistry
- University of Cambridge
- CB2 1EW Cambridge
- UK
- Instituto de Medicina Molecular
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Rai RK, Singh C, Sinha N. Predominant role of water in native collagen assembly inside the bone matrix. J Phys Chem B 2014; 119:201-11. [PMID: 25530228 DOI: 10.1021/jp511288g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Bone is one of the most intriguing biomaterials found in nature consisting of bundles of collagen helixes, hydroxyapatite, and water, forming an exceptionally tough, yet lightweight material. We present here an experimental tool to map water-dependent subtle changes in triple helical assembly of collagen protein in its absolute native environment. Collagen being the most abundant animal protein has been subject of several structural studies in last few decades, mostly on an extracted, overexpressed, and synthesized form of collagen protein. Our method is based on a (1)H detected solid-state nuclear magnetic resonance (ssNMR) experiment performed on native collagen protein inside intact bone matrix. Recent development in (1)H homonuclear decoupling sequences has made it possible to observe specific atomic resolution in a large complex system. The method consists of observing a natural-abundance two-dimensional (2D) (1)H/(13)C heteronuclear correlation (HETCOR) and(1)H double quantum-single quantum (DQ-SQ) correlation ssNMR experiment. The 2D NMR experiment maps three-dimensional assembly of native collagen protein and shows that extracted form of collagen protein is significantly different from protein in the native state. The method also captures native collagen subtle changes (of the order of ∼1.0 Å) due to dehydration and H/D exchange, giving an experimental tool to map small changes. The method has the potential to be of wide applicability to other collagen containing biomaterials.
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Affiliation(s)
- Ratan Kumar Rai
- Centre of Biomedical Research , SGPGIMS Campus, Raibarelly Road, Lucknow 226014, India
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Singh C, Rai RK, Aussenac F, Sinha N. Direct Evidence of Imino Acid-Aromatic Interactions in Native Collagen Protein by DNP-Enhanced Solid-State NMR Spectroscopy. J Phys Chem Lett 2014; 5:4044-4048. [PMID: 26276492 DOI: 10.1021/jz502081j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Aromatic amino acids (AAAs) have rare presence (∼1.4% abundance of Phe) inside of collagen protein, which is the most abundant animal protein playing a functional role in skin, bone, and connective tissues. The role of AAAs is very crucial and has been debated. We present here experimental results depicting interaction of AAAs with imino acids in a native collagen protein sample. The interaction is probed by solid-state NMR (ssNMR) spectroscopy experiments such as (1)H-(13)C heteronuclear correlation (HETCOR) performed on a native collagen sample. The natural abundance (13)C spectrum was obtained by dynamic nuclear polarization (DNP) sensitivity enhancement coupled with ssNMR, providing ∼30-fold signal enhancement. Our results also open up new avenues of probing collagen structure/dynamics closest to the native state by ssNMR experiments coupled with DNP.
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Affiliation(s)
- Chandan Singh
- †Centre of Biomedical Research, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS) Campus, Raebarelly Road, Lucknow 226014, India
- §School of Biotechnology, Banaras Hindu University, Varanasi 221005, India
| | - Ratan Kumar Rai
- †Centre of Biomedical Research, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS) Campus, Raebarelly Road, Lucknow 226014, India
| | - Fabien Aussenac
- ‡Bruker Biospin, 34 Rue Industrie, 67160 Wissembourg, France
| | - Neeraj Sinha
- †Centre of Biomedical Research, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS) Campus, Raebarelly Road, Lucknow 226014, India
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