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Chow WY, Rajan R, Muller KH, Reid DG, Skepper JN, Wong WC, Brooks RA, Green M, Bihan D, Farndale RW, Slatter DA, Shanahan CM, Duer MJ. NMR spectroscopy of native and in vitro tissues implicates polyADP ribose in biomineralization. Science 2014; 344:742-6. [PMID: 24833391 DOI: 10.1126/science.1248167] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is useful to determine molecular structure in tissues grown in vitro only if their fidelity, relative to native tissue, can be established. Here, we use multidimensional NMR spectra of animal and in vitro model tissues as fingerprints of their respective molecular structures, allowing us to compare the intact tissues at atomic length scales. To obtain spectra from animal tissues, we developed a heavy mouse enriched by about 20% in the NMR-active isotopes carbon-13 and nitrogen-15. The resulting spectra allowed us to refine an in vitro model of developing bone and to probe its detailed structure. The identification of an unexpected molecule, poly(adenosine diphosphate ribose), that may be implicated in calcification of the bone matrix, illustrates the analytical power of this approach.
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Affiliation(s)
- W Ying Chow
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Rakesh Rajan
- Orthopaedic Research Unit, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Karin H Muller
- Department of Physiology, Development, and Neuroscience, University of Cambridge, Downing Site, Cambridge CB2 3DY, UK
| | - David G Reid
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Jeremy N Skepper
- Department of Physiology, Development, and Neuroscience, University of Cambridge, Downing Site, Cambridge CB2 3DY, UK
| | - Wai Ching Wong
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Roger A Brooks
- Orthopaedic Research Unit, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Maggie Green
- Central Biomedical Resources, University of Cambridge, School of Clinical Medicine, West Forvie Building, Forvie Site, Robinson Way, Cambridge CB2 0SZ, UK
| | - Dominique Bihan
- Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK
| | - Richard W Farndale
- Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK
| | - David A Slatter
- Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK
| | - Catherine M Shanahan
- British Heart Foundation Centre of Research Excellence, Cardiovascular Division, James Black Centre, King's College London, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Melinda J Duer
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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Bouchemal-Chibani N, du Penhoat CH, Abdelkafi M, Ghomi M, Turpin PY. Characterization of the dynamic behavior of r(ACC) and r(AAC) with NMR relaxation data and both metropolis monte carlo and molecular dynamics simulations. Biopolymers 1998. [DOI: 10.1002/(sici)1097-0282(199610)39:4<549::aid-bip7>3.0.co;2-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Giessner-Prettre C, Pullman B. Quantum mechanical calculations of NMR chemical shifts in nucleic acids. Q Rev Biophys 1987; 20:113-72. [PMID: 3327086 DOI: 10.1017/s0033583500004169] [Citation(s) in RCA: 122] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
During the last twenty-five years the development of quantum mechanical calculations and experimental measurements of chemical shifts of the different type of nuclei present in nucleic acids have run parallel in close relation to each other. The first calculations dealt with intramolecular effects on base proton shifts (Veillard, 1962) but the real breakthrough of the theory occurred with the advent of computations of intermolecular shielding due to the ring current effect of the nucleic acid bases (Giessner-Prettre & Pullman, 1970).
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Affiliation(s)
- C Giessner-Prettre
- Laboratoire de Biochimie Théorique associé au C.N.R.S., Institut de Biologie Physico-Chimique, Paris, France
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Giessner-Prettre C, Cung MT, Marraud M. Ab initio quantum mechanical calculations of the variation of the 1H and 13C nuclear magnetic shielding constants in proline as a function of the angle psi. EUROPEAN JOURNAL OF BIOCHEMISTRY 1987; 163:79-87. [PMID: 3028796 DOI: 10.1111/j.1432-1033.1987.tb10739.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The variation of the nuclear magnetic shielding constant of the different protons and carbons of trans HCO-L-Pro-NH2 with the value of the angle psi is calculated by a non-empirical method for three conformations of the proline ring. The results concerning the CH protons show that the chemical shift of the alpha, beta and gamma endo hydrogens can vary by more than 1 ppm when psi goes from -30 degrees to 180 degrees. The theoretical variation of the chemical shift difference between alpha and gamma or beta and gamma carbons is found to be sensitive to the puckering of the proline ring. For the second of these differences the theoretical results are in agreement with Siemion's relation only for a limited range of molecular conformations. Additional calculations show that the variations of the proton shifts with the value of psi are due to the magnetic anisotropy of the proline carbonyl group and to the polarization of the CH bonds by the multipolar charge distribution carried by this carbonyl. The results are discussed in relation to experiment and the possibility of using 1H and 13C chemical shifts for the determination of the value of the torsion angle about the C alpha C' bond.
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