NMR spectroscopy of large molecules and multimolecular assemblies in solution

Current Opinion in Structural Biology

Volumn 9, Issue 5, 1999, Pages 594-601

  Wider, Gerhard ^a   Wüthrich, Kurt ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

NITROGEN 15; NUCLEIC ACID; PROTEIN;

AQUEOUS SOLUTION; CHEMICAL STRUCTURE; HYDROGEN BOND; ISOTOPE LABELING; MOLECULAR WEIGHT; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE; REVIEW;

EID: 0344994534     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(99)00011-1     Document Type: Review

References (53)

1. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanoucghi T The protein data bank: a computer-based archival file for macromolecular structures. J Mol Biol. 112:1977;535-542.
2. Güntert P Structure calculation of biological macromolecules from NMR data. Q Rev Biophys. 31:1998;145-237.
3. Wüthrich K NMR - this other method for protein and nucleic acid structure determination. Acta Crystallogr D. 51:1995;249-270.
4. Borman S Scaling up protein NMR. Chem Eng News. February 15:1999;65-67.
5. Wüthrich K The second decade - into the third millennium. Nat Struct Biol. 5:1998;492-495.
6. Yu H Extending the size limit of protein nuclear magnetic resonance. Proc Natl Acad Sci USA. 96:1999;332-334.
7. Pellecchia M, Sebbel P, Hermanns U, Wüthrich K, Glockshuber R Pilus chaperone FimC-adhesin FimH interactions mapped by TROSY-NMR. Nat Struct Biol. 6:1999;336-339. First application of transverse relaxation-optimized spectroscopy (TROSY) chemical shift mapping of intermolecular contacts between two proteins in a complex of molecular weight 51 kDa, which could previously not be achieved with conventional NMR methods. This use of TROSY opens a new avenue for NMR studies of supramolecular structures with high molecular weights.
8. Shuker SB, Hajduk PJ, Meadows RP, Fesik SW Discovering high-affinity ligands for proteins: SAR by NMR. Science. 274:1996;1531-1534.
9. Wagner G Prospects for NMR of large proteins. J Biomol NMR. 3:1993;375-385.
10. Kay LE, Gardner KH Solution NMR spectroscopy beyond 25 kDa. Curr Opin Struct Biol. 7:1997;722-731.
11. Clore GM, Gronenborn AM NMR structure determination of proteins and protein complexes larger than 20 kDa. Curr Opin Chem Biol. 2:1998;564-570.
12. Wider G Technical aspects of NMR spectroscopy with biological macromolecules and studies of hydration in solution. Prog Nucl Magn Reson Spectros. 32:1998;193-275.
13. 2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc Natl Acad Sci USA. 94:1997;12366-12371.
14. Riek R, Wider G, Pervushin K, Wüthrich K Polarization transfer by cross-correlated relaxation in solution NMR with very large proteins. Proc Natl Acad Sci USA. 96:1999;4918-4923. For structures with molecular weights beyond 100 kDa, transverse relaxation during magnetization transfers using scalar spin-spin couplings becomes a limiting factor. Cross-correlated relaxation-enhanced polarization transfer (CRINEPT) makes use of the fact that the rate of polarization transfer by cross-correlated relaxation is proportional to the rotational correlation time and thus generates efficient transfer for solution NMR spectroscopy of very high molecular weight structures.
15. Bax A, Grzesiek S Methodological advances in protein NMR. Accounts Chem Res. 26:1993;131-138.
16. 1H polarization.
17. 1H transition, which affords a √2 sensitivity enhancement in transverse relaxation-optimized spectroscopy (TROSY) pulse sequences.
18. Freeman R, Kupce E Decoupling: theory and practice I. Current methods and recent concepts. NMR Biomed. 10:1997;372-380.
19. 15N chemical shift anisotropy in solution. J Am Chem Soc. 120:1998;10947-10952.
20. 1H dipolar cross-correlation rates. J Magn Resonance. 127:1997;128-133.
21. Wand AJ, Ehrhardt MR, Flynn PF High-resolution NMR of encapsulated proteins dissolved in low-viscosity fluids. Proc Natl Acad Sci USA. 95:1998;15299-15302. In a novel approach to reducing transverse relaxation, the protein ubiquitin was introduced into a reversed micelle, which, in turn, was dissolved in a low viscosity solvent that enables rapid rotational movement of the micelles. For large proteins, the mobility of the micelles could potentially be significantly faster than that of the free protein in water.
22. Salzmann M, Pervushin K, Wider G, Senn H, Wüthrich K TROSY in triple-resonance experiments: new perspectives for sequential NMR assignment of large proteins. Proc Natl Acad Sci USA. 95:1998;13585-13590. With the implementation of transverse relaxation-optimized spectroscopy (TROSY) elements in triple-resonance experiments, a severalfold increase in sensitivity can be obtained for proteins with molecular weights around 25 kDa. Sensitivity enhancements of one to two orders of magnitude are predicted for proteins of 100 kDa or somewhat larger.
23. Salzmann M, Wider G, Pervushin K, Senn H, Wüthrich K TROSY type triple-resonance experiments for sequential NMR assignments of large proteins. J Am Chem Soc. 121:1999;844-848.
24. Yamazaki T, Otomo T, Oda N, Kyogoku Y, Uegaki K, Ito N, Ishino Y, Nakamura H Segmental isotope labeling for protein NMR using peptide splicing. J Am Chem Soc. 120:1998;5591-5592.
25. Otomo T, Teruya K, Uegaki K, Yamazaki T, Kyogoku Y Improved segmental isotope labeling of proteins and application to a larger protein. J Biolmol NMR. 14:1999;105-114. Improved and more versatile techniques for the segmental isotope labeling of proteins using trans-splicing are introduced.
26. Muir TW, Sondhi D, Cole PA Expressed protein ligation: a general method for protein engineering. Proc Natl Acad Sci USA. 95:1998;6705-6710.
27. Xu R, Ayers B, Cowburn D, Muir TW Chemical ligation of folded recombinant proteins: segmental isotopic labeling of domains for NMR studies. Proc Natl Acad Sci USA. 96:1999;388-393. Improved and more versatile techniques for the segmental isotope labeling of proteins using chemical semisynthesis are described.
28. Wüthrich K NMR of proteins and nucleic acids. 1986;Wiley, New York.
29. Salzmann M: The use of TROSY for the sequential NMR assignment of very large proteins. Zürich: ETH Zürich; no. 13189.
30. 1H]-TROSY-HNCA for sequential assignments of large proteins. J Biomol NMR. 14:1999;85-88.
31. Weigelt J Single scan, sensitivity- and gradient-enhanced TROSY for multidimensional NMR experiments. J Am Chem Soc. 120:1998;10778-10779.
32. Czisch M, Boelens R Sensitivity enhancement in the TROSY experiment. J Mag Resonance. 134:1998;158-160.
33. 1H]-correlation experiments with improved sensitivity and resolution were obtained by implementing transverse relaxation-optimization spectroscopy (TROSY) and a standard sensitivity enhancement routine. Applications using isotope-labeled RNA yielded spectra of impressive quality.
34. Meissner A, Schulte-Herbrüggen T, Briand J, Sørensen OW Double spin-state-selective coherence transfer. Application for two-dimensional selection of multiplet components with long transverse relaxation times. Mol Phys. 95:1998;1137-1142.
35. Rance M, Loria JP, Palmer AG Sensitivity improvement of transverse relaxation-optimized spectroscopy. J Magn Resonance. 136:1999;92-101.
36. 1H-detected triple resonance TROSY-based experiments. J Biomol NMR. 13:1999;3-10.
37. 1H dimension were achieved by the implementation of transverse relaxation-optimization spectroscopy (TROSY) and a standard sensitivity enhancement routine in triple-resonance experiments. Four-dimensional spectra of a 46 kDa protein were presented as illustrations for the use of this approach.
38. 13C nuclear-magnetic-resonance chemical-shifts. J Am Chem Soc. 113:1991;5490-5492.
39. 13C chemical-shift data. J Biomol NMR. 4:1994;171-180.
40. Zhu G, Kong XM, Sze KH Gradient and sensitivity enhancement of 2D TROSY with water flip-back, 3D NOESY-TROSY and TOCSY-TROSY experiments. J Biomol NMR. 13:1999;77-81.
41. 15N-labeled proteins.
42. Prestegard JH New techniques in structural NMR - anisotropic interactions. Nat Struct Biol. 5:1998;517-522.
43. Gayathra C, Bothner-By AA, van Zijl PCM, MacLean C Dipolar magnetic field effects in NMR spectroscopy. Chem Phys Lett. 87:1982;192-196.
44. Tolman JR, Flanagan JM, Kennedy MA, Prestegard JH Nuclear magnetic dipole interactions in field-oriented proteins - information for structure determination in solution. Proc Natl Acad Sci USA. 92:1995;9279-9283.
45. Tjandra N, Bax A Direct measurement of distances and angles in biomolecules by NMR in dilute liquid crystalline medium. Science. 278:1997;1111-1114.
46. Hansen MR, Mueller L, Pardi A Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions. Nat Struct Biol. 5:1998;1065-1074. Filamentous phage is introduced as an alternative to dilute liquid-crystal media for the alignment of macromolecules in studies of residual dipole-dipole couplings.
47. Koenig BW, Hu JS, Ottiger M, Bose S, Hendler RW, Bax A NMR measurement of dipolar couplings in proteins aligned by transient binding to purple membrane fragments. J Am Chem Soc. 121:1999;1385-1386. Purple membrane fragments are introduced as an alternative medium for the alignment of macromolecules in studies of residual dipole-dipole couplings.
48. Dötsch V, Wagner G New approaches to structure determination by NMR spectroscopy. Curr Opin Struct Biol. 8:1998;619-623.
49. 15N scalar couplings across the hydrogen bonds in RNA base pairs are reported, with values of about 7 Hz. These new NMR parameters have great potential in structural studies of RNAs and are of keen interest with regard to the theory of hydrogen bonds and scalar couplings.
50. 13C-labeled DNA duplex, with values of about 7 Hz and 3 Hz, respectively. These new NMR parameters are of keen interest with regard to structural studies of DNA, as well as to theoretical investigations of hydrogen bonds and scalar coupling constants.
51. 15N nuclei with widely separated chemical shifts. J Biomol NMR. 14:1999;67-70.
52. 13C′ couplings of about 0.5 Hz across hydrogen bonds in proteins. This direct detection of hydrogen bonds is of keen interest in structural studies of proteins by NMR spectroscopy.
53. 13C′ couplings of about 0.5 Hz across hydrogen bonds in proteins. This direct detection of hydrogen bonds is of keen interest for structural studies of proteins by NMR spectroscopy.