Rapid NMR data collection

Methods in Enzymology

Volumn 394, Issue , 2005, Pages 78-108

  Atreya, Hanudatta S ^a   Szyperski, Thomas ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

ANALYSIS OF VARIANCE; ANALYTIC METHOD; BIOLISTIC TRANSFORMATION; CARBON NUCLEAR MAGNETIC RESONANCE; CHEMICAL MODIFICATION; CORRELATION ANALYSIS; DATA ANALYSIS; DECOMPOSITION; ENERGY YIELD; ENTROPY; FOURIER ANALYSIS; FREQUENCY ANALYSIS; GENOME ANALYSIS; MASS SPECTROMETRY; MATHEMATICAL COMPUTING; MOLECULAR INTERACTION; MOLECULAR MECHANICS; MOLECULAR PROBE; NITROGEN NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR OVERHAUSER EFFECT; POLARIZATION; PRIORITY JOURNAL; REACTION OPTIMIZATION; REDUCTION KINETICS; RELIABILITY; REVIEW; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS; SIGNAL DETECTION; SPECTRAL SENSITIVITY; STRUCTURE ANALYSIS;

EID: 16244388547     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(05)94004-4     Document Type: Article

References (90)

1. Atreya H.S., Szyperski T. G-matrix Fourier transform NMR spectroscopy for complete protein resonance assignment. Proc. Natl. Acad. Sci. USA. 101:2004;9642-9647
2. Barna J.C.J., Laue E.D. Conventional and exponential sampling for 2D NMR experiments with application to a 2D NMR spectrum of a protein. J. Magn. Reson. 75:1987;384-389
3. Barna J.C.J., Laue E.D., Mayger M.R., Skilling J., Worall S.J.P. Exponential sampling, an alternate method for sampling in two-dimensional NMR experiments. J. Magn. Reson. 73:1987;69-77
4. Bircher H.R., Müller C., Bigler P. Improvements for the 1D HOHAHA experiment. J. Magn. Reson. 89:1990;146-152
5. Bircher H.R., Müller C., Bigler P. Improved sensitivity for the 2D analogue of the 3D HOHAHA-COSY experiment. Magn. Reson. Chem. 29:1991;726-729
6. Blechta V., Freeman R. Multisite Hadamard NMR spectroscopy. Chem. Phys. Lett. 215:1993;341-346
7. Bodenhausen G., Ernst R.R. The accordion experiment, a simple approach to 3-dimensional NMR-spectroscopy. J. Magn. Reson. 45:1981;367-373
8. Boelens R., Burgering M., Fogh R.H., Kaptein R. Time-saving methods for heteronuclear multidimensional NMR of (C-13, N-15) doubly labeled protein. J. Biomol. NMR. 4:1994;201-213
9. Bolinger L., Leigh J.S. Hadamard spectroscopic imaging (HSI) for multivolume localization. J. Magn. Reson. 80:1988;162-167
10. Brutscher B. Combined frequency- and time-domain NMR spectroscopy. Application to fast protein resonance assignment. J. Biomol. NMR. 29:2004;57-64
11. Brutscher B., Morelle N., Cordier F., Marion D. Determination of an initial set of NOE-derived distance contraints for the structure determination of N-15/C-13-labeled proteins. J. Magn. Reson. B109:1995a;238-242
12. Brutscher B., Cordier F., Simorre J.-P., Caffrey M.S., Marion D. High-resolution 3D HNCOCA experiment applied to a 28-kDa paramagnetic protein. J. Biomol. NMR. 5:1995b;202-206
13. Brutscher B., Simorre J.-P., Caffrey M.S., Marion D. Design of a complete set of 2-dimensional triple resonance experiments for assigning labeled proteins. J. Magn. Reson. B105:1994;77-82
14. Carroll J.D., Chang J. Analysis of individual differences in multidimensional scaling via an N-way generalization of the 'Eckart-Young' decomposition. Psychometrica. 35:1970;283-319
15. Cavanagh C., Fairbrother W.J., Palmer A.G., Skelton N.J. "Protein NMR Spectroscopy." 1996;Academic Press, San Diego, CA
16. Cieslar C., Ross A., Zink T., Holak T.A. Efficiency in multidimensional NMR by optimized recording of time point-phase pairs in evolution periods and their selective linear transformation. J. Magn. Reson. B101:1993;97-101
17. Coggins B.E., Venters R.A., Zhou P. Generalized reconstruction of n-D NMR spectra from multiple projections: Application to the 5-D HACACONH spectrum of protein G B1 domain. J. Am. Chem. Soc. 126:2004;1000-1001
18. Ding K., Gronenborn A.M. Novel 2D triple-resonance NMR experiments for sequential resonance assignments of proteins. J. Magn. Reson. 156:2002;262-268
19. Ernst R.R., Bodenhausen G., Wokaun A. "Principles of Nuclear Magnetic Resonance in One and Two Dimensions." 1987;Oxford University Press (Clarendon), London
20. 15N]-HMQC, a pseudo-triple-resonance experiment. J. Magn. Reson. 93:1991;635-641
21. Farmer B.T., Mueller L. Simultaneous acquisition of [13C,15N]- and [15N,15N]-separated 4D gradient-enhanced NOESY spectra in proteins. J. Biomol. NMR. 4:1994;673-687
22. Frydman L., Lupulescu A., Scherf T. Principles and features of single scan two-dimensional NMR spectroscopy. J. Am. Chem. Soc. 125:2003;9204-9217
23. Frydman L., Scherf T., Lupulescu A. The acquisition of multidimensional NMR spectra within a single scan. Proc. Natl. Acad. Sci. USA. 99:2002;15858-15862
24. 15N multidimensional NMR to study the structure and dynamics of proteins. Annu. Rev. Biophys. Biomol. Struct. 27:1998;357-406
25. Goelman G. Fast Handamard spectroscopic imaging techniques. J. Magn. Reson. B104:1994;212
26. Goelman G., Subramanium V.H., Leigh J.S. Transverse Hadamard spectroscopic imaging technique. J. Magn. Reson. 89:1990;437-454
27. 15N-NOESY-HSQC. J. Biomol. NMR. 24:2002;191-201
28. Hoch J.C. Maximum entropy signal processing of two-dimensional NMR data. J. Magn. Reson. 64:1985;436-440
29. Hoch J.C. Modern spectrum analysis in nuclear magnetic resonance - alteratives to the Fourier transform. Methods Enzymol. 176:1989;216-241
30. Hoch J.C., Stern A.S. "NMR Data Processing." 1996;Wiley-Liss, New York
31. Hoch J.C., Stern A.S. Maximum entropy reconstruction, analysis and deconvolution in multidimensional nuclear magnetic resonance. Methods Enzymol. 338:2001;159-178
32. Hoch J.C., Stern A.S., Donoho D.L., Johnstone I.M. Maximum entropy reconstruction of complex (phase-sensitive) spectra. J. Magn. Reson. 86:1990;236-246
33. Hore P.J. NMR data processing using the maximum entropy method. J. Magn. Reson. 62:1985;561-567
34. Hu W.D., Gosser Y.Q., Xu W.J., Patel D.J. Novel 2D and 3D multiple-quantum bi-directional HCNCH experiments for the correlation of ribose and base protons/carbons in 13C/15N labeled RNA. J. Biomol. NMR. 20:2001;167-172
35. Ibraghimov I. Application of the three-way decomposition for matrix compression. Numer. Linear Algebra Appl. 9:2002;551-565
36. Jaynes E.T. Where do we stand on maximum entropy? Levine R.D., Tribus M. "The Maximum Entropy Formalism" 1979;15-118 MIT Press, Cambridge, MA
37. Kay L.E., Prestegard J.H. Spin-lattice relaxation of coupled spins from 2D accordion spectroscopy. J. Magn. Reson. 77:1988;599-605
38. Kay L.E., Keifer P., Saarinen T. Pure absorption gradient enhanced heteronuclear single quantum coherence spectroscopy with increased sensitivity. J. Am. Chem. Soc. 114:1992;10663-10665
39. Kessler H., Mronga S., Gemmecker G. Multi-dimensional NMR experiments using selective pulses. Magn. Reson. Chem. 29:1991;527-557
40. Kim S., Szyperski T. GFT NMR, a new approach to rapidly obtain precise high-dimensional spectral information. J. Am. Chem. Soc. 125:2003;1385-1393
41. β chemical shift assignment. J. Biomol. NMR. 28:2004;117-130
42. Köck M., Griesinger C. FAST NOESY experiments - An approach for fast structure determination. Angew. Chem. Int. Ed. Engl. 33:1994;332-334
43. Kontaxis G., Keeler J. The accordion approach for "Taylored" TOCSY. J Magn. Reson. 115:1995;35-41
44. Korzhnev D.M., Ibraghimov I.V., Billeter M., Orehov V.Y. MUNIN: Application of three-way decomposition to the analysis of heteronuclear NMR relaxation data. J. Biomol. NMR. 21:2001;263-268
45. Kozminski W., Zhukov I. Multiple quadrature detection in reduced dimensionality experiments. J. Biomol. NMR. 26:2003;157-166
46. Kupče E., Freeman R. Multisite correlation spectoscopy with soft pulses. A new phase-encoding scheme. J. Magn. Reson. A105:1993;310-315
47. Kupče E., Freeman R. Frequency-domain Hadamard spectroscopy. J. Magn. Reson. 162:2003a;158-165
48. Kupče E., Freeman R. Two-dimensional Hadamard spectoscopy. J. Magn. Reson. 162:2003b;300-310
49. Kupče E., Freeman R. Reconstruction of the three-dimensional NMR spectrum of a protein from a set of plane projections. J. Biomol. NMR. 27:2003c;383-387
50. Kupče E., Freeman R. Projection-reconstruction of three-dimensional NMR spectra. J. Am. Chem. Soc. 125:2003d;13958-13959
51. Kupče E., Freeman R. Fast reconstruction of four-dimensional NMR spectra from plane projections. J. Biomol. NMR. 28:2004;391-395
52. Laue E.D., Skilling J., Staunton J., Sibisi S., Brereton R.G. Maximum entropy method in nuclear magnetic resonance spectroscopy. J. Magn. Reson. 62:1985;437-452
53. Löhr F., Rüterjans H. A new experiment for the sequential assignment of backbone resonances in proteins. J. Biomol. NMR. 6:1995;189-197
54. Mandel A.M., Palmer A.G. Measurement of relaxation-rate constants using constant-time accordion NMR spectroscopy. J. Magn. Reson. 110:1994;62-72
55. Mariani M., Tessari M., Boelens R., Vis H., Kaptein R. Assignment of the protein backbone from a single 3D, N-15, C-13, time-shared HXYH experiment. J. Magn. Reson. B104:1994;294-297
56. 1H spin-spin coupling-constants in proteins. Biochem. Biophys. Res. Commun. 113:1983;967-974
57. Monleón D., Colson K., Moseley H.N.B., Anklin C., Oswald R., Szyperski T., Montelione G.T. Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools. J. Struct. Funct. Genom. 2:2002;93-101
58. Montelione G.T., Zheng D., Huang Y., Gunsalus C., Szyperski T. Protein NMR spectroscopy for structural genomics. Nat. Struct. Biol. 7:2000;982-984
59. Moseley H.N.B., Riaz N., Aramini J.M., Szyperski T., Montelione G.T. A generalized approach to automated NMR peak list editing: Application to reduced dimensionality triple resonance spectra. J. Magn. Reson. 170:2004;263-277
60. Orekhov V.Y., Ibraghimov I., Billeter M. MUNIN: A new approach to multi-dimensional NMR spectra interpretation. J. Biomol. NMR. 20:2001;49-60
61. Orekhov V.Y., Ibraghimov I., Billeter M. Optimizing resolution in multidimensional NMR by three-way decomposition. J. Biomol. NMR. 27:2003;165-173
62. Pang Y.X., Zeng L., Kurochkin A.V., Zuiderweg E.R.P. High-resolution detection of five frequencies in a single 3D spectrum: HNHCACO - a bidirectional coherence transfer experiment. J. Biomol. NMR. 11:1998;185-190
63. 2O. J. Magn. Reson. B103:1994;197-201
64. Pervushin K., Riek R., Wider G., Wüthrich K. Attenuated T-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
65. 1H relaxation optimization in TROSY NMR spectroscopy. J. Am. Chem. Soc. 124:2002;12898-12902
66. Rexroth A., Schmidt P., Szalma S., Geppert T., Schwalbe H., Griesinger C. New principle for the determination of coupling constants that largely suppresses differential relaxation effects. J. Am. Chem. Soc. 117:1995;10389-10390
67. Schmieder P., Stern A.S., Wagner G., Hoch J.C. Application of nonlinear sampling schemes to COSY-type spectra. J. Biomol. NMR. 3:1993;569-576
68. Schmieder P., Stern A.S., Wagner G., Hoch J.C. Improved resolution in triple-resonance spectra by nonlinear sampling in the constant-time domain. J. Biomol. NMR. 4:1994;483-490
69. Shapira B., Karton A., Aronzon D., Frydman L. Real-time 2D NMR identification of analytes undergoing continuous chromatographic separation. J. Am. Chem. Soc. 126:2004a;1262-1265
70. Shapira B., Lupulescu A., Shrot Y., Frydman L. Line shape considerations in ultrafast 2D NMR. J. Magn. Reson. 166:2004b;152-163
71. α splitting in protein NMR spectra by deconvolution with maximum entropy reconstruction. J. Am. Chem. Soc. 125:2003;2382-2383
72. Shrot Y., Frydman L. Single-scan NMR spectroscopy in arbitrary dimensions. J. Am. Chem. Soc. 125:2003;11385-11396
73. Sibisi S. Two-dimensional reconstructions from one-dimensional data by maximum entropy. Nature. 301:1983;134-136
74. Sibisi S., Skilling J., Brereton R.G., Laue E.D., Staunton J. Maximum entropy signal processing in practical NMR spectroscopy. Nature. 311:1984;446-447
75. Simorre J.-P., Brutscher B., Caffrey M.S., Marion D. Asignment of NMR-spectra of proteins using triple-resonance 2-dimensional experiments. J. Biomol. NMR. 4:1994;325-333
76. Stephenson D.S. Linear prediction and maximum entropy methods in NMR spectroscopy. Prog. NMR Spectrosc. 20:1988;515-626
77. Stern A.S., Li K.B., Hoch J.C. Modern spectrum analysis in multidimensional NMR spectroscopy: Comparison of linear-prediction extrapolation and maximum-entropy reconstruction. J. Am. Chem. Soc. 124:2002;1982-1993
78. 15N-double labeled proteins. J. Biomol. NMR. 3:1993a;127-132
79. Szyperski T., Wider G., Bushweller J.H., Wüthrich K. Reduced dimensionality in triple resonance NMR experiments. J. Am. Chem. Soc. 115:1993b;9307
80. N chemical shifts. J. Magn. Reson. B105:1994;188-191
81. Szyperski T., Braun D., Fernandez C., Bartels C., Wüthrich K. A novel reduced-dimensionality triple resonance experiment for efficient polypeptide backbone assignment, 3D CO HNN CA. J. Magn. Reson. B108:1995;197-203
82. Szyperski T., Braun D., Banecki B., Wüthrich K. Useful information from axial peak magnetization in projected NMR experiments. J. Am. Chem. Soc. 118:1996;8147-8148
83. 13C-labeled proteins with projected 4D triple resonance NMR experiments. J. Biomol. NMR. 11:1998;387-405
84. Szyperski T., Yeh D.C., Sukumaran D.K., Moseley H.N.B., Montelione G.T. Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment. Proc. Natl. Acad. Sci. USA. 99:2002;8009-8014
85. Tashiro M., Tejero R., Zimmerman D.E., Celda B., Nilsson B., Montelione G.T. High-resolution solution NMR structure of the Z domain of staphylococcal protein A. J. Mol. Biol. 272:1997;573-590
86. 1H one-bond couplings in proteins using accordion heteronuclear shift correlation experiments. J. Magn. Reson. B112:1996;269-274
87. Wüthrich K. "NMR of Proteins and Nucleic Acids." 1986;Wiley, New York
88. Xia Y., Arrowsmith C., Szyperski T. Novel projected 4D triple resonance experiments for polypeptide chemical shift assignment. J. Biomol. NMR. 24:2002;41-51
89. 2 dimensions for simultaneous data acquisition. J. Biomol. NMR. 27:2003;193-203
90. Zheng D., Aramini J.M., Montelione G.T. Validation of helical tilt angles in the solution NMR structure of the Z domain of staphylococcal protein A by combined analysis of residual dipolar coupling and NOE data. Protein Sci. 13:2004;549-554