Abstract
Application of Fourier Transform for processing 3D NMR spectra with random sampling of evolution time space is presented. The 2D FT is calculated for pairs of frequencies, instead of conventional sequence of one-dimensional transforms. Signal to noise ratios and linewidths for different random distributions were investigated by simulations and experiments. The experimental examples include 3D HNCA, HNCACB and 15N-edited NOESY-HSQC spectra of 13C 15N labeled ubiquitin sample. Obtained results revealed general applicability of proposed method and the significant improvement of resolution in comparison with conventional spectra recorded in the same time.
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Armstrong G.S., Mandelshtam V.A., Shaka A.J., Bendiak B. (2005) J. Magn. Reson. 173:160–168
Barna, J.C.J., Laue, E.D., Mayger, M.R., Skilling, J., Worrall, S.J.P. (1987) J. Magn. Reson., 73, 69–77
Berkovitz A., Rusnak I. (1992) IEEE Trans. Signal Process. 40:2816–2819
Bodenhausen G., Ernst R.R. (1981) J. Magn. Reson. 45:367–373
Bodenhausen G., Ernst R.R. (1982) J. Am. Chem. Soc. 104:1304–1309
Coggins B.E., Venters R.A., Zhou P. (2004) J. Am. Chem. Soc. 126:1000–1001
Coggins B.E., Venters R.A., Zhou P. (2005) J. Am. Chem. Soc. 127:11562–11563
Delsuc M.A., Tramesel D. (2006) CR Chim. 9:364–373
Ding K., Gronenborn A.M. (2002) J. Magn. Reson. 156:262–268
Dutt A., Rokhlin V. (1995) Appl. Comp. Harm. Anal. 2:85–100
Eghbalnia H.R., Bahrami A., Tonelli M., Hallenga K., Markley J.L. (2005) J. Am. Chem. Soc. 127:12528–12536
Ernst R.R., Anderson W.A. (1966) Rev. Sci. Instrum. 37:93–102
Ferreira P. (1999) IEEE Trans. Circuits Syst. II 46:475–478
Freeman R., Kupče Ē. (2003) J. Biomol. NMR 27:101–113
Frueh D.P., Sun Z.-Y. J., Vosburg D.A., Walsh C.T., Hoch J.C., Wagner G. (2006) J. Am. Chem. Soc. 128:5757–5763
Frydman L., Scherf T., Lupulescu A. (2002) Proc. Natl. Acad. Sci. USA 99: 15858–15662
Galassi, M., Davies, J., Theiler, J., Gough, B., Jungman, G., Booth, M. and Rossi, F. (2003) GNU Scientific Library Reference Manual, 2nd edn. Network Theory Ltd. ISBN 0954161734
Goddard, T.D. and Kneller, D.G. (2002) SPARKY 3. University of California, San Francisco, http://www.cgl.ucsf.edu/home/sparky
Hamilton W.R. (1847) Proc. Roy. Irish Acad. 3:1–16
Kazimierczuk K., Koźmiński W., Zhukov I. (2006) J. Magn. Reson. 179:323–328
Kim S., Szyperski T. (2003) J. Am. Chem. Soc. 125:1385–1393
Koźmiński W., Zhukov I. (2003) J. Biomol. NMR 26:157–166
Kupče Ē., Freeman R. (2003) J. Am. Chem. Soc. 125:13958–13959
Kupče Ē., Freeman R. (2004a) J. Biomol. NMR 28:391–395
Kupče Ē., Freeman R. (2004b) Concept Magnetic Res. 22A:4–11
Lauterbur P.C. (1973) Nature 242:190–191
Luan T., Jaravine V., Yee A., Arrowsmith C.H., Orekhov V.Y. (2005) Optimization of resolution and sensitivity of 4D NOESY using multi-dimensional decomposition. J. Biomol. NMR 33:1–14
Mandelshtam V.A., Taylor H.S., Shaka A.J. (1998) J. Magn. Reson. 133:304–312
Malmodin D., Billeter M. (2005a) J. Magn. Reson. 176:47–53
Malmodin D., Billeter M. (2005b) J. Am. Chem. Soc. 127:13486–13487
Marion D. (2005) J. Biomol. NMR 32: 141–150
Marvasti F. (1996) IEEE Trans. Signal Process. 44:572–576
Marvasti F. (2001) Nonuniform Sampling, Theory and Practice. New York, Kluwer/Plenum
Orekhov V., Ibraghimov I., Billeter M. (2003) J. Biomol. NMR 27:165–173
Rovnyak D., Frueh D.P., Sastry M., Sun Z.Y.J., Stern A.S., Hoch J.C., Wagner G. (2004) J. Magn. Reson. 170:15–21
Sattler M., Schleuchter J., Griesinger C. (1999) Prog. NMR Spectrosc. 34:93–158
Sun Z.Y.J., Frueh D.P., Selenko P., Hoch J.C., Wagner G. (2005) J. Biomol. NMR 33:43–50
Szyperski T., Yeh D.C., Sukumaran D.K., Moseley H.N.B., Montelione G.T. (2002) Proc. Natl. Acad. Sci. USA 99:8009–8014
Tarczynski A., Allay N. (2004) IEEE Trans. Signal Process. 52:3324–3334
Tarczyński A., Qu D. (2005) Int. J. Appl. Math. Comput. Sci. 15:463–469
Tugarinov V., Kay L.E., Ibraghimov I., Orekhov V.Y. (2005) J. Am. Chem. Soc. 127:2767–2775
Yeh T. (1997) Appl. Math. Comp. 87: 227–246
Yoon J.W., Godsill S., Kupče Ē., Freeman R. (2006) Magn. Reson. Chem. 44:197–209
Acknowledgements
Authors are grateful to Prof. Andrew R. Byrd (Structural Biophysics Laboratory, National Cancer Institute-Frederick, Frederick, Maryland, USA) for the sample of 13C, 15N-double labeled human ubiquitin.
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Kazimierczuk, K., Zawadzka, A., Koźmiński, W. et al. Random sampling of evolution time space and Fourier transform processing. J Biomol NMR 36, 157–168 (2006). https://doi.org/10.1007/s10858-006-9077-y
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DOI: https://doi.org/10.1007/s10858-006-9077-y