Publication date: Available online 26 December 2014 Source:Biochemical and Biophysical Research Communications
Author(s): Yoshiki Shigemitsu , Teppei Ikeya , Akihiro Yamamoto , Yuusuke Tsuchie , Masaki Mishima , Brian O. Smith , Peter Güntert , Yutaka Ito
Despite their advantages in analysis, 4D NMR experiments are still infrequently used as a routine tool in protein NMR projects due to the long duration of the measurement and limited digital resolution. Recently, new acquisition techniques for speeding up multidimensional NMR experiments, such as nonlinear sampling, in combination with non-Fourier transform data processing methods have been proposed to be beneficial for 4D NMR experiments. Maximum entropy (MaxEnt) methods have been utilised for reconstructing nonlinearly sampled multi-dimensional NMR data. However, the artefacts arising from MaxEnt processing, particularly, in NOESY spectra have not yet been clearly assessed in comparison with other methods, such as quantitative maximum entropy, multidimensional decomposition, and compressed sensing. We compared MaxEnt with other methods in reconstructing 3D NOESY data acquired with variously reduced sparse sampling schedules and found that MaxEnt is robust, quick and competitive with other methods. Next, nonlinear sampling and MaxEnt processing were applied to 4D NOESY experiments, and the effect of the artefacts of MaxEnt was evaluated by calculating 3D structures from the NOE-derived distance restraints. Our results demonstrated that sufficiently converged and accurate structures (RMSD of 0.91 Å to the mean and 1.36 Å to the reference structures) were obtained even with NOESY spectra reconstructed from 1.6% randomly selected sampling points for indirect dimensions. This suggests that 3D MaxEnt processing in combination with nonlinear sampling schedules is still a useful and advantageous option for rapid acquisition of high-resolution 4D NOESY spectra of proteins.
Compressed sensing reconstruction of undersampled 3D NOESY spectra: application to large membrane proteins
Compressed sensing reconstruction of undersampled 3D NOESY spectra: application to large membrane proteins
Abstract Central to structural studies of biomolecules are multidimensional experiments. These are lengthy to record due to the requirement to sample the full Nyquist grid. Time savings can be achieved through undersampling the indirectly-detected dimensions combined with non-Fourier Transform (FT) processing, provided the experimental signal-to-noise ratio is sufficient. Alternatively, resolution and signal-to-noise can be improved within a given experiment time. However, non-FT...
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[NMRpipe Yahoo group] How to collapse multiplets into singlets by Maximum entropy algorith
How to collapse multiplets into singlets by Maximum entropy algorith
Hi, Recently, I ran a 3D HCC-TOCSY experiment on a uniformly 13C labeled sample. Therefore, all peaks are split due to carbon-carbon coupling. The paper
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Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids
Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids
Abstract Unravelling the complex correlation between chemical shifts of 13 C α, 13 C β, 13 C�, 1 H α, 15 N, 1 H N atoms in amino acids of proteins from NMR experiment and local structural environments of amino acids facilitates the assignment of secondary structures of proteins. This is an important impetus for both determining the three-dimensional structure and understanding the biological function of proteins. The previous...
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11-14-2011 08:45 AM
[NMR paper] Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE).
Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE).
Related Articles Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE).
J Biomol NMR. 2002 Aug;23(4):271-87
Authors: Gronwald W, Moussa S, Elsner R, Jung A, Ganslmeier B, Trenner J, Kremer W, Neidig KP, Kalbitzer HR
Automated assignment of NOESY spectra is a prerequisite for automated structure determination of biological macromolecules. With the program KNOWNOE we present a novel, knowledge based approach to this problem. KNOWNOE...
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11-24-2010 08:58 PM
[NMR paper] Reconstructing NMR spectra of "invisible" excited protein states using HSQC and HMQC
Reconstructing NMR spectra of "invisible" excited protein states using HSQC and HMQC experiments.
Related Articles Reconstructing NMR spectra of "invisible" excited protein states using HSQC and HMQC experiments.
J Am Chem Soc. 2002 Oct 16;124(41):12352-60
Authors: Skrynnikov NR, Dahlquist FW, Kay LE
Carr-Purcell-Meiboom-Gill (CPMG) relaxation measurements employing trains of 180 degrees pulses with variable pulse spacing provide valuable information about systems undergoing millisecond-time-scale chemical exchange. Fits of the CPMG relaxation...
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11-24-2010 08:58 PM
[NMR paper] Suppression of diagonal peaks in TROSY-type 1H NMR NOESY spectra of 15N-labeled prote
Suppression of diagonal peaks in TROSY-type 1H NMR NOESY spectra of 15N-labeled proteins.
Related Articles Suppression of diagonal peaks in TROSY-type 1H NMR NOESY spectra of 15N-labeled proteins.
J Magn Reson. 1999 Oct;140(2):499-503
Authors: Meissner A, Sørensen OW
A novel method for suppression of diagonal peaks in the amide region of NOESY NMR spectra of 15N-labeled proteins is presented. The method is particularly useful for larger proteins at high magnetic fields where interference between dipolar and chemical shift anisotropy relaxation...
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11-18-2010 08:31 PM
[NMR paper] A general method for assigning NMR spectra of denatured proteins using 3D HC(CO)NH-TO
A general method for assigning NMR spectra of denatured proteins using 3D HC(CO)NH-TOCSY triple resonance experiments.
Related Articles A general method for assigning NMR spectra of denatured proteins using 3D HC(CO)NH-TOCSY triple resonance experiments.
J Biomol NMR. 1993 Mar;3(2):225-31
Authors: Logan TM, Olejniczak ET, Xu RX, Fesik SW
A general approach for assigning the resonances of uniformly 15N- and 13C-labeled proteins in their unfolded state is presented. The assignment approach takes advantage of the spectral dispersion of the amide...
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08-21-2010 11:53 PM
Automatic maximum entropy spectral reconstruction in NMR
Automatic maximum entropy spectral reconstruction in NMR
Mehdi Mobli, Mark W. Maciejewski, Michael R. Gryk and Jeffrey C. Hoch
Journal of Biomolecular NMR; 2007; 39(2) pp 133 - 139
Abstract:
Developments in superconducting magnets, cryogenic probes, isotope labeling strategies, and sophisticated pulse sequences together have enabled the application, in principle, of high-resolution NMR spectroscopy to biomolecular systems approaching 1 megadalton. In practice, however, conventional approaches to NMR that utilize the fast Fourier transform, which require data collected at uniform time...
Evaluation of the reliability of the maximum entropy method for reconstructing 3D and 4D NOESY-type NMR spectra of proteins
Linear Mode
