We have previously reported on the measurement of exact NOEs (eNOEs), which yield a wealth of additional information in comparison to conventional NOEs. We have used these eNOEs in a variety of applications, including calculating high-resolution structures of proteins and RNA molecules. The collection of eNOEs is challenging, however, due to the need to measure a NOESY buildup series consisting of typically four NOESY spectra with varying mixing times in a single measurement session. While the 2D version can be completed in a few days, a fully sampled 3D-NOESY buildup series can take 10Â*days or more to acquire. This can be both expensive as well as problematic in the case of samples that are not stable over such a long period of time. One potential method to significantly decrease the required measurement time of eNOEs is to use non-uniform sampling (NUS) to decrease the number of points measured in the indirect dimensions. The effect of NUS on the extremely tight distance restraints extracted from eNOEs may be very pronounced. Therefore, we investigated the fidelity of eNOEs measured from three test cases at decreasing NUS densities: the 18.4Â*kDa protein human Pin1, the 4.1Â*kDa WW domain of Pin1 (both in 3D), and a 4.6Â*kDa 14mer RNA UUCG tetraloop (2D). Our results show that NUS imparted negligible error on the eNOE distances derived from good quality data down to 10% sampling for all three cases, but there is a noticeable decrease in the eNOE yield that is dependent upon the underlying sparsity, and thus complexity, of the sample. For Pin1, this transition occurred at roughly 40% while for the WW domain and the UUCG tetraloop it occurred at lower NUS densities of 20% and 10%, respectively. We rationalized these numbers through reconstruction simulations under various conditions. The extent of this loss depends upon the number of scans taken as well as the number of peaks to be reconstructed. Based on these findings, we have created guidelines for choosing an optimal NUS density depending on the number of peaks needed to be reconstructed in the densest region of a 2D or 3D NOESY spectrum.
Joint non-uniform sampling of all incremented time delays for quicker acquisition in protein relaxation studies
Joint non-uniform sampling of all incremented time delays for quicker acquisition in protein relaxation studies
Abstract
NMR relaxometry plays crucial role in studies of protein dynamics. The measurement of longitudinal and transverse relaxation rates of \(^{15}\) N is the main source of information on backbone motions. However, even the most basic approach exploiting a series of \(^{15}\) ...
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05-16-2017 06:53 AM
[U. of Ottawa NMR Facility Blog] Non-uniform Sampling (NUS)
Non-uniform Sampling (NUS)
Collecting 2D or 3D NMR data can be very time consuming. The indirect dimension of a 2D experiment is sampled linearly via the t1 increments in the pulse sequence. An FID must be collected for every single linearly spaced t1 increment. In the interest in collecting 2D or 3D NMR data in a more time efficient manner, a great deal of effort is made towards faster data collection techniques. While some of these methods are based on spatial selectivity, others are based on sparse sampling techniques in the indirect dimensions of nD NMR sequences. One such sparse...
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05-11-2016 08:04 PM
[NMR paper] Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics.
Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics.
Related Articles Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics.
J Struct Biol. 2015 Jul 20;
Authors: Vögeli B, Olsson S, Riek R, Güntert P
Abstract
The study of the spatial sampling of biomolecules is essential to understanding the structure-dynamics-function relationship. We have established a protocol for the determination of...
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07-25-2015 01:54 PM
Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics
Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics
Publication date: Available online 20 July 2015
Source:Journal of Structural Biology</br>
Author(s): Beat Vögeli, Simon Olsson, Roland Riek, Peter Güntert</br>
The study of the spatial sampling of biomolecules is essential to understanding the structure-dynamics-function relationship. We have established a protocol for the determination of multiple-state ensembles based on exact measurements of the nuclear Overhauser effect (eNOE). The...
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07-20-2015 09:54 PM
[NMR paper] Towards a true protein movie: A perspective on the potential impact of the ensemble-based structure determination using exact NOEs
Towards a true protein movie: A perspective on the potential impact of the ensemble-based structure determination using exact NOEs
Publication date: April 2014
Source:Journal of Magnetic Resonance, Volume 241</br>
Author(s): Beat Vögeli , Julien Orts , Dean Strotz , Celestine Chi , Martina Minges , Marielle Aulikki Wälti , Peter Güntert , Roland Riek</br>
Confined by the Boltzmann distribution of the energies of the states, a multitude of structural states are inherent to biomolecules. For a detailed understanding of a protein’s function, its entire...
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03-22-2014 01:28 AM
[NMR paper] Time-resolved multidimensional NMR with non-uniform sampling.
Time-resolved multidimensional NMR with non-uniform sampling.
Time-resolved multidimensional NMR with non-uniform sampling.
J Biomol NMR. 2014 Jan 17;
Authors: Mayzel M, Rosenlöw J, Isaksson L, Orekhov VY
Abstract
Time-resolved experiments demand high resolution both in spectral dimensions and in time of the studied kinetic process. The latter requirement traditionally prohibits applications of the multidimensional experiments, which, although capable of providing invaluable information about structure and dynamics and almost unlimited...
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01-18-2014 11:31 AM
[NMR analysis blog] Non Uniform Sampling (NUS) NMR Processing
Non Uniform Sampling (NUS) NMR Processing
Background
In the last few years, Non-Uniform Sampling (NUS) has emerged as a very powerful tool to significantly speed up the acquisition of multidimensional NMR experiments due to the fact that only a subset of the usual linearly sampled data in the Nyquist grid is measured.
Unfortunately, this fast acquisition modality introduces a new challenge as the normal Fourier Transform will fail and consequently, special processing techniques are required.
A number of sophisticated methods have been proposed for reconstructing sparsely sampled 2D...