Non-Uniform Sampling has the potential to exploit the optimal resolution of high-field NMR instruments. This is not possible in 3D and 4D NMR experiments when using traditional uniform sampling due to the long overall measurement time. Nominally, uniformly sampled time domain data acquired to a maximum evolution time tmax can be extended to high resolution via a virtual maximum evolution time t*max while extrapolating with linear prediction or iterative soft thresholding (IST). At the high resolution obtainable with extrapolation of US data, however, the accuracy of peak positions is compromised as observed when comparing inter- and intra-residue peaks in a 3D HNCA experiment. However, the accuracy of peak positions is largely improved by spreading the same number of acquired time domain data points non-uniformly over a larger evolution time to an optimal tmax followed by extrapolation to a total t*max and processing the data with an appropriate reconstruction method, such as hmsIST. To explore the optimum value of experimentally measured tmax to be reached non-uniformly with a given number of sampling points we have created test situations of time-equivalent experiments and evaluate sensitivity and accuracy of peak positions. Here we use signal-to-maximum-noise ratio as the decisive measure of sensitivity. We find that both sensitivity and resolution are optimal when PoissonGap sampling to a tmax of about ½*T2 *. Digital resolution is further enhanced by extrapolating the range of acquired time domain data to 2*T2 * but without measuring experimental points beyond ½*T2 *.
A 3D time-shared NOESY experiment designed to provide optimal resolution for accurate assignment of NMR distance restraints in large proteins
A 3D time-shared NOESY experiment designed to provide optimal resolution for accurate assignment of NMR distance restraints in large proteins
Abstract
Structure determination of proteins by solution NMR has become an established method, but challenges increase steeply with the size of proteins. Notably, spectral crowding and signal overlap impair the analysis of cross-peaks in NOESY spectra that provide distance restraints for structural models. An optimal spectral resolution can alleviate overlap but requires prohibitively long experimental time...
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11-11-2014 11:57 AM
[NMR paper] A 3D time-shared NOESY experiment designed to provide optimal resolution for accurate assignment of NMR distance restraints in large proteins.
A 3D time-shared NOESY experiment designed to provide optimal resolution for accurate assignment of NMR distance restraints in large proteins.
Related Articles A 3D time-shared NOESY experiment designed to provide optimal resolution for accurate assignment of NMR distance restraints in large proteins.
J Biomol NMR. 2014 Nov 9;
Authors: Mishra SH, Harden BJ, Frueh DP
Abstract
Structure determination of proteins by solution NMR has become an established method, but challenges increase steeply with the size of proteins. Notably,...
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11-10-2014 10:59 PM
[NMR paper] Toward optimal-resolution NMR of intrinsically disordered proteins.
Toward optimal-resolution NMR of intrinsically disordered proteins.
Related Articles Toward optimal-resolution NMR of intrinsically disordered proteins.
J Magn Reson. 2014 Apr;241:41-52
Authors: Nová?ek J, Zídek L, Sklená? V
Abstract
Proteins, which, in their native conditions, sample a multitude of distinct conformational states characterized by high spatiotemporal heterogeneity, most often termed as intrinsically disordered proteins (IDPs), have become a target of broad interest over the past 15years. With the growing evidence of their...
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03-25-2014 11:49 AM
Toward optimal-resolution NMR of intrinsically disordered proteins
Toward optimal-resolution NMR of intrinsically disordered proteins
Publication date: April 2014
Source:Journal of Magnetic Resonance, Volume 241</br>
Author(s): Ji?í Nová?ek , Lukáš Žídek , Vladimír Sklená?</br>
Proteins, which, in their native conditions, sample a multitude of distinct conformational states characterized by high spatiotemporal heterogeneity, most often termed as intrinsically disordered proteins (IDPs), have become a target of broad interest over the past 15years. With the growing evidence of their important roles in fundamental cellular...
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03-21-2014 12:52 AM
[NMR paper] Homonuclear decoupling for enhancing resolution and sensitivity in NOE and RDC measurements of peptides and proteins
Homonuclear decoupling for enhancing resolution and sensitivity in NOE and RDC measurements of peptides and proteins
Publication date: Available online 22 November 2013
Source:Journal of Magnetic Resonance</br>
Author(s): Jinfa Ying , Julien Roche , Ad Bax</br>
Application of band-selective homonuclear (BASH) 1H decoupling pulses during acquisition of the 1H free induction decay is shown to be an efficient procedure for removal of scalar and residual dipolar couplings between amide and aliphatic protons. BASH decoupling can be applied in both dimensions of a...
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11-23-2013 04:05 AM
[NMR paper] Sensitivity and resolution enhancement of oriented solid-state NMR: Application to membrane proteins.
Sensitivity and resolution enhancement of oriented solid-state NMR: Application to membrane proteins.
Related Articles Sensitivity and resolution enhancement of oriented solid-state NMR: Application to membrane proteins.
Prog Nucl Magn Reson Spectrosc. 2013 Nov;75:50-68
Authors: Gopinath T, Mote KR, Veglia G
Abstract
Oriented solid-state NMR (O-ssNMR) spectroscopy is a major technique for the high-resolution analysis of the structure and topology of transmembrane proteins in native-like environments. Unlike magic angle spinning (MAS)...
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10-29-2013 08:21 PM
Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency
Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency
Abstract The 1H dipolar network, which is the major obstacle for applying proton detection in the solid-state, can be reduced by deuteration, employing the RAP (Reduced Adjoining Protonation) labeling scheme, which yields random protonation at non-exchangeable sites. We present here a systematic study on the optimal degree of random sidechain protonation in RAP samples as a function of the MAS (magic angle spinning) frequency. In particular, we compare 1H...
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08-25-2012 08:56 AM
[NMR paper] High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection.
High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection.
Related Articles High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection.
J Am Chem Soc. 2005 Sep 14;127(36):12528-36
Authors: Eghbalnia HR, Bahrami A, Tonelli M, Hallenga K, Markley JL
We describe a novel approach to the rapid collection and processing of multidimensional NMR data: "high-resolution iterative frequency identification for NMR" (HIFI-NMR). As with...
Interpolating and extrapolating with hmsIST:Â*seeking a t max for optimal sensitivity, resolution and frequency accuracy
Linear Mode
