Related ArticlesEffects of NMR spectral resolution on protein structure calculation.
PLoS One. 2013;8(7):e68567
Authors: Tikole S, Jaravine V, Orekhov VY, Güntert P
Abstract
Adequate digital resolution and signal sensitivity are two critical factors for protein structure determinations by solution NMR spectroscopy. The prime objective for obtaining high digital resolution is to resolve peak overlap, especially in NOESY spectra with thousands of signals where the signal analysis needs to be performed on a large scale. Achieving maximum digital resolution is usually limited by the practically available measurement time. We developed a method utilizing non-uniform sampling for balancing digital resolution and signal sensitivity, and performed a large-scale analysis of the effect of the digital resolution on the accuracy of the resulting protein structures. Structure calculations were performed as a function of digital resolution for about 400 proteins with molecular sizes ranging between 5 and 33 kDa. The structural accuracy was assessed by atomic coordinate RMSD values from the reference structures of the proteins. In addition, we monitored also the number of assigned NOESY cross peaks, the average signal sensitivity, and the chemical shift spectral overlap. We show that high resolution is equally important for proteins of every molecular size. The chemical shift spectral overlap depends strongly on the corresponding spectral digital resolution. Thus, knowing the extent of overlap can be a predictor of the resulting structural accuracy. Our results show that for every molecular size a minimal digital resolution, corresponding to the natural linewidth, needs to be achieved for obtaining the highest accuracy possible for the given protein size using state-of-the-art automated NOESY assignment and structure calculation methods.
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
January 2012
Publication year: 2012
Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 60</br>
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The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we present a new and highly accurate, precise, and robust formulation for the prediction...
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12-01-2012 06:10 PM
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Publication year: 2012
Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 60</br>
Jakob T. Nielsen, Hamid R. Eghbalnia, Niels Chr. Nielsen</br>
The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we present a new and highly accurate, precise,...
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03-09-2012 09:16 AM
[U. of Ottawa NMR Facility Blog] Nitrogen Pressure and Spectral Resolution
Nitrogen Pressure and Spectral Resolution
Super-conducting NMR magnets are cooled with liquid helium. The boil off rate of the liquid helium is minimized by surrounding it with a high vacuum and a liquid nitrogen cryostat. The liquid nitrogen cryostat may either be vented directly to the atmosphere or it may be maintained at a pressure slightly above atmospheric pressure with the use of pressure relief valves. NMR users should be aware that the homogeneity of an NMR magnet is affected drastically by the pressure in the liquid nitrogen cryostat. The left-hand panel of the figure below shows...
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08-25-2011 06:00 AM
Cryogenic temperature effects and resolution upon slow cooling of protein preparations in solid state NMR
Cryogenic temperature effects and resolution upon slow cooling of protein preparations in solid state NMR
Abstract X-ray crystallography using synchrotron radiation and the technique of dynamic nuclear polarization (DNP) in nuclear magnetic resonance (NMR) require samples to be kept at temperatures below 100 K. Protein dynamics are poorly understood below the freezing point of water and down to liquid nitrogen temperatures. Therefore, we investigate the α-spectrin SH3 domain by magic angle spinning (MAS) solid state NMR (ssNMR) at various temperatures while cooling slowly. Cooling down...
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08-13-2011 02:47 AM
Cryogenic temperature effects and resolution upon slow cooling of protein preparations in solid state NMR.
Cryogenic temperature effects and resolution upon slow cooling of protein preparations in solid state NMR.
Cryogenic temperature effects and resolution upon slow cooling of protein preparations in solid state NMR.
J Biomol NMR. 2011 Aug 9;
Authors: Linden AH, Franks WT, Akbey U, Lange S, van Rossum BJ, Oschkinat H
X-ray crystallography using synchrotron radiation and the technique of dynamic nuclear polarization (DNP) in nuclear magnetic resonance (NMR) require samples to be kept at temperatures below 100*K. Protein dynamics are poorly understood...
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08-10-2011 12:30 PM
Protein structure calculation with data imputation: the use of substitute restraints
Protein structure calculation with data imputation: the use of substitute restraints
Abstract The amount of experimental restraints e.g., NOEs is often too small for calculating high quality three-dimensional structures by restrained molecular dynamics. Considering this as a typical missing value problem we propose here a model based data imputation technique that should lead to an improved estimation of the correct structure. The novel automated method implemented in AUREMOL makes a more efficient use of the experimental information to obtain NMR structures with higher accuracy. It...
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01-09-2011 12:46 PM
[NMR paper] Protein structure calculation from NMR data.
Protein structure calculation from NMR data.
Related Articles Protein structure calculation from NMR data.
Methods Mol Biol. 2002;173:267-83
Authors: Mal TK, Bagby S, Ikura M
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11-24-2010 08:49 PM
protein structure calculation
Hi! every one!
I wanted to get in contact with people solving the structure of protein by using NMR. I am learning the process and i have many basics problem related with the work.
cheers!
Effects of NMR spectral resolution on protein structure calculation.
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