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Effects of NMR spectral resolution on protein structure calculation.

Tikole S, Jaravine V, Orekhov VY, Güntert P - PLoS ONE (2013)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute of Advanced Studies, Goethe University Frankfurt am Main, Frankfurt am Main, Germany.

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.

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Median RMSDs to reference structures and chemical shift spectral overlap (CSSO) indices for protein structures of different size groups.(A) Median of the heavy atom RMSD to the reference structures are shown for 280 protein structures in the molecular size range from 10 to 15 kDa (solid), 76 protein structures in the molecular size range 15–20 kDa (dashed) and 25 protein structures in the molecular size range 20–35 kDa (dotted). RMSD values were calculated for the residue ranges determined by the CYRANGE algorithm. (B) Average CSSO index for 13C-resolved NOESY (black) and 15N-resolved NOESY (red) peak lists for the proteins structures of the same size-groups as in A.
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pone-0068567-g002: Median RMSDs to reference structures and chemical shift spectral overlap (CSSO) indices for protein structures of different size groups.(A) Median of the heavy atom RMSD to the reference structures are shown for 280 protein structures in the molecular size range from 10 to 15 kDa (solid), 76 protein structures in the molecular size range 15–20 kDa (dashed) and 25 protein structures in the molecular size range 20–35 kDa (dotted). RMSD values were calculated for the residue ranges determined by the CYRANGE algorithm. (B) Average CSSO index for 13C-resolved NOESY (black) and 15N-resolved NOESY (red) peak lists for the proteins structures of the same size-groups as in A.

Mentions: We obtained for each of the 381 protein structures the RMSD values as a function of digital resolution, to which we refer here as ‘profiles’. All profiles are shown in Figure S4. These profiles were grouped by molecular size or by RMSD values of calculated structures. The result is shown in Figure 2. The histogram of all RMSD values obtained from the profiles at the highest resolution is shown in Figure 3. The RMSD values and the fitted gamma distribution show a statistically significant fit. For the same data, we computed the CSSO indices, which are shown in Figure 4.


Effects of NMR spectral resolution on protein structure calculation.

Tikole S, Jaravine V, Orekhov VY, Güntert P - PLoS ONE (2013)

Median RMSDs to reference structures and chemical shift spectral overlap (CSSO) indices for protein structures of different size groups.(A) Median of the heavy atom RMSD to the reference structures are shown for 280 protein structures in the molecular size range from 10 to 15 kDa (solid), 76 protein structures in the molecular size range 15–20 kDa (dashed) and 25 protein structures in the molecular size range 20–35 kDa (dotted). RMSD values were calculated for the residue ranges determined by the CYRANGE algorithm. (B) Average CSSO index for 13C-resolved NOESY (black) and 15N-resolved NOESY (red) peak lists for the proteins structures of the same size-groups as in A.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3713035&req=5

pone-0068567-g002: Median RMSDs to reference structures and chemical shift spectral overlap (CSSO) indices for protein structures of different size groups.(A) Median of the heavy atom RMSD to the reference structures are shown for 280 protein structures in the molecular size range from 10 to 15 kDa (solid), 76 protein structures in the molecular size range 15–20 kDa (dashed) and 25 protein structures in the molecular size range 20–35 kDa (dotted). RMSD values were calculated for the residue ranges determined by the CYRANGE algorithm. (B) Average CSSO index for 13C-resolved NOESY (black) and 15N-resolved NOESY (red) peak lists for the proteins structures of the same size-groups as in A.
Mentions: We obtained for each of the 381 protein structures the RMSD values as a function of digital resolution, to which we refer here as ‘profiles’. All profiles are shown in Figure S4. These profiles were grouped by molecular size or by RMSD values of calculated structures. The result is shown in Figure 2. The histogram of all RMSD values obtained from the profiles at the highest resolution is shown in Figure 3. The RMSD values and the fitted gamma distribution show a statistically significant fit. For the same data, we computed the CSSO indices, which are shown in Figure 4.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute of Advanced Studies, Goethe University Frankfurt am Main, Frankfurt am Main, Germany.

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.

Show MeSH