Effects of NMR spectral resolution on protein structure calculation.
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...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2013-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3713035?pdf=render |
| _version_ | 1819070884059545600 |
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| author | Suhas Tikole Victor Jaravine Vladislav Yu Orekhov Peter Güntert |
| author_facet | Suhas Tikole Victor Jaravine Vladislav Yu Orekhov Peter Güntert |
| author_sort | Suhas Tikole |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-21T17:13:01Z |
| format | Article |
| id | doaj.art-0c1ee625418e4504b8ed02c17e97ec2e |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-21T17:13:01Z |
| publishDate | 2013-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-0c1ee625418e4504b8ed02c17e97ec2e2022-12-21T18:56:21ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-0187e6856710.1371/journal.pone.0068567Effects of NMR spectral resolution on protein structure calculation.Suhas TikoleVictor JaravineVladislav Yu OrekhovPeter GüntertAdequate 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.http://europepmc.org/articles/PMC3713035?pdf=render |
| spellingShingle | Suhas Tikole Victor Jaravine Vladislav Yu Orekhov Peter Güntert Effects of NMR spectral resolution on protein structure calculation. PLoS ONE |
| title | Effects of NMR spectral resolution on protein structure calculation. |
| title_full | Effects of NMR spectral resolution on protein structure calculation. |
| title_fullStr | Effects of NMR spectral resolution on protein structure calculation. |
| title_full_unstemmed | Effects of NMR spectral resolution on protein structure calculation. |
| title_short | Effects of NMR spectral resolution on protein structure calculation. |
| title_sort | effects of nmr spectral resolution on protein structure calculation |
| url | http://europepmc.org/articles/PMC3713035?pdf=render |
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