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Automatic (13)C chemical shift reference correction for unassigned protein NMR spectra
Poor chemical shift referencing, especially for (13)C in protein Nuclear Magnetic Resonance (NMR) experiments, fundamentally limits and even prevents effective study of biomacromolecules via NMR, including protein structure determination and analysis of protein dynamics. To solve this problem, we co...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer Netherlands
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6209040/ https://www.ncbi.nlm.nih.gov/pubmed/30097912 http://dx.doi.org/10.1007/s10858-018-0202-5 |
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author | Chen, Xi Smelter, Andrey Moseley, Hunter N. B. |
author_facet | Chen, Xi Smelter, Andrey Moseley, Hunter N. B. |
author_sort | Chen, Xi |
collection | PubMed |
description | Poor chemical shift referencing, especially for (13)C in protein Nuclear Magnetic Resonance (NMR) experiments, fundamentally limits and even prevents effective study of biomacromolecules via NMR, including protein structure determination and analysis of protein dynamics. To solve this problem, we constructed a Bayesian probabilistic framework that circumvents the limitations of previous reference correction methods that required protein resonance assignment and/or three-dimensional protein structure. Our algorithm named Bayesian Model Optimized Reference Correction (BaMORC) can detect and correct (13)C chemical shift referencing errors before the protein resonance assignment step of analysis and without three-dimensional structure. By combining the BaMORC methodology with a new intra-peaklist grouping algorithm, we created a combined method called Unassigned BaMORC that utilizes only unassigned experimental peak lists and the amino acid sequence. Unassigned BaMORC kept all experimental three-dimensional HN(CO)CACB-type peak lists tested within ± 0.4 ppm of the correct (13)C reference value. On a much larger unassigned chemical shift test set, the base method kept (13)C chemical shift referencing errors to within ± 0.45 ppm at a 90% confidence interval. With chemical shift assignments, Assigned BaMORC can detect and correct (13)C chemical shift referencing errors to within ± 0.22 at a 90% confidence interval. Therefore, Unassigned BaMORC can correct (13)C chemical shift referencing errors when it will have the most impact, right before protein resonance assignment and other downstream analyses are started. After assignment, chemical shift reference correction can be further refined with Assigned BaMORC. These new methods will allow non-NMR experts to detect and correct (13)C referencing error at critical early data analysis steps, lowering the bar of NMR expertise required for effective protein NMR analysis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10858-018-0202-5) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6209040 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Springer Netherlands |
record_format | MEDLINE/PubMed |
spelling | pubmed-62090402018-11-13 Automatic (13)C chemical shift reference correction for unassigned protein NMR spectra Chen, Xi Smelter, Andrey Moseley, Hunter N. B. J Biomol NMR Article Poor chemical shift referencing, especially for (13)C in protein Nuclear Magnetic Resonance (NMR) experiments, fundamentally limits and even prevents effective study of biomacromolecules via NMR, including protein structure determination and analysis of protein dynamics. To solve this problem, we constructed a Bayesian probabilistic framework that circumvents the limitations of previous reference correction methods that required protein resonance assignment and/or three-dimensional protein structure. Our algorithm named Bayesian Model Optimized Reference Correction (BaMORC) can detect and correct (13)C chemical shift referencing errors before the protein resonance assignment step of analysis and without three-dimensional structure. By combining the BaMORC methodology with a new intra-peaklist grouping algorithm, we created a combined method called Unassigned BaMORC that utilizes only unassigned experimental peak lists and the amino acid sequence. Unassigned BaMORC kept all experimental three-dimensional HN(CO)CACB-type peak lists tested within ± 0.4 ppm of the correct (13)C reference value. On a much larger unassigned chemical shift test set, the base method kept (13)C chemical shift referencing errors to within ± 0.45 ppm at a 90% confidence interval. With chemical shift assignments, Assigned BaMORC can detect and correct (13)C chemical shift referencing errors to within ± 0.22 at a 90% confidence interval. Therefore, Unassigned BaMORC can correct (13)C chemical shift referencing errors when it will have the most impact, right before protein resonance assignment and other downstream analyses are started. After assignment, chemical shift reference correction can be further refined with Assigned BaMORC. These new methods will allow non-NMR experts to detect and correct (13)C referencing error at critical early data analysis steps, lowering the bar of NMR expertise required for effective protein NMR analysis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10858-018-0202-5) contains supplementary material, which is available to authorized users. Springer Netherlands 2018-08-10 2018 /pmc/articles/PMC6209040/ /pubmed/30097912 http://dx.doi.org/10.1007/s10858-018-0202-5 Text en © The Author(s) 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. |
spellingShingle | Article Chen, Xi Smelter, Andrey Moseley, Hunter N. B. Automatic (13)C chemical shift reference correction for unassigned protein NMR spectra |
title | Automatic (13)C chemical shift reference correction for unassigned protein NMR spectra |
title_full | Automatic (13)C chemical shift reference correction for unassigned protein NMR spectra |
title_fullStr | Automatic (13)C chemical shift reference correction for unassigned protein NMR spectra |
title_full_unstemmed | Automatic (13)C chemical shift reference correction for unassigned protein NMR spectra |
title_short | Automatic (13)C chemical shift reference correction for unassigned protein NMR spectra |
title_sort | automatic (13)c chemical shift reference correction for unassigned protein nmr spectra |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6209040/ https://www.ncbi.nlm.nih.gov/pubmed/30097912 http://dx.doi.org/10.1007/s10858-018-0202-5 |
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