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Amino-acid selective isotope labeling enables simultaneous overlapping signal decomposition and information extraction from NMR spectra

Signal overlapping is a major bottleneck for protein NMR analysis. We propose a new method, stable-isotope-assisted parameter extraction (SiPex), to resolve overlapping signals by a combination of amino-acid selective isotope labeling (AASIL) and tensor decomposition. The basic idea of Sipex is that...

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Autores principales: Kasai, Takuma, Ono, Shunsuke, Koshiba, Seizo, Yamamoto, Masayuki, Tanaka, Toshiyuki, Ikeda, Shiro, Kigawa, Takanori
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Netherlands 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7080692/
https://www.ncbi.nlm.nih.gov/pubmed/32002710
http://dx.doi.org/10.1007/s10858-019-00295-9
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author Kasai, Takuma
Ono, Shunsuke
Koshiba, Seizo
Yamamoto, Masayuki
Tanaka, Toshiyuki
Ikeda, Shiro
Kigawa, Takanori
author_facet Kasai, Takuma
Ono, Shunsuke
Koshiba, Seizo
Yamamoto, Masayuki
Tanaka, Toshiyuki
Ikeda, Shiro
Kigawa, Takanori
author_sort Kasai, Takuma
collection PubMed
description Signal overlapping is a major bottleneck for protein NMR analysis. We propose a new method, stable-isotope-assisted parameter extraction (SiPex), to resolve overlapping signals by a combination of amino-acid selective isotope labeling (AASIL) and tensor decomposition. The basic idea of Sipex is that overlapping signals can be decomposed with the help of intensity patterns derived from quantitative fractional AASIL, which also provides amino-acid information. In SiPex, spectra for protein characterization, such as (15)N relaxation measurements, are assembled with those for amino-acid information to form a four-order tensor, where the intensity patterns from AASIL contribute to high decomposition performance even if the signals share similar chemical shift values or characterization profiles, such as relaxation curves. The loading vectors of each decomposed component, corresponding to an amide group, represent both the amino-acid and relaxation information. This information link provides an alternative protein analysis method that does not require “assignments” in a general sense; i.e., chemical shift determinations, since the amino-acid information for some of the residues allows unambiguous assignment according to the dual selective labeling. SiPex can also decompose signals in time-domain raw data without Fourier transform, even in non-uniformly sampled data without spectral reconstruction. These features of SiPex should expand biological NMR applications by overcoming their overlapping and assignment problems. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10858-019-00295-9) contains supplementary material, which is available to authorized users.
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spelling pubmed-70806922020-03-23 Amino-acid selective isotope labeling enables simultaneous overlapping signal decomposition and information extraction from NMR spectra Kasai, Takuma Ono, Shunsuke Koshiba, Seizo Yamamoto, Masayuki Tanaka, Toshiyuki Ikeda, Shiro Kigawa, Takanori J Biomol NMR Article Signal overlapping is a major bottleneck for protein NMR analysis. We propose a new method, stable-isotope-assisted parameter extraction (SiPex), to resolve overlapping signals by a combination of amino-acid selective isotope labeling (AASIL) and tensor decomposition. The basic idea of Sipex is that overlapping signals can be decomposed with the help of intensity patterns derived from quantitative fractional AASIL, which also provides amino-acid information. In SiPex, spectra for protein characterization, such as (15)N relaxation measurements, are assembled with those for amino-acid information to form a four-order tensor, where the intensity patterns from AASIL contribute to high decomposition performance even if the signals share similar chemical shift values or characterization profiles, such as relaxation curves. The loading vectors of each decomposed component, corresponding to an amide group, represent both the amino-acid and relaxation information. This information link provides an alternative protein analysis method that does not require “assignments” in a general sense; i.e., chemical shift determinations, since the amino-acid information for some of the residues allows unambiguous assignment according to the dual selective labeling. SiPex can also decompose signals in time-domain raw data without Fourier transform, even in non-uniformly sampled data without spectral reconstruction. These features of SiPex should expand biological NMR applications by overcoming their overlapping and assignment problems. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10858-019-00295-9) contains supplementary material, which is available to authorized users. Springer Netherlands 2020-01-30 2020 /pmc/articles/PMC7080692/ /pubmed/32002710 http://dx.doi.org/10.1007/s10858-019-00295-9 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Kasai, Takuma
Ono, Shunsuke
Koshiba, Seizo
Yamamoto, Masayuki
Tanaka, Toshiyuki
Ikeda, Shiro
Kigawa, Takanori
Amino-acid selective isotope labeling enables simultaneous overlapping signal decomposition and information extraction from NMR spectra
title Amino-acid selective isotope labeling enables simultaneous overlapping signal decomposition and information extraction from NMR spectra
title_full Amino-acid selective isotope labeling enables simultaneous overlapping signal decomposition and information extraction from NMR spectra
title_fullStr Amino-acid selective isotope labeling enables simultaneous overlapping signal decomposition and information extraction from NMR spectra
title_full_unstemmed Amino-acid selective isotope labeling enables simultaneous overlapping signal decomposition and information extraction from NMR spectra
title_short Amino-acid selective isotope labeling enables simultaneous overlapping signal decomposition and information extraction from NMR spectra
title_sort amino-acid selective isotope labeling enables simultaneous overlapping signal decomposition and information extraction from nmr spectra
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7080692/
https://www.ncbi.nlm.nih.gov/pubmed/32002710
http://dx.doi.org/10.1007/s10858-019-00295-9
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