
The Library
SOMSpec as a general purpose validated self-organising map tool for rapid protein secondary structure prediction from infrared absorbance data
Tools
Pinto Corujo, Marco, Olamoyesan, Adewale, Tukova, Anastasiia, Ang, Dale, Goormaghtigh, Erik, Peterson, Jason, Sharov, Victor, Chmel, Nikola Paul and Rodger, Alison (2022) SOMSpec as a general purpose validated self-organising map tool for rapid protein secondary structure prediction from infrared absorbance data. Frontiers in Chemistry, 9 . 784625. doi:10.3389/fchem.2021.784625 ISSN 2296-2646.
|
PDF
WRAP-SOMSpec-general-purpose-validated-self-organising-map-tool-rapid-protein-secondary-structure-prediction-infrared-absorbance data-Rodger-2022.pdf - Published Version - Requires a PDF viewer. Available under License Creative Commons Attribution 4.0. Download (1849Kb) | Preview |
Official URL: https://doi.org/10.3389/fchem.2021.784625
Abstract
A protein’s structure is the key to its function. As protein structure can vary with environment, it is important to be able to determine it over a wide range of concentrations, temperatures, formulation vehicles, and states. Robust reproducible validated methods are required for applications including batch-batch comparisons of biopharmaceutical products. Circular dichroism is widely used for this purpose, but an alternative is required for concentrations above 10 mg/mL or for solutions with chiral buffer components that absorb far UV light. Infrared (IR) protein absorbance spectra of the Amide I region (1,600–1700 cm−1) contain information about secondary structure and require higher concentrations than circular dichroism often with complementary spectral windows. In this paper, we consider a number of approaches to extract structural information from a protein infrared spectrum and determine their reliability for regulatory and research purpose. In particular, we compare direct and second derivative band-fitting with a self-organising map (SOM) approach applied to a number of different reference sets. The self-organising map (SOM) approach proved significantly more accurate than the band-fitting approaches for solution spectra. As there is no validated benchmark method available for infrared structure fitting, SOMSpec was implemented in a leave-one-out validation (LOOV) approach for solid-state transmission and thin-film attenuated total reflectance (ATR) reference sets. We then tested SOMSpec and the thin-film ATR reference set against 68 solution spectra and found the average prediction error for helix (α + 310) and β-sheet was less than 6% for proteins with less than 40% helix. This is quantitatively better than other available approaches. The visual output format of SOMSpec aids identification of poor predictions. We also demonstrated how to convert aqueous ATR spectra to and from transmission spectra for structure fitting. Fourier self-deconvolution did not improve the average structure predictions.
Item Type: | Journal Article | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Subjects: | Q Science > QC Physics Q Science > QD Chemistry |
||||||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Chemistry | ||||||||||||
SWORD Depositor: | Library Publications Router | ||||||||||||
Library of Congress Subject Headings (LCSH): | Proteins -- Structure -- Research, Absorption spectra, Infrared spectra, Self-organizing maps | ||||||||||||
Journal or Publication Title: | Frontiers in Chemistry | ||||||||||||
Publisher: | Frontiers Research Foundation | ||||||||||||
ISSN: | 2296-2646 | ||||||||||||
Official Date: | 27 January 2022 | ||||||||||||
Dates: |
|
||||||||||||
Volume: | 9 | ||||||||||||
Article Number: | 784625 | ||||||||||||
DOI: | 10.3389/fchem.2021.784625 | ||||||||||||
Status: | Peer Reviewed | ||||||||||||
Publication Status: | Published | ||||||||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||||||||
Date of first compliant deposit: | 8 March 2022 | ||||||||||||
Date of first compliant Open Access: | 15 March 2022 | ||||||||||||
RIOXX Funder/Project Grant: |
|
Request changes or add full text files to a record
Repository staff actions (login required)
![]() |
View Item |
Downloads
Downloads per month over past year