Issue 39, 2021, Issue in Progress

Circular dichroism for secondary structure determination of proteins with unfolded domains using a self-organising map algorithm SOMSpec

Abstract

Many proteins and peptides are increasingly being recognised to contain unfolded domains or populations that are key to their function, whether it is in ligand binding or material assembly. We report an approach to determine the secondary structure for proteins with suspected significant unfolded domains or populations using our neural network approach SOMSpec. We proceed by derandomizing spectra by removing fractions of random coil (RC) spectra prior to secondary structure fitting and then regenerating α-helical and β-sheet contents for the experimental proteins. Application to bovine serum albumin spectra as a function of temperature proved to be straightforward, whereas lysozyme and insulin have hidden challenges. The importance of being able to interrogate the SOMSpec output to understand the best matching units used in the predictions is illustrated with lysozyme and insulin whose partially melted proteins proved to have significant βII content and their CD spectrum looks the same as that for a random coil.

Graphical abstract: Circular dichroism for secondary structure determination of proteins with unfolded domains using a self-organising map algorithm SOMSpec

Supplementary files

Article information

Article type
Paper
Submitted
14 Apr 2021
Accepted
27 Jun 2021
First published
07 Jul 2021
This article is Open Access
Creative Commons BY license

RSC Adv., 2021,11, 23985-23991

Circular dichroism for secondary structure determination of proteins with unfolded domains using a self-organising map algorithm SOMSpec

A. Olamoyesan, D. Ang and A. Rodger, RSC Adv., 2021, 11, 23985 DOI: 10.1039/D1RA02898G

This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. You can use material from this article in other publications without requesting further permissions from the RSC, provided that the correct acknowledgement is given.

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