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Hidden information on protein function in censuses of proteome foldedness.

Published version
Peer-reviewed

Type

Article

Change log

Authors

Ang, Ching-Seng 
Nillegoda, Nadinath B  ORCID logo  https://orcid.org/0000-0002-9980-3991
Reid, Gavin E 

Abstract

Methods that assay protein foldedness with proteomics have generated censuses of apparent protein folding stabilities in biological milieu. However, different censuses poorly correlate with each other. Here, we show that the reason for this is that methods targeting foldedness through monitoring amino acid sidechain reactivity also detect changes in conformation and ligand binding, which can be a substantial fraction of the data. We show that the reactivity of only one quarter of cysteine or methionine sidechains in proteins in a urea denaturation curve of mammalian cell lysate can be confidently explained by a two-state unfolding isotherm. Contrary to that expected from unfolding, up to one third of the cysteines decreased reactivity. These cysteines were enriched in proteins with functions relating to unfolded protein stress. One protein, chaperone HSPA8, displayed changes arising from ligand and cofactor binding. Unmasking this hidden information using the approaches outlined here should improve efforts to understand both folding and the remodeling of protein function directly in complex biological settings.

Description

Keywords

Animals, Censuses, Circular Dichroism, Cysteine, Kinetics, Ligands, Mammals, Protein Conformation, Protein Denaturation, Protein Folding, Proteome, Thermodynamics, Urea

Journal Title

Nat Commun

Conference Name

Journal ISSN

2041-1723
2041-1723

Volume Title

13

Publisher

Springer Science and Business Media LLC