Global analysis of methionine oxidation provides a census of folding stabilities for the human proteome

ABSTRACT: Most natural proteins fold into a native conformation stabilized by non-covalent interactions. The energy difference between native and denatured states (Gfolding) is highly variable between proteins and can range from less than -10 kcal per mole for highly stable proteins to positive values for intrinsically disordered proteins. Folding stability is a dynamic property of proteins and can be modulated by molecular chaperones and binding interactions. The stability of a protein influences its tendency to aggregate, degrade or become covalently modified in cells. Despite its significance to understanding protein folding and function, quantitative analyses of thermodynamic stability have been mostly limited to small soluble proteins in purified systems. Here, we have used a highly multiplexed bottom-up proteomics approach, based on analyses of rates of methionine oxidation, to quantify the thermodynamic stabilities of the human proteome in crude extracts obtained from dermal fibroblasts. Our data provide structural and stability information for more than 10,000 unique regions and domains within more than 3,200 proteins. The data identifies lysosomal and extracellular proteins as the most stable ontological subsets of the proteome. We show that the stability of proteins can impact their tendency to become oxidized and are globally altered by the osmolyte trimethylamine-N-oxide (TMAO). We also show that most proteins designated as IDPs retain their unfolded structure in the complex milieu of the cell and most cannot be refolded by TMAO. Together, the data provide a census of the stability of the human proteome and validate a methodology for global analysis of protein thermodynamic stabilities.

INSTRUMENT(S): Orbitrap Fusion Lumos, Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Fibroblast

SUBMITTER: Ethan Walker  

LAB HEAD: Sina Ghaemmaghami

PROVIDER: PXD011456 | Pride | 2018-11-21

REPOSITORIES: Pride