Global analysis of protein structural changes in complex proteomes

• Published in: Nature biotechnology Vol. 32; no. 10; pp. 1036 - 1044
• Main Authors: Feng, Yuehan, De Franceschi, Giorgia, Kahraman, Abdullah, Soste, Martin, Melnik, Andre, Boersema, Paul J, de Laureto, Patrizia Polverino, Nikolaev, Yaroslav, Oliveira, Ana Paula, Picotti, Paola
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01-10-2014; Nature Publishing Group
• Subjects: 101/28; 14/63; 631/61/475; 82/58; Agriculture; Amino Acid Sequence; Amyloid; Bioinformatics; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; Cells; Conformation; Data analysis; Fructosediphosphates; Life Sciences; Mass Spectrometry; Molecular Sequence Data; Nutrients; Peptide Fragments; Prions; Protein Conformation; Protein research; Proteins; Proteins - analysis; Proteins - chemistry; Proteolysis; Proteome - analysis; Proteome - chemistry; Proteomics; Proteomics - methods; Structure; Trypsin; Yeasts; United States
• ISSN: 1087-0156; 1546-1696
• DOI: 10.1038/nbt.2999

Coupling limited proteolysis and a proteomics workflow enables measurement of both subtle and wholesale protein conformational changes in a eukaryotic proteome.
Changes in protein conformation can affect protein function, but methods to probe these structural changes on a global scale in cells have been lacking. To enable large-scale analyses of protein conformational changes directly in their biological matrices, we present a method that couples limited proteolysis with a targeted proteomics workflow. Using our method, we assessed the structural features of more than 1,000 yeast proteins simultaneously and detected altered conformations for ∼300 proteins upon a change of nutrients. We find that some branches of carbon metabolism are transcriptionally regulated whereas others are regulated by enzyme conformational changes. We detect structural changes in aggregation-prone proteins and show the functional relevance of one of these proteins to the metabolic switch. This approach enables probing of both subtle and pronounced structural changes of proteins on a large scale.