Global analysis of protein structural changes in complex proteomes

Nat Biotechnol. 2014 Oct;32(10):1036-44. doi: 10.1038/nbt.2999. Epub 2014 Sep 14.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Amyloid
  • Fructosediphosphates
  • Mass Spectrometry
  • Molecular Sequence Data
  • Peptide Fragments
  • Prions
  • Protein Conformation
  • Proteins / analysis*
  • Proteins / chemistry*
  • Proteolysis
  • Proteome / analysis*
  • Proteome / chemistry*
  • Proteomics / methods*
  • Trypsin

Substances

  • Amyloid
  • Fructosediphosphates
  • Peptide Fragments
  • Prions
  • Proteins
  • Proteome
  • Trypsin
  • fructose-1,6-diphosphate