Global Analysis of Protein Folding Thermodynamics for Disease State Characterization

Current
methods for the large-scale characterization of disease
states generally rely on the analysis of gene and/or protein expression
levels. These existing methods fail to detect proteins with disease-related
functions and unaltered expression levels. Here we describe the large-scale
use of thermodynamic measurements of protein folding and stability
for the characterization of disease states. Using the Stable Isotope
Labeling with Amino Acids in Cell Culture and Stability of Proteins
from Rates of Oxidation (SILAC-SPROX) technique, we assayed ∼800
proteins for protein folding and stability changes in three different
cell culture models of breast cancer including the MCF-10A, MCF-7,
and MDA-MB-231 cell lines. The thermodynamic stability profiles generated
here created distinct molecular markers to differentiate the three
cell lines, and a significant fraction (∼45%) of the differentially
stabilized proteins did not have altered expression levels. Thus,
the differential thermodynamic profiling strategy reported here created
novel molecular signatures of breast cancer and provided additional
insight into the molecular basis of the disease. Our results establish
the utility of protein folding and stability measurements for the
study of disease processes, and they suggest that such measurements
may be useful for biomarker discovery in disease.