title: Global analysis of protein folding thermodynamics for disease state characterization.
abstract: 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.
authors.affiliation: #Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27708, United States.
authors.forename: Jagat
authors.initials: J
authors.lastname: Adhikari
authors.affiliation: †Department of Mass Spectrometry and Proteomics, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States.
authors.forename: Graham M
authors.initials: GM
authors.lastname: West
authors.affiliation: #Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27708, United States.|∥Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.
authors.forename: Michael C
authors.initials: MC
authors.lastname: Fitzgerald
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D014408:Biomarkers, Tumor / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification*; D001943:Breast Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000473:pathology; D045744:Cell Line, Tumor; D005260:Female; D015870:Gene Expression; D006801:Humans; D007553:Isotope Labeling; D058977:Molecular Sequence Annotation; D009363:Neoplasm Proteins / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification*; D010084:Oxidation-Reduction; D017510:Protein Folding; D055550:Protein Stability; D020543:Proteome / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification*; D040901:Proteomics / Q000379:methods; D013816:Thermodynamics
chemical_list: D000596:Amino Acids; D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins; D020543:Proteome
keywords: MCF-10A; MCF-7; MDA-MB-231; SILAC; breast cancer; chemical denaturation; mass spectrometry; protein folding; proteomics
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