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Thermodynamic analysis of protein-ligand interactions in complex biological mixtures using a shotgun proteomics approach.

Publication ,  Journal Article
Dearmond, PD; Xu, Y; Strickland, EC; Daniels, KG; Fitzgerald, MC
Published in: Journal of proteome research
November 2011

Shotgun proteomics protocols are widely used for the identification and/or quantitation of proteins in complex biological samples. Described here is a shotgun proteomics protocol that can be used to identify the protein targets of biologically relevant ligands in complex protein mixtures. The protocol combines a quantitative proteomics platform with a covalent modification strategy, termed Stability of Proteins from Rates of Oxidation (SPROX), which utilizes the denaturant dependence of hydrogen peroxide-mediated oxidation of methionine side chains in proteins to assess the thermodynamic properties of proteins and protein-ligand complexes. The quantitative proteomics platform involves the use of isobaric mass tags and a methionine-containing peptide enhancement strategy. The protocol is evaluated in a ligand binding experiment designed to identify the proteins in a yeast cell lysate that bind the well-known enzyme cofactor, β-nicotinamide adenine dinucleotide (NAD+). The protocol is also used to investigate the protein targets of resveratrol, a biologically active ligand with less well-understood protein targets. A known protein target of resveratrol, cytosolic aldehyde dehydrogenase, was identified in addition to six other potential new proteins targets including four that are associated with the protein translation machinery, which has previously been implicated as a target of resveratrol.

Duke Scholars

Published In

Journal of proteome research

DOI

EISSN

1535-3907

ISSN

1535-3893

Publication Date

November 2011

Volume

10

Issue

11

Start / End Page

4948 / 4958

Related Subject Headings

  • Thermodynamics
  • Tandem Mass Spectrometry
  • Stilbenes
  • Saccharomyces cerevisiae Proteins
  • Resveratrol
  • Proteome
  • Protein Binding
  • Peptide Fragments
  • Oxidation-Reduction
  • Oxidants
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Dearmond, P. D., Xu, Y., Strickland, E. C., Daniels, K. G., & Fitzgerald, M. C. (2011). Thermodynamic analysis of protein-ligand interactions in complex biological mixtures using a shotgun proteomics approach. Journal of Proteome Research, 10(11), 4948–4958. https://doi.org/10.1021/pr200403c
Dearmond, Patrick D., Ying Xu, Erin C. Strickland, Kyle G. Daniels, and Michael C. Fitzgerald. “Thermodynamic analysis of protein-ligand interactions in complex biological mixtures using a shotgun proteomics approach.Journal of Proteome Research 10, no. 11 (November 2011): 4948–58. https://doi.org/10.1021/pr200403c.
Dearmond PD, Xu Y, Strickland EC, Daniels KG, Fitzgerald MC. Thermodynamic analysis of protein-ligand interactions in complex biological mixtures using a shotgun proteomics approach. Journal of proteome research. 2011 Nov;10(11):4948–58.
Dearmond, Patrick D., et al. “Thermodynamic analysis of protein-ligand interactions in complex biological mixtures using a shotgun proteomics approach.Journal of Proteome Research, vol. 10, no. 11, Nov. 2011, pp. 4948–58. Epmc, doi:10.1021/pr200403c.
Dearmond PD, Xu Y, Strickland EC, Daniels KG, Fitzgerald MC. Thermodynamic analysis of protein-ligand interactions in complex biological mixtures using a shotgun proteomics approach. Journal of proteome research. 2011 Nov;10(11):4948–4958.
Journal cover image

Published In

Journal of proteome research

DOI

EISSN

1535-3907

ISSN

1535-3893

Publication Date

November 2011

Volume

10

Issue

11

Start / End Page

4948 / 4958

Related Subject Headings

  • Thermodynamics
  • Tandem Mass Spectrometry
  • Stilbenes
  • Saccharomyces cerevisiae Proteins
  • Resveratrol
  • Proteome
  • Protein Binding
  • Peptide Fragments
  • Oxidation-Reduction
  • Oxidants