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Proteome-Wide Structural Biology: An Emerging Field for the Structural Analysis of Proteins on the Proteomic Scale.

Publication ,  Journal Article
Kaur, U; Meng, H; Lui, F; Ma, R; Ogburn, RN; Johnson, JHR; Fitzgerald, MC; Jones, LM
Published in: Journal of proteome research
November 2018

Over the past decade, a suite of new mass-spectrometry-based proteomics methods has been developed that now enables the conformational properties of proteins and protein-ligand complexes to be studied in complex biological mixtures, from cell lysates to intact cells. Highlighted here are seven of the techniques in this new toolbox. These techniques include chemical cross-linking (XL-MS), hydroxyl radical footprinting (HRF), Drug Affinity Responsive Target Stability (DARTS), Limited Proteolysis (LiP), Pulse Proteolysis (PP), Stability of Proteins from Rates of Oxidation (SPROX), and Thermal Proteome Profiling (TPP). The above techniques all rely on conventional bottom-up proteomics strategies for peptide sequencing and protein identification. However, they have required the development of unconventional proteomic data analysis strategies. Discussed here are the current technical challenges associated with these different data analysis strategies as well as the relative analytical capabilities of the different techniques. The new biophysical capabilities that the above techniques bring to bear on proteomic research are also highlighted in the context of several different application areas in which these techniques have been used, including the study of protein ligand binding interactions (e.g., protein target discovery studies and protein interaction network analyses) and the characterization of biological states.

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Published In

Journal of proteome research

DOI

EISSN

1535-3907

ISSN

1535-3893

Publication Date

November 2018

Volume

17

Issue

11

Start / End Page

3614 / 3627

Related Subject Headings

  • Thermodynamics
  • Sequence Analysis, Protein
  • Proteomics
  • Proteome
  • Proteolysis
  • Proteins
  • Protein Stability
  • Protein Processing, Post-Translational
  • Protein Folding
  • Protein Binding
 

Citation

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Chicago
ICMJE
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Kaur, U., Meng, H., Lui, F., Ma, R., Ogburn, R. N., Johnson, J. H. R., … Jones, L. M. (2018). Proteome-Wide Structural Biology: An Emerging Field for the Structural Analysis of Proteins on the Proteomic Scale. Journal of Proteome Research, 17(11), 3614–3627. https://doi.org/10.1021/acs.jproteome.8b00341
Kaur, Upneet, He Meng, Fang Lui, Renze Ma, Ryenne N. Ogburn, Julia H. R. Johnson, Michael C. Fitzgerald, and Lisa M. Jones. “Proteome-Wide Structural Biology: An Emerging Field for the Structural Analysis of Proteins on the Proteomic Scale.Journal of Proteome Research 17, no. 11 (November 2018): 3614–27. https://doi.org/10.1021/acs.jproteome.8b00341.
Kaur U, Meng H, Lui F, Ma R, Ogburn RN, Johnson JHR, et al. Proteome-Wide Structural Biology: An Emerging Field for the Structural Analysis of Proteins on the Proteomic Scale. Journal of proteome research. 2018 Nov;17(11):3614–27.
Kaur, Upneet, et al. “Proteome-Wide Structural Biology: An Emerging Field for the Structural Analysis of Proteins on the Proteomic Scale.Journal of Proteome Research, vol. 17, no. 11, Nov. 2018, pp. 3614–27. Epmc, doi:10.1021/acs.jproteome.8b00341.
Kaur U, Meng H, Lui F, Ma R, Ogburn RN, Johnson JHR, Fitzgerald MC, Jones LM. Proteome-Wide Structural Biology: An Emerging Field for the Structural Analysis of Proteins on the Proteomic Scale. Journal of proteome research. 2018 Nov;17(11):3614–3627.
Journal cover image

Published In

Journal of proteome research

DOI

EISSN

1535-3907

ISSN

1535-3893

Publication Date

November 2018

Volume

17

Issue

11

Start / End Page

3614 / 3627

Related Subject Headings

  • Thermodynamics
  • Sequence Analysis, Protein
  • Proteomics
  • Proteome
  • Proteolysis
  • Proteins
  • Protein Stability
  • Protein Processing, Post-Translational
  • Protein Folding
  • Protein Binding