Investigation of Stable and Transient Protein-protein Interactions: Past, Present, and Future

Overview

Journal Proteomics

Date 2012 Nov 30

PMID 23193082

Citations 42

Authors

Armand G Ngounou Wetie

Izabela Sokolowska

Alisa G Woods

Urmi Roy

Joseph A Loo

Costel C Darie

Affiliations

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Abstract

This article presents an overview of the literature and a review of recent advances in the analysis of stable and transient protein-protein interactions (PPIs) with a focus on their function within cells, organs, and organisms. The significance of PTMs within the PPIs is also discussed. We focus on methods to study PPIs and methods of detecting PPIs, with particular emphasis on electrophoresis-based and MS-based investigation of PPIs, including specific examples. The validation of PPIs is emphasized and the limitations of the current methods for studying stable and transient PPIs are discussed. Perspectives regarding PPIs, with focus on bioinformatics and transient PPIs are also provided.

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References

Fields S, Song O . A novel genetic system to detect protein-protein interactions. Nature. 1989; 340(6230):245-6. DOI: 10.1038/340245a0. View

Wolbink G, Brouwer M, Buysmann S, ten Berge I, Hack C . CRP-mediated activation of complement in vivo: assessment by measuring circulating complement-C-reactive protein complexes. J Immunol. 1996; 157(1):473-9. View

Synowsky S, van den Heuvel R, Mohammed S, Pijnappel P, Heck A . Probing genuine strong interactions and post-translational modifications in the heterogeneous yeast exosome protein complex. Mol Cell Proteomics. 2006; 5(9):1581-92. DOI: 10.1074/mcp.M600043-MCP200. View

Jares-Erijman E, Jovin T . FRET imaging. Nat Biotechnol. 2003; 21(11):1387-95. DOI: 10.1038/nbt896. View

Lomeli S, Peng I, Yin S, Ogorzalek Loo R, Loo J . New reagents for increasing ESI multiple charging of proteins and protein complexes. J Am Soc Mass Spectrom. 2009; 21(1):127-31. PMC: 2821426. DOI: 10.1016/j.jasms.2009.09.014. View

Dziembowski A, Seraphin B . Recent developments in the analysis of protein complexes. FEBS Lett. 2004; 556(1-3):1-6. DOI: 10.1016/s0014-5793(03)01357-7. View

MacBeath G, Schreiber S . Printing proteins as microarrays for high-throughput function determination. Science. 2000; 289(5485):1760-3. DOI: 10.1126/science.289.5485.1760. View

Nickell S, Kofler C, Leis A, Baumeister W . A visual approach to proteomics. Nat Rev Mol Cell Biol. 2006; 7(3):225-30. DOI: 10.1038/nrm1861. View

SVEDBERG T . Molecular sedimentation in the ultracentrifuge. Endeavour. 2010; 6(22):89-95. View

10.

Darie C, Deinhardt K, Zhang G, Cardasis H, Chao M, Neubert T . Identifying transient protein-protein interactions in EphB2 signaling by blue native PAGE and mass spectrometry. Proteomics. 2011; 11(23):4514-28. PMC: 3563432. DOI: 10.1002/pmic.201000819. View

11.

Schagger H . Native electrophoresis for isolation of mitochondrial oxidative phosphorylation protein complexes. Methods Enzymol. 1995; 260:190-202. DOI: 10.1016/0076-6879(95)60137-6. View

12.

Fried M, Crothers D . Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res. 1981; 9(23):6505-25. PMC: 327619. DOI: 10.1093/nar/9.23.6505. View

13.

Zhang Z, Smith D . Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation. Protein Sci. 1993; 2(4):522-31. PMC: 2142359. DOI: 10.1002/pro.5560020404. View

14.

Breitkreutz B, Stark C, Tyers M . The GRID: the General Repository for Interaction Datasets. Genome Biol. 2003; 4(3):R23. PMC: 153463. DOI: 10.1186/gb-2003-4-3-r23. View

15.

Yuan J, Galbraith D, Dai S, Griffin P, Stewart Jr C . Plant systems biology comes of age. Trends Plant Sci. 2008; 13(4):165-71. DOI: 10.1016/j.tplants.2008.02.003. View

16.

Nogales E, Wolf S, Downing K . Structure of the alpha beta tubulin dimer by electron crystallography. Nature. 1998; 391(6663):199-203. DOI: 10.1038/34465. View

17.

Hubbard S, Till J . Protein tyrosine kinase structure and function. Annu Rev Biochem. 2000; 69:373-98. DOI: 10.1146/annurev.biochem.69.1.373. View

18.

Gamberi T, Puglia M, Guidi F, Magherini F, Bini L, Marzocchini R . A proteomic approach to identify plasma proteins in patients with abdominal aortic aneurysm. Mol Biosyst. 2011; 7(10):2855-62. DOI: 10.1039/c1mb05107e. View

19.

Hedin L, Illergard K, Elofsson A . An introduction to membrane proteins. J Proteome Res. 2011; 10(8):3324-31. DOI: 10.1021/pr200145a. View

20.

Shell S, Hess S, Kvaratskhelia M, Zou Y . Mass spectrometric identification of lysines involved in the interaction of human replication protein a with single-stranded DNA. Biochemistry. 2005; 44(3):971-8. PMC: 1450108. DOI: 10.1021/bi048208a. View