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The authors presented an overview of different experimental and bioinformatic methods to …


Biology Articles » Bioinformatics » Experimental and bioinformatic approaches for interrogating protein–protein interactions to determine protein function » Figures

Figures
- Experimental and bioinformatic approaches for interrogating protein–protein interactions to determine protein function

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Figure 1 Representation of methods employing mass spectrometric identification of proteins.

Figure 1

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Figure 2 Mapping protein interactions using the ß-lactamase assay. (A) A ribbon diagram of ß-lactamase. (B) A construct is made to create a fusion protein of a protein-bait and the {omega} fragment of ß-lactamase. A second construct is designed to create a fusion protein between a protein-prey and the {alpha} fragment of ß-lactamase. (C) If the bait protein binds to the prey protein, ß-lactamase activity is observed.

Figure 2

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Figure 3 Experimental approach to determine protein–protein interactions. (A) Sequence and structure of the TAP tag. The various domains constituting the tag are indicated. (B) The purification protein assemblies are separated by denaturing gel electrophoresis. The separated proteins are then digested by trypsin, and the resulting peptides are analyzed by mass spectrometry. (C) Using bioinformatics methods, interacting proteins can be characterized.

Figure 3

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Figure 4 Reconstruction of two metabolic pathways in E. coli. Pathways A and C are the known pathways for biosynthesis of shikimate and purine. Pathways B and D are constructed from the proteins in pathways A and C with connections predicted by the domain fusion method to interact with other proteins of the pathway. Taken from Marcotte et al.(1999) and reproduced with permission from Science.

Figure 4

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Figure 5: Screenshot from Cytoscape (website: http://www.cytoscape.org) showing a portion of an interaction network.

Figure 5

 

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Source: Journal of Molecular Endocrinology (2005) 34, 263-280.


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