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Protein-Protein Interactions

Protein-Protein Interactions. Protein Quaternary Structure. No covalent bonding. Homo- oligimer vs Hetero- oligimer. Protein Complex. Subunits = each protein Protein complex performs a biological function. To the left is the proteasome. Degrades unneeded and damaged proteins

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Protein-Protein Interactions

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  1. Protein-Protein Interactions

  2. Protein Quaternary Structure No covalent bonding

  3. Homo-oligimervs Hetero-oligimer

  4. Protein Complex Subunits = each protein Protein complex performs a biological function. To the left is the proteasome. Degrades unneeded and damaged proteins Complexes are amazing cellular “machines.”

  5. Graph or Network Abstraction of Protein-Protein Interactions Mass spectrometry A important technique for discovering edges in this graph.

  6. Bait, prey, and contaminant proteins

  7. Affinity Purification http://www.lamondlab.com/MSResource/separations/affinityIsolation.php

  8. Finding Specific Interaction Partners What does the MS1 data look like? http://www.lamondlab.com/MSResource/separations/affinityPurification.php

  9. SILAC Ratio Distribution http://www.lamondlab.com/MSResource/separations/DataMining/visualisations.php

  10. For the triple labeling experiment

  11. Interactions that increase and decrease in the experiment

  12. “big data” approach to uncovering protein complexes

  13. This looks weird. Strange interactions between “ground truth complexes”

  14. Machine learning to the rescue?

  15. Looks better now

  16. Correlation to protein-protein interactions in another species and cross validation looks good Look back at the ML procedure… something is weird here no? Wasn’t fly used In the “training procedure”?

  17. 385 novel protein complexes discovered! Supported by Affinity purification experiments.

  18. All of the data with representative examples

  19. Complexes Associated with Disease

  20. Knockdown of genes confirms functional role

  21. New complexes tend to have conserved protein interactions in other species

  22. Complexes occur in other species and members seen to be expressed in the same tissues

  23. Stoichiometry is used in a difference sense here:

  24. Comments? • Is this paper a triumph of machine learning and big data?

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