Predicted 'wiring landscape' of Ras-effector interactions in 29 human tissues

NPJ Syst Biol Appl. 2021 Feb 12;7(1):10. doi: 10.1038/s41540-021-00170-0.

Abstract

Ras is a plasma membrane (PM)-associated signaling hub protein that interacts with its partners (effectors) in a mutually exclusive fashion. We have shown earlier that competition for binding and hence the occurrence of specific binding events at a hub protein can modulate the activation of downstream pathways. Here, using a mechanistic modeling approach that incorporates high-quality proteomic data of Ras and 56 effectors in 29 (healthy) human tissues, we quantified the amount of individual Ras-effector complexes, and characterized the (stationary) Ras "wiring landscape" specific to each tissue. We identified nine effectors that are in significant amount in complex with Ras in at least one of the 29 tissues. We simulated both mutant- and stimulus-induced network re-configurations, and assessed their divergence from the reference scenario, specifically discussing a case study for two stimuli in three epithelial tissues. These analyses pointed to 32 effectors that are in significant amount in complex with Ras only if they are additionally recruited to the PM, e.g. via membrane-binding domains or domains binding to activated receptors at the PM. Altogether, our data emphasize the importance of tissue context for binding events at the Ras signaling hub.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Guanosine Triphosphate / metabolism
  • Humans
  • Membrane Proteins / metabolism
  • Models, Theoretical
  • Phosphatidylinositol 3-Kinases / metabolism
  • Protein Binding / physiology
  • Proteomics / methods
  • Proto-Oncogene Proteins c-raf / metabolism*
  • Signal Transduction / physiology
  • ras Proteins / genetics
  • ras Proteins / metabolism*
  • ras Proteins / physiology

Substances

  • Membrane Proteins
  • Guanosine Triphosphate
  • Proto-Oncogene Proteins c-raf
  • ras Proteins