Modeling and subtleties of K-Ras and Calmodulin interaction

PLoS Comput Biol. 2018 Oct 30;14(10):e1006552. doi: 10.1371/journal.pcbi.1006552. eCollection 2018 Oct.

Abstract

K-Ras, one of the most common small GTPases of the cell, still presents many riddles, despite the intense efforts to unveil its mysteries. Such is the case of its interaction with Calmodulin, a small acidic protein known for its role as a calcium ion sensor. Although the interaction between these two proteins and its biological implications have been widely studied, a model of their interaction has not been performed. In the present work we analyse this intriguing interaction by computational means. To do so, both conventional molecular dynamics and scaled molecular dynamics have been used. Our simulations suggest a model in which Calmodulin would interact with both the hypervariable region and the globular domain of K-Ras, using a lobe to interact with each of them. According to the presented model, the interface of helixes α4 and α5 of the globular domain of K-Ras would be relevant for the interaction with a lobe of Calmodulin. These results were also obtained when bringing the proteins together in a step wise manner with the umbrella sampling methodology. The computational results have been validated using SPR to determine the relevance of certain residues. Our results demonstrate that, when mutating residues of the α4-α5 interface described to be relevant for the interaction with Calmodulin, the interaction of the globular domain of K-Ras with Calmodulin diminishes. However, it is to be considered that our simulations indicate that the bulk of the interaction would fall on the hypervariable region of K-Ras, as many more interactions are identified in said region. All in all our simulations present a suitable model in which K-Ras could interact with Calmodulin at membrane level using both its globular domain and its hypervariable region to stablish an interaction that leads to an altered signalling.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Calmodulin / chemistry*
  • Calmodulin / metabolism*
  • Humans
  • Molecular Dynamics Simulation
  • Protein Binding
  • Proto-Oncogene Proteins p21(ras) / chemistry*
  • Proto-Oncogene Proteins p21(ras) / metabolism*
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / metabolism
  • Signal Transduction / physiology*

Substances

  • Calmodulin
  • KRAS protein, human
  • Recombinant Proteins
  • Proto-Oncogene Proteins p21(ras)

Grants and funding

This work was supported by Ministerio de Economía y Competitividad (Spanish government) grant SAF2016-76239-R to NA, by “Red Temática de Investigación Cooperativa en Cancer” grant RD 12/0036/0049 (Spanish government) and by AGAUR-Generalitat de Cataluny projects 2017SGR1033 and 2017 SGR 1225. EG was granted a FI predoctoral fellowship from AGAUR (Generalitat de Catalunya). Open access charges were funded by Ministerio de Economia y Competitividad, grant SAF2016-76239-R and University of Barcelona. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.