Modeling and subtleties of K-Ras and Calmodulin interaction

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.Author summary: K-Ras is one of the most mutated oncogenes in human cancer. Although several studies validate K-Ras protein as good candidate for direct therapeutic targeting, pharmacologic targeting has not been successful. During the last years increasing evidences demonstrate that oncogenic K-Ras activity can be modulated in vivo by dimerization, nanoclustering at the plasma membrane or interaction with non-effector proteins, consequently opening new therapeutic strategies. We have previously demonstrated that Calmodulin, an ubiquitous Ca2+-binding protein, is one of this K-Ras interacting proteins and that it negatively modulates K-Ras signaling. Although experimental data were available showing the relevant regions for this interaction, a model of K-Ras and Calmodulin interaction was missing. In the present work by using different computational modeling techniques we obtained a model for this interaction that agrees with the experimental data. We believe the present model will help to better understand K-Ras regulation, and to design new inhibitors. For instance, base on our model, we can predict that the interaction can take place at the plasma membrane, and that since the surface of K-Ras that interact with Calmodulin is the same that it uses for dimerization, that Calmodulin could be inhibiting K-Ras dimerization.