Simulations of K-Ras GTPase Mutagenesis ; Simulacije mutageneze K-Ras GTPaze

Kirsten rat sarcoma (K-Ras) protein is a signaling GTPase which has an important role in the Mitogen-activated protein kinase (MAPK) pathway. Using the methods of molecular dynamics (MD) simulations, in this thesis we will investigate if and how does the specific mutagenesis of K-Ras protein affect its signaling properties. The mutation studied here is G12C, as it is predominant in humans. K-Ras exists in an active state when it binds to a GTP molecule, and then it signals the activation of MAPK pathway, whose functions include proliferation and growth of cells. By a hydrolysis GTP to GDP molecule, K-Ras gets into an inactive state. As it is observed that irregularities in K-Ras signaling lead to development of cancer, simulations of its mutagenesis become more relevant to show the exact mechanisms of binding GTP/GDP molecules. In this thesis we have calculated the free energy using the method of thermodynamic integration on MD simulations and performed the analysis of the trajectories from the same set of simulations. The results reveal that the binding affinity of GTP/GDP molecule changes depending on whether it binds to the wild type or mutated protein. Apparent inconsistencies in results between identical replicas, as well as a prominent hysteresis between different directions in simulations of the same perturbation system is discussed. In order to understand these inconsistencies, a thorough analysis of simulation trajectories is exploited. It is shown that such a lack of the full reproducibility of the simulation replicas emerges from the inconsistencies in the formation of h-bond between cysteine and GTP molecule, whereas the hysteresis is a consequence of the conformational changes in the Switch loops of K-Ras protein. In other words, a mutated protein favours the active state, which directly influences the activity of the MAPK pathway, which in turn leads to a cancer development. ; K-Ras (eng. Kirsten rat sarcoma) protein je signalna GTPaza koja igra važnu ulogu u radu signalnog puta ...