K-Ras4B ve c-Raf etkileşimlerinin moleküler dinamik simülasyonları ve hesaplamalı analizi

Ras proteins are activated through their upstream regulators. Upon activation, Ras proteins recruit their downstream effectors to the plasma membrane and activate them. Activated downstream effectors, then activate other proteins and this signaling cascades lead several responses within the cell. Although Ras proteins are activated through guanine exchange factor protein, specific mutations result with constitutively activate Ras. Those mutations are found in many cancer types and several developmental diseases. Therefore, targeting the mutations on Ras has been the main focus in the treatment of Ras-related diseases. However, Ras proteins are still classified as "undruggable protein". Effects of the mutations on Ras proteins and the interaction dynamics between their effectors are unclear. In this thesis, K-Ras4B and c-Raf interaction studied within two subsystems through molecular dynamics simulations. Computationally, K-Ras4B and c-Raf interaction were predicted by using PRISM (PRotein Interactions by Structural Matching). Residues on Ras and Raf interaction complex were identified using HotRegion. The results gave an idea about the specific amino acids involved in K-Ras4B and c-Raf interaction. To confirm the predictions, R41E/K42D double charge reversal mutations, called B3 mutation, were introduced to the control (G12D). MD simulations were performed on control and B3 mutated subsystems. In the system, which contains K-Ras4B1-166, the mutation slightly changed the binding free energy levels. According to the result, B3 mutation decreased the binding free energy levels. However, the difference in the energy levels was not significant enough. The unexpected energy levels can be studied further by introducing a membrane and a cysteine rich domain (CRD) to the system.