Investigating the effect of the oncogenic mutation E545K of the PI3Ka protein with enhanced sampling MD simulations

Project reference: 1815

The PI3Ka protein is the most commonly mutated kinase in human malignancies. One of the most common mutations is located in amino acid E545K, where a glutamic acid is replaced by lysine. It has been recently proposed that in this oncogenic mutation, a detachment of the protein catalytic subunit from the protein regulatory subunit happens, resulting in loss of regulation and constitutive PI3Ka activation, which can lead to oncogenesis. To test the mechanism of protein overactivation, enhanced sampling MetaDynamics Molecular Dynamics simulations will be used here to examine the dynamics and  conformations of the mutant PI3Ka protein as they occur in microsecond simulations. The dynamics and structural evolution of this E545K oncogenic protein, as described by our simulations, might reveal possible binding pockets, which will then be exploited in order to design small molecules that will target only the oncogenic mutant protein.

PI3Kα, a lipid kinase that attaches to the cell membrane to function, is the most frequently mutated kinase in human cancers. Understanding the mechanism of overactivation of the most common mutation of the PI3Kα protein, E545K, is central to developing mutant-specific therapeutics for cancer. Using MD simulations we would like to gain insights into the overactivation mechanism of the PI3Kα mutant E545K. The catalytic and regulatory subunits of the protein are shown in purple and green, respectively and the membrane is represented in grey. 

Project Mentor: Dr. Zoe Cournia

Project Co-mentor: Dr Dimitris Dellis

Site Co-ordinator: Aristeidis Sotiropoulos

Learning Outcomes:
Learn how to setup and perform enhanced MD simulations. Analyze enhanced MD simulations with standard tools. Develop own tools and scripts for MD simulation analysis. Understand the protein function and dynamics.

Student Prerequisites (compulsory):
Natural science student (Chemistry, Physics, Engineer) that have familiarity with  or want to learn how to perform computer simulations.

Student Prerequisites (desirable):
Basic programming skills and linux would be desirable.

Training Materials:
See www.drugdesign.gr

Workplan:

  • Week 1. Perform GROMACS and PLUMED Tutorial. Familiarize with linux.
  • Week 2. Setup the protein system. Read the literature on PI3Ka.
  • Week 3. Submit the Work Plan. Familiarize with HPC resources on ARIS, creating and running batch scripts. Submit the MD jobs.
  • Week 4. Familiriaze with analyses tools and perform test calculations on the trajectories.
  • Week 5. Produce enhanced sampling MD trajectories.
  • Week 6. Analyze the trajectories
  • Week 7. Rationalize the results and gain insights into the mechanism of PI3Ka mutant function.
  • Week 8. Write the final report.

Adapting the Project: Increasing the Difficulty:
The project can be made more difficult depending on the analyses that will be performed.

Adapting the Project: Decreasing the Difficulty
The project can be made less difficult by choosing easier analyses.

Resources:
The student will need to have access to ARIS supercomputer facility, the necessary software and analysis tools to run and analyse the trajectories. Local resources for analyses will be provided (office space and desktop).

Organisation:
Greek Research and Technology Network and Biomedical Research Foundation
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