Molecular Dynamics Simulations of Biological Macromolecules

The Guanylate Kinase (GK) enzyme catalyzes the conversion of ATP to ADP which provides energy for cellular processes. Lab research on this important enzyme has shown that the behavior of the molecule follows a viscoelastic regime, and this research project has attempted to model the GK enzyme via computational software. The research required becoming familiar with the Python programming language and doing research into molecular dynamics simulations. The project looked into visualization software such as Anaconda and LAMMPS to create the model. This research project was able to obtain a simple visualization of the GK enzyme using VMD, and is in the process of obtaining further simulations using GROMACS software. Given the complexity of the field of computational biology and the associated programming, full scale representations of the GK enzyme are very difficult, and the work is ongoing. The GK enzyme model will be useful to better understand the molecular dynamics of the enzyme and assist with more targeted research in the fields of biophysics and biochemistry.