Molecular Dynamics Simulations: Analyzing and Understanding Protein Vibrations

Protein vibrations may enable protein structure to efficiently access structural changes necessary for function.  In addition, the motions may effect biochemistry by bringing catalytic partners together.  Anisotropic THz spectroscopy provides a spectrum of vibrational excitations, but to understand what the spectra mean, we need to compare these to calculations.  Calculations enable us to more readily see trends with changes in temperature, ligand binding and mutation.  However the calculations may be inaccurate for such complex systems.  By combining calculations and measurements we can both improve the computational accuracy and analyze what the data mean.  We use a number of different software packages to perform molecular dynamics simulations (mainly charmm and NAMD), and analyze the results using different visualization software (VMD and PyMOL).  We have developed some python/TCL scripts to more readily visualize the data within VMD.