Deborah A. Kallick, Principal Investigator

Molecular Simulations of Biomolecules

  Research in this laboratory used data derived from Nuclear Magnetic Resonance (NMR) Spectroscopy to supplement holonomic constraints in restrained molecular dynamic simulations of RNA (ribonucleic acid) and proteins. The majority of NMR spectroscopy laboratories determining structures of biological macromolecules in solution use approximations to the force field that lead to errors, especially in the treatment of electrostatic interactions. Typically, the NMR spectroscopy laboratory simulates the molecule in vacuo and simply turns off electrostatics.

  A more realistic approach is to use the particle mesh Ewald method as implemented in amber, which has been shown computationally to result in stable simulations for large nucleic acids. The implementation of this method with the experimental restraints determined from solution NMR was applied to RNA. The goal was to generate more realistic structures of macromolecules using both experimental data and computational techniques.

  Other work performed by these researchers involved analysis of NMR data and correlation of chemical shifts with structure. Additional work included the calculation of protein structures using NMR and molecular simulations.

  All work performed by these researchers involved visualization and computation using the Basic Sciences Computation Laboratory (BSCL) and Visualization Workstation Laboratory (VWL).