Developing a Coarse-Grained Model of Protein Dynamics

Marina Guenza, Chemistry

Site-specific dynamics of proteins in their isolated and bound forms affect their capability of binding to their target sites and performing their biological roles. Developing a better understanding of how proteins interact with substrates, including nucleic acids, requires answers to a number of questions, such as how molecules interact and move relative to each other, how this motion is guided by the chemical structure of the molecules involved and the nature of their fluctuations. On the local scale, computer simulations are useful because they show how their motions are guided by the chemical structure of the molecules and their fluctuations, how water molecules can mediate dynamical processes, what is the ionic environment around proteins and DNA, and more. On the larger scale of the macromolecular 1UBQ_environment-2de1kgocomplexes, atomistic computer simulations can hardly provide information even with the help of state of the art super computers. Because of the wide range of timescales involved, protein and nucleic acid dynamics need to be approached by multiscale models that combine atomistic simulations and coarse-grained descriptions.

The Guenza group develops theory and computational models for the dynamics of biological systems represented as coarse-grained units. The theory is a Langevin Equation for Protein Dynamics (LE4PD), which relates local flexibility to the biological function of the molecule, protein and DNA. The REU student involved in this project will work closely with Chemistry and Physics graduate students to learn and perform Molecular Dynamics computer simulations of biological systems, which are input to the LE4PD approach.