Modeling the role of water and ions in the structure and function of biomolecules

Dr. Tyler Luchko, Associate Professor of Physics and Astronomy, CSU Northridge

When dissolved in water, salt, such as sodium-chloride, becomes ions that play a critical role in the structure and function of proteins, RNA and DNA. Modeling the equilibrium distribution of ions around these molecules is important for understanding biology at the molecular level and the development of new drugs. However, the most common approach, molecular dynamics, is computationally prohibitive, especially at millimolar concentrations typical for ions like magnesium and calcium, and for complexes of protein molecules. To address this, we have been developing the 3D-reference interaction site model (3D-RISM) of molecular solvation. Rather than simulating the motions of ions, 3D-RISM uses statistical physics to calculate equilibrium distributions of ions, from which we can calculate thermodynamic properties. In this talk, I will discuss how we can use statistical physics to study biology at the molecular level and our efforts to make 3D-RISM faster and more accurate. I will illustrate these numerical and modeling advances with applications to protein complexes, like microtubules, and highly charged systems, such as RNA hairpins.