Molecular simulations of polymeric and biological systems: Protein-polyelectrolyte complexes and bacterial motility

Computer simulations have been performed to study polymeric and biological systems such as protein-polyelectrolyte complexes and bacterial gliding motility. In polymeric systems, we have studied complex formation between proteins (polyampholytes) and polyelectrolyte chains in dilute and semidilute solutions. Using Monte Carlo (MC) and molecular dynamics (MD) simulations we have shown that the complexation between polyampholyte and polyelectrolyte chains is due to polarization induced attractive interactions between molecules. A polyampholyte chain binds to a polyelectrolyte in such a way to maximize the electrostatic attraction between oppositely charged ionic groups and minimize the electrostatic repulsion between similarly charged ones. In dilute solutions, a complex is usually formed by one polyampholyte and one polyelectrolyte chain. The complex structure changes from double helical structure to three-arm star-like complex depending on the strength of electrostatic interaction and the charge sequence along polyampholyte backbone. In dilute solutions of moderate polymer concentration, diblock polyampholytes and polyelectrolytes form micellar aggregates that bind together resulting in a network of micelles spanning the entire system in semidilute solutions. On the contrary, the structure of multichain aggregates formed by random polyampholytes and polyelectrolytes resembles that of branched polymers. ^ In biological systems, we have studied how the slime secretion by Cyanobacteria and Myxobacteria is related to their gliding motility over surfaces. The slime is produced by the nozzle-like pores located on the bacteria surface. To understand the mechanism of gliding motion and its relation to the slime polymerization, we have performed molecular dynamics simulations of a molecular nozzle with growing inside polymer chains. These simulations show that the compression of polymer chains inside the nozzle is a driving force for its motion. There is a linear relationship between the average nozzle velocity and the chain polymerization rate with a proportionality coefficient dependent on the geometric characteristics of the nozzle such as its length and friction coefficient. This minimal model of the molecular engine was used to explain the gliding motion of bacteria over surfaces.