Colloquium on July 20, 2009

Alexander S. Mikhailov
Department of Physical Chemistry
Fritz Haber Institute of the Max Planck Society
Faradeyweg 4-6, 14195 Berlin

"Nonlinear relaxation properties of elastic networks and nonequilibrium dynamics of protein machines"

Protein machines operating as mechanical motors, enzymes or ion pumps play a fundamental role in biological cells. To execute their functions, they use energy supplied with ATP molecules. Binding and hydrolysis of ATP induce large-scale conformational relaxation motions in such machines. While the structure of most machine proteins is known, modeling of dynamics of their operation cycles presents difficulties. Because the cycles of molecular machines are slow and typically lie in the range from tens of milliseconds to a second, they cannot be followed in all-atom molecular dynamics simulations. On the other hand, phenomenological models of molecular motors, such as mechanical ratchets or stochastic oscillators, provide an oversimplified view of their operation, reducing it to effective motions along a single mechanical coordinate. More realistic coarse-grained descriptions are therefore needed to fill the gap between simple phenomenology and full atomic dynamics. Elastic network models, picturing the protein as a network made up of beads connected by elastic springs can yield such a middle-level description. In this talk, I give an overview of our recent investigations of nonlinear relaxation dynamics in the elastic networks corresponding to several real protein machines and show how artificial elastic networks with similar conformational relaxation properties can be constructed.