High-resolution computational simulations and advanced visualizations are enabling researchers at Oak Ridge National Laboratory to identify and gain a better understanding of proteins. Until recently, protein complexes have been viewed as static entities with biological function understood in terms of direct interactions between components. Now, Pratul Agarwal and colleagues at ORNL are using the lab's Cheetah supercomputer and EVEReST 35 megapixel visualization facility to study protein function in far greater detail. "Based on computational simulations, we're seeing proteins as very efficient molecular machines that are dynamically active and where internal protein dynamics are closely associated with their structure and function," Agarwal said. This emerging view has broad implications for protein engineering and drug design. Using biomolecular simulations, Agarwal has identified a network of protein vibrations in the enzyme cyclophilin A., which is involved in many biological reactions. These include protein folding and intracellular protein transport. Cyclophilin A is also required for the infectious activity of HIV-1. Funding is provided by DOE's Office of Science, Office of Biological and Environmental Research.
Menu