Biology

Dr. Avisek Das
Department of Biochemistry and Molecular Biology, University of Chicago, USA

Complex macromolecular systems such as enzymes, channels, transporters and pumps need to change their shapes and visit many conformational states in order to perform their functions. Most experimental techniques inform us on the long-lived stable functional states of biological macromolecules. To understand the molecular mechanism of a specific biological process, one needs to go beyond the static information and determine how macromolecules change their conformations as a function of time. Computational methods can help generate physically plausible pathways for conformational transitions, which can then serve as ‘‘hypotheses’’ to be tested and refined experimentally. In the first part of my talk, I will describe a simple method for calculating coarse-grained transition pathways between two experimentally resolved states of a protein. The protein is represented as a double well elastic network model, where the nodes of the network are placed at the Cα atoms of the protein. The method is extremely efficient; it can produce a physically meaningful transition pathway for a thousand residue protein within an hour on a single CPU. In the second part of my talk, I will present our recent results on the molecular mechanism of ATP-driven calcium pump sarco/endoplasmic reticulum Ca2+-ATPase (SERCA). SERCA is an integral membrane protein that uses ATP hydrolysis as a source of free energy to pump two calcium ions per ATP molecule from the calcium poor cytoplasm of the muscle cell to the calcium rich lumen of the sarcoplasmic reticulum, thereby maintaining a ten thousand fold concentration gradient. Detailed structural studies of the pump under different conditions provided analogues of various intermediates in the transport cycle and revealed important changes in the tertiary structure of the protein both in the cytoplasmic and in the transmembrane parts. We have calculated transition pathways, with all-tom resolutions, between the experimentally resolved functional states of the pump. The resulting information provides a molecular movie of the entire transport cycle and elucidates the key elements of active transport not revealed by the structures of the stable states.