Conformational Transitions in ATP-Driven Calcium Pump SERCA

Abstract

Sarco/endoplasmic reticulum Ca2+-ATPase (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 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 reaction cycle and revealed important changes in the tertiary structure of the protein both in the cytoplasmic and in the transmembrane parts. Two major outstanding issues are the pathways of the ions to and from the transmembrane binding sites and a detailed understanding of the large scale conformational changes among various functionally relevant states. We have applied all-atom molecular dynamics (MD) and string method with swarms-of-trajectories to study transition pathways among various experimental structures. The size of the system (291,000) and the time-scale involved in the large scale motions prohibit the use of brute-force unbiased simulations to obtain statistically meaningful information. To circumvent this challenge, the string method with swarms-of-trajectories is used to discover the optimal minimum free energy path between the two end-states. The path, which is represented as a chain of states or images in the space of relevant collective variables, is optimized by iterating two steps: moving each image along the drift calculated from an ensemble (swarm) of short unbiased MD trajectories initiated from the image and a reparametrization procedure that keeps all the images equidistant. We hope to understand the molecular details of the complex motions involved in the conformational transitions by studying the pathways produced by the string method and correlating these observations to available structural and biochemical experiments.