The role of domain: Domain interactions versus domain: Water interactions in the coarse-grained simulations of the E1P to E2P transitions in Ca-ATPase (SERCA)

SERCA is an important model system for understanding the molecular details of conformational change in membrane transport systems. This reflects the large number of solved X‐ray structures and the equally large database of mutations that have been assayed. In this computational study, we provide a molecular dynamics description of the conformational changes during the E1P → E2P transitions. This set of states further changes with insertion mutants in the A‐M3 linker region. These mutants were experimentally shown to lead to significant shifts in rates between the E1P → E2P states. Using the population shift framework and dynamic importance sampling method along with coarse‐grained representations of the protein, lipid, and water, we suggest why these changes are found. The calculations sample on intermediates and suggest that changes in interactions, individual helix interactions, and water behavior are key elements in the molecular compositions that underlie shifts in kinetics. In particular, as the insertion length grows, it attracts more water and disrupts domain interactions, creating changes as well at the sites of key helix interactions between the A‐Domain and the P‐Domain. This provides a conceptual picture that aids understanding of the experimental results. Proteins 2012;. © 2012 Wiley Periodicals, Inc.