A computational investigation of the conformational transitions in the catalytic cycle of SERCA

Ca-ATPase or SERCA is structurally and functionally the most well studied protein in the P-type ATPase family. X-ray structures of intermediate states and extensive mutational studies contribute to the information about this pump. In spite of the wealth of information, the dynamics of the pump moving from one state to another is not understood on a molecular level. Molecular dynamics (MD) simulations and dynamics importance sampling (DIMS) was used to explore conformational changes in the E2 -> E1 and the E1P -> E2P transitions. Our study is based on experiments showing a shift in kinetics with the insertions and deletions in the A-M3 linker region. To identify the underlying mechanism that drives these changes, the free energy changes and its components were studied. In order to estimate the free energy, enthalpic and entropic estimates were computed. The enthalpy-entropy compensation is found to be important for the E2 -> E1 transitions. The interactions of water with the A-M3 linker region is critical in that regard. Although the estimates of free energies use a coarse grained model, the trends seen among the mutants is in good correlation with the experimental results. In the second transition, the water interactions are significant for the E1P -> E2P large conformational change. Domain-water interactions compete with domain-domain interactions to alter the free energy changes during this transition in the mutations. Finally, the E2 -> E1 transition using the all-atom model reveals that making and breaking of three main inter-domain salt-bridges is central to the conformational transition. A comparison of the free energy changes in the all-atom transition show similar enthalpy-entropy compensations to that found in the coarse-grained study.