Sets of Local Entropy-Enthalpy Change Leads to Global Entropy-Enthalpy Change in SERCA

Abstract

Major conformational changes are involved in the multi-step catalytic cycle of the sarcoplasmic endoplasmic reticulum calcium ATPase (SERCA) pump. The movement and rotation of the Actuator (A) domain is crucial for ion translocation. The A-domain is connected to the trans-membrane helices through linker regions. Mutational studies on the A-M3 linker region show that varying the length of this region causes significant changes in the rate of the conformational transitions (JBC (2009),284,12258-12265 ). The focus of this research is to study the impact of these mutations on the structural changes during the transition from E1 to E2, the behavior of the A-M3 linker region, and the overall rate of the conformational transitions. In order to achieve faster computation of transitions, we implemented the MARTINI coarse-grained protein and lipid model in CHARMM. We used Dynamic Importance Sampling (DIMS) to compute transitions from the E1 to the E2 state for both directions of each mutant in both coarse-grained and all atom models. Analysis of the transitions across mutants shows that the angle formed by A-P-N domains changes by up to 20 degrees with an increasing number of inserts into the A-M3 linker region. Estimates of barrier crossing time from the simulation and experimental values are highly correlated (R2=0.934). Quasiharmonic analysis on the domains, linkers and transmembrane helices show entropic changes between the mutants and compensation effects. Interaction energies of the same regions indicate entropic-enthalpic compensation. Further investigation of the end state simulations shows changes in the number of high density water sites around the A-M3 linker region across the mutants. The varying degree of the change in volume due to water sites across all the mutants indicates a ripple effect where the local entropy-enthaply changes translate to global entropy-enthalpy changes.