Quaternary Structure Analysis of Calcium/Calmodulin-Dependent Protein Kinase II Alpha by Cryo-Electron Microscopy
Calcium-dependent protein kinase II alpha (CaMKIIα) is a highly abundant protein within the hippocampus, the region of the brain responsible for memory and learning. CaMKII has both structural and signaling roles in the regulation of the connective strength of synapses in excitatory neurons. It has a unique structure comprised of twelve subunits that form a dynamic assembly and is highly flexible. Its structural behavior has been shown to affect its activity, and a comprehensive mechanism of structure and function is still not fully understood. The determination of the quaternary structure of the CaMKII holoenzyme has been attempted for nearly 20 years by a variety of methods, with no one method giving a definitive structure. Problems in obtaining a structure originated with observation methods that estimated quaternary shape from low-resolution ensemble averages or required significant alteration of the protein to enforce a particular conformation. In this work, experiments were conducted to remove these limitations and provide a path towards the quaternary structure of CaMKIIα. Different expression and purification methods were evaluated to produce an optimal protocol for the generation of samples of concentrated, monodisperse, autoinhibited full-length wild-type CaMKIIα for study with cryo-electron microscopy. Strategies for microscopy sample preparation were investigated, including affinity girds, graphene-coated grids, and holey carbon grids. Lastly, experiments using negative stain electron microscopy, cryo-electron microscopy with single particle analysis, and cryo-electron tomography with subtomogram averaging were conducted to reveal the conditions required to produce an unambiguous three-dimensional structure. It was found that the assembly of the hexameric hub rings appeared to have flexible orientation, and superposition problems inherent in two-dimensional projection averaging requires the use of cryo-electron tomography to unravel the ambiguity in both hub orientation and catalytic module placement within the reconstructed volume. A subtomogram average of a limited number of particles revealed a hub domain that matched the morphology of prior reports, but the determination of catalytic module placement was not resolved. The cumulative result of this work establishes a strategy for the large-scale data collection needed to fully elucidate the structure of this challenging and fascinating protein.