a School of Pharmacy , Kitasato University , Shirokane 5-9-1, Minato-ku, Tokyo 108-8641 , Japan.
J Biomol Struct Dyn. 2019 Apr;37(6):1567-1581. doi: 10.1080/07391102.2018.1462730. Epub 2018 May 7.
Calmodulin (CaM) is a multifunctional calcium-binding protein, which regulates various biochemical processes. CaM acts via structural changes and complex forming with its target enzymes. CaM has two globular domains (N-lobe and C-lobe) connected by a long linker region. Upon calcium binding, the N-lobe and C-lobe undergo local conformational changes, after that, entire CaM wraps the target enzyme through a large conformational change. However, the regulation mechanism, such as allosteric interactions regulating the conformational changes, is still unclear. In order to clarify the allosteric interactions, in this study, experimentally obtained 'real' structures are compared to 'model' structures lacking the allosteric interactions. As the allosteric interactions would be absent in calcium-free CaM (apo-CaM), allostery-eliminated calcium-bound CaM (holo-CaM) models were constructed by combining the apo-CaM's linker and the holo-CaM's N- and C-lobe. Before the comparison, the 'real' and 'model' structures were clustered and cluster-cluster relationship was determined by a principal component analysis. The structures were compared based on the relationship, then, a distance map and a contact probability analysis clarified that the inter-domain motion is regulated by several groups of inter-domain contacting residue pairs. The analyses suggested that these residues cause inter-domain translation and rotation, and as a consequence, the motion encourage structural diversity. The resultant diversity would contribute to the functional versatility of CaM.
钙调蛋白（CaM）是一种多功能的钙结合蛋白，调节着各种生化过程。CaM 通过结构变化和与靶酶形成复合物来发挥作用。CaM 有两个球状结构域（N 结构域和 C 结构域），通过一个长的连接区连接。钙结合后，N 结构域和 C 结构域发生局部构象变化，之后，整个 CaM 通过一个大的构象变化包裹靶酶。然而，调节机制，如调节构象变化的变构相互作用，仍不清楚。为了阐明变构相互作用，在这项研究中，将实验获得的“真实”结构与缺乏变构相互作用的“模型”结构进行了比较。由于无钙钙调蛋白（apo-CaM）中不存在变构相互作用，因此通过将 apo-CaM 的连接区与 holo-CaM 的 N 结构域和 C 结构域组合，构建了变构消除的钙结合 CaM（holo-CaM）模型。在比较之前，通过主成分分析确定了“真实”和“模型”结构的聚类和聚类间关系。然后，根据这种关系对结构进行了比较，距离图和接触概率分析表明，结构域间的运动受几组结构域间接触残基对的调节。这些分析表明，这些残基引起结构域间的平移和旋转，从而促进结构的多样性。由此产生的多样性将有助于 CaM 的多功能性。
