Department of Physics, University of Houston, Houston, Texas, United States of America.
PLoS Comput Biol. 2011 Jul;7(7):e1002114. doi: 10.1371/journal.pcbi.1002114. Epub 2011 Jul 28.
The flexibility in the structure of calmodulin (CaM) allows its binding to over 300 target proteins in the cell. To investigate the structure-function relationship of CaM, we combined methods of computer simulation and experiments based on circular dichroism (CD) to investigate the structural characteristics of CaM that influence its target recognition in crowded cell-like conditions. We developed a unique multiscale solution of charges computed from quantum chemistry, together with protein reconstruction, coarse-grained molecular simulations, and statistical physics, to represent the charge distribution in the transition from apoCaM to holoCaM upon calcium binding. Computationally, we found that increased levels of macromolecular crowding, in addition to calcium binding and ionic strength typical of that found inside cells, can impact the conformation, helicity and the EF hand orientation of CaM. Because EF hand orientation impacts the affinity of calcium binding and the specificity of CaM's target selection, our results may provide unique insight into understanding the promiscuous behavior of calmodulin in target selection inside cells.
钙调蛋白（CaM）结构的灵活性使其能够与细胞内的 300 多种靶蛋白结合。为了研究 CaM 的结构-功能关系，我们结合计算机模拟和基于圆二色性（CD）的实验方法，研究了影响 CaM 靶识别的结构特征在拥挤的细胞样条件下。我们开发了一种独特的多尺度电荷解决方案，该解决方案是根据量子化学计算得出的，并结合蛋白质重建、粗粒度分子模拟和统计物理，以表示钙结合时从 apoCaM 到 holoCaM 的电荷分布。从计算上，我们发现除了细胞内常见的钙结合和离子强度外，大分子拥挤程度的增加也会影响 CaM 的构象、螺旋和 EF 手的取向。由于 EF 手的取向会影响钙结合的亲和力和 CaM 靶选择的特异性，我们的结果可能为理解钙调蛋白在细胞内靶选择中的混杂行为提供独特的见解。
