Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India.
J Chem Phys. 2018 Sep 21;149(11):114902. doi: 10.1063/1.5042290.
The dissociation of an insulin dimer to two monomers is an important life process. Although the monomer is the biologically active form of the hormone, it is stored in the β-cells of the pancreas in the hexameric form. The latter, when the need comes, dissociates to dimers and the dimers in turn to monomers to maintain the endogenous delivery of the hormone. In order to understand insulin dimer dissociation at a molecular level, we perform biased molecular dynamics simulations (parallel tempering metadynamics in the well-tempered ensemble) of the dissociation of the insulin dimer in water using two order parameters and an all-atom model of the protein in explicit water. The two order parameters selected (after appropriate studies) are the distance (R) between the center of mass of two monomers and the number of contacts (N) among the backbone-Cα atoms of the two monomers. We calculated the free energy landscape as a function of these two order parameters and determined the minimum free energy pathway of dissociation. We find that the pathway involves multiple minima and multiple barriers. In the initial stage of dissociation, the distance between the monomers does not change significantly but the N decreases rapidly. In the latter stage of separation, the opposite occurs, that is, the distance R increases at nearly a constant low value of N. The configurations of the two monomeric proteins so formed are found to be a bit different due to the entropic reasons. Water is seen to play a key role in the dissociation process stabilizing the intermediates along the reaction path. Our study reveals interesting molecular details during the dissociation, such as the variation in the structural and relative orientational arrangement of the amino acid residues along the minimum energy path. The conformational changes of monomeric insulin in the stable dimer and in the intermediate states during dimer dissociation have been studied in detail.
胰岛素二聚体解离为两个单体是一个重要的生命过程。虽然单体是激素的生物活性形式，但它以六聚体的形式储存在胰腺的β细胞中。当需要时，后者会解离为二聚体，二聚体又会解离为单体，以维持激素的内源性释放。为了在分子水平上理解胰岛素二聚体的解离，我们使用两个序参数和蛋白质的全原子模型在显式水中对胰岛素二聚体在水中的解离进行了有偏分子动力学模拟（well-tempered 系综中的平行温度化元动力学）。选择的两个序参数（经过适当的研究）是两个单体的质心之间的距离（R）和两个单体的骨干-Cα原子之间的接触数（N）。我们计算了作为这两个序参数的函数的自由能景观，并确定了解离的最小自由能途径。我们发现该途径涉及多个最小值和多个势垒。在解离的初始阶段，单体之间的距离没有明显变化，但 N 值迅速下降。在分离的后期阶段，情况正好相反，即 R 距离以几乎恒定的低 N 值增加。由于熵的原因，形成的两个单体蛋白质的构象被发现略有不同。水在解离过程中起着关键作用，稳定反应路径上的中间体。我们的研究揭示了解离过程中的一些有趣的分子细节，例如沿着最小能量路径的氨基酸残基的结构和相对取向排列的变化。还详细研究了单体胰岛素在稳定二聚体和二聚体解离过程中的中间状态下的构象变化。
