Zoete Vincent, Meuwly Markus, Karplus Martin
Laboratoire de Chimie Biophysique, ISIS/Université Louis Pasteur, 8, allée Gaspard Monge, BP 70028, 67083 Strasbourg Cedex, France.
J Mol Biol. 2004 Sep 17;342(3):913-29. doi: 10.1016/j.jmb.2004.07.033.
Molecular dynamics (MD) simulations (5-10ns in length) and normal mode analyses were performed for the monomer and dimer of native porcine insulin in aqueous solution; both starting structures were obtained from an insulin hexamer. Several simulations were done to confirm that the results obtained are meaningful. The insulin dimer is very stable during the simulation and remains very close to the starting X-ray structure; the RMS fluctuations calculated from the MD simulation agree with the experimental B-factors. Correlated motions were found within each of the two monomers; they can be explained by persistent non-bonded interactions and disulfide bridges. The correlated motions between residues B24 and B26 of the two monomers are due to non-bonded interactions between the side-chains and backbone atoms. For the isolated monomer in solution, the A chain and the helix of the B chain are found to be stable during 5ns and 10ns MD simulations. However, the N-terminal and the C-terminal parts of the B chain are very flexible. The C-terminal part of the B chain moves away from the X-ray conformation after 0.5-2.5ns and exposes the N-terminal residues of the A chain that are thought to be important for the binding of insulin to its receptor. Our results thus support the hypothesis that, when monomeric insulin is released from the hexamer (or the dimer in our study), the C-terminal end of the monomer (residues B25-B30) is rearranged to allow binding to the insulin receptor. The greater flexibility of the C-terminal part of the beta chain in the B24 (Phe-->Gly) mutant is in accord with the NMR results. The details of the backbone and side-chain motions are presented. The transition between the starting conformation and the more dynamic structure of the monomers is characterized by displacements of the backbone of Phe B25 and Tyr B26; of these, Phe B25 has been implicated in insulin activation.
对水溶液中天然猪胰岛素的单体和二聚体进行了分子动力学(MD)模拟(时长5 - 10纳秒)和简正模式分析;两种起始结构均取自胰岛素六聚体。进行了多次模拟以确认所得结果是有意义的。胰岛素二聚体在模拟过程中非常稳定,并且与起始X射线结构非常接近;从MD模拟计算得到的均方根波动与实验B因子相符。在两个单体中的每一个内部都发现了相关运动;它们可以通过持续的非键相互作用和二硫键来解释。两个单体的B24和B26残基之间的相关运动是由于侧链与主链原子之间的非键相互作用。对于溶液中的孤立单体,在5纳秒和10纳秒的MD模拟过程中,A链和B链的螺旋结构是稳定的。然而,B链的N端和C端部分非常灵活。B链的C端部分在0.5 - 2.5纳秒后偏离X射线构象,并暴露了A链的N端残基,这些残基被认为对胰岛素与其受体的结合很重要。因此,我们的结果支持这样一种假设,即当单体胰岛素从六聚体(或我们研究中的二聚体)中释放出来时,单体的C端(残基B25 - B30)会重新排列以允许与胰岛素受体结合。B24(苯丙氨酸→甘氨酸)突变体中β链C端部分更大的灵活性与核磁共振结果一致。文中给出了主链和侧链运动的详细情况。单体从起始构象到更具动态结构的转变以苯丙氨酸B25和酪氨酸B26主链的位移为特征;其中,苯丙氨酸B25与胰岛素激活有关。