PDF(Pubmed)
Abstract：
The present study aims at numerically describing to what extent substrate - enzyme complexes in solution may change over time as a natural process of conformational changes for a liganded enzyme in comparison to those movements which occur independently from substrate interaction, i.e. without a ligand. To this end, we selected structurally known pairs of liganded / unliganded CYP450 3A4 enzymes with different geometries hinting at induced fit events. We carried out molecular dynamics simulations (MD) comparing the trajectories in a \"cross-over\" protocol: (i) we added the ligand to the unliganded crystal form which should adopt geometries similar to the known geometry of the liganded crystal structure during MD, and - conversely - (ii) we removed the bound ligand form the known liganded complex to test if a geometry similar to the known unliganded (apo-) form can be adopted during MD. To compare continues changes we measured root means square deviations and frequencies. Results for case (i) hint at larger conformational changes required for accepting the substrate during its approach to final position - in contrast to case (ii) when mobility is fairly reduced by ligand binding (strain energy). In conclusion, a larger conformational sampling prior to ligand binding and the freezing-in (rigidity) of conformations for bound ligands can be interpreted as two conditions linked to induced-fit.
摘要：
本研究旨在通过数值描述，与独立于底物相互作用而发生的运动相比，作为配体酶的构象变化的自然过程，溶液中的底物-酶复合物可能随时间变化的程度。即没有配体。为此,我们选择了结构已知的成对的配体/非配体CYP4503A4酶,这些酶具有不同的几何形状,提示诱导的拟合事件.我们进行了分子动力学模拟（MD）比较了“交叉”协议中的轨迹：（i）我们将配体添加到未配位的晶体形式中，该形式应采用与已知的配位晶体结构相似的几何形状在MD期间，相反，（ii）我们从已知的配体复合物中去除结合的配体，以测试在MD期间是否可以采用类似于已知的无配体（载脂蛋白）形式的几何形状。为了比较连续的变化，我们测量了均方根偏差和频率。情况（i）的结果表明，在接近最终位置的过程中，接受底物所需的构象变化更大-与情况（ii）相反，当配体结合（应变能）使迁移率相当降低时。总之,配体结合之前的较大构象采样和结合配体的构象的冻结（刚性）可以解释为与诱导拟合有关的两个条件。
