CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France.
Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France.
J Struct Biol. 2021 Sep;213(3):107769. doi: 10.1016/j.jsb.2021.107769. Epub 2021 Jul 3.
In this work, we combined biochemical and structural investigations with molecular dynamics (MD) simulations to analyze the very different thermal-dependent allosteric behavior of two lactate dehydrogenases (LDH) from thermophilic bacteria. We found that the enzyme from Petrotoga mobilis (P. mob) necessitates an absolute requirement of the allosteric effector (fructose 1, 6-bisphosphate) to ensure functionality. In contrast, even without allosteric effector, the LDH from Thermus thermophilus (T. the) is functional when the temperature is raised. We report the crystal structure of P. mob LDH in the Apo state solved at 1.9 Å resolution. We used this structure and the one from T. the, obtained previously, as a starting point for MD simulations at various temperatures. We found clear differences between the thermal dynamics, which accounts for the behavior of the two enzymes. Our work demonstrates that, within an allosteric enzyme, some areas act as local gatekeepers of signal transmission, allowing the enzyme to populate either the T-inactive or the R-active states with different degrees of stringency.
在这项工作中，我们将生化和结构研究与分子动力学（MD）模拟相结合，分析了两种来自嗜热细菌的乳酸脱氢酶（LDH）非常不同的热依赖性变构行为。我们发现，来自 Petrotoga mobilis（P. mob）的酶需要变构效应物（果糖 1,6-二磷酸）的绝对需求来确保其功能。相比之下，即使没有变构效应物，来自 Thermus thermophilus（T. the）的 LDH 在温度升高时也具有功能。我们报告了在 1.9 Å分辨率下解决的 P. mob LDH 在 apo 状态下的晶体结构。我们以前使用这个结构和 T. the 的结构作为起点，在不同的温度下进行 MD 模拟。我们发现了热动力学之间的明显差异，这解释了两种酶的行为。我们的工作表明，在变构酶中，一些区域充当信号传递的局部门卫，允许酶以不同的严格程度进入 T-无活性或 R-活性状态。
