Groß Christine, Hamacher Kay, Schmitz Katja, Jager Sven
Department of Biology, Computational Biology & Simulation Group, Technische Universität Darmstadt , Schnittspahnstraße 2, 64287 Darmstadt, Germany.
Department of Chemistry, Biological Chemistry Group, Technische Universität Darmstadt , Alarich-Weiss-Straße 8, 64287 Darmstadt, Germany.
J Chem Inf Model. 2017 Feb 27;57(2):243-255. doi: 10.1021/acs.jcim.6b00556. Epub 2017 Jan 27.
The Fusarium solani cutinase (FsC) is a promising candidate for the enzymatic degradation of the synthetic polyester polyethylene terephthalate (PET) but still suffers from a lack of activity. Using atomic MD simulations with different concentrations of cleavage product ethylene glycol (EG), we show influences of EG on the dynamic of FsC. We observed accumulation of EG in the active site region reducing the local flexibility of FsC. Furthermore, we used a coarse-grained mechanical model to investigate whether substrate binding in the active site causes an induced fit. We observed this supposed induced fit or "breath-like" movement during substrate binding indicating that the active site has to be flexible for substrate conversion. This guides rational design: mutants with an increased flexibility near the active site should be considered to compensate the solvent-mediated reduction in activity.
茄病镰刀菌角质酶（FsC）是用于酶促降解合成聚酯聚对苯二甲酸乙二酯（PET）的一个有前景的候选酶，但它仍然存在活性不足的问题。通过使用不同浓度裂解产物乙二醇（EG）的原子分子动力学模拟，我们展示了EG对FsC动力学的影响。我们观察到EG在活性位点区域积累，降低了FsC的局部灵活性。此外，我们使用粗粒度力学模型来研究活性位点中的底物结合是否会引起诱导契合。我们在底物结合过程中观察到了这种假定的诱导契合或“呼吸样”运动，这表明活性位点必须具有灵活性才能进行底物转化。这为合理设计提供了指导：应考虑在活性位点附近具有更高灵活性的突变体，以补偿溶剂介导的活性降低。
