Świderek Katarzyna, Tuñón Iñaki, Moliner Vicent, Bertran Joan
Departament de Química Física i Analítica, Universitat Jaume I, 12071, Castellón, Spain.
Institute of Applied Radiation Chemistry, Lodz University of Technology, 90-924, Lodz, Poland.
Chemistry. 2017 Jun 1;23(31):7582-7589. doi: 10.1002/chem.201700807. Epub 2017 May 15.
The design of new biocatalysts is a goal in biotechnology to improve the rate, selectivity and environmental impact of industrial chemical processes. In this regard, the use of computational techniques has provided valuable assistance in the design of new enzymes with remarkable catalytic activity. In this paper, hybrid QM/MM molecular dynamics simulations have allowed insights to be gained on the origin of the limited efficiency of a computationally designed enzyme for the Kemp elimination; the HG-3. Comparison of results derived from this enzyme with those of a more evolved protein containing additional point mutations, HG-3.17, rendered important information that should be taken into account in the design of new enzymes. For this Kemp eliminase reaction, higher reactivity has been demonstrated to be related to a better electrostatic preorganisation of an environment that creates a more favourable electrostatic potential for the reaction to proceed. The limitations of HG-3 can be related to a lack of flexibility, a not well-fitted active site, and a lack of protein electrostatic preorganisation, which decrease the reorganisation around the oxyanion hole.
新型生物催化剂的设计是生物技术领域的一个目标，旨在提高工业化学过程的反应速率、选择性以及对环境的影响。在这方面，计算技术的应用为设计具有卓越催化活性的新型酶提供了宝贵的帮助。在本文中，量子力学/分子力学（QM/MM）混合分子动力学模拟使我们能够深入了解一种通过计算设计的用于肯普消除反应的酶——HG-3效率有限的根源。将该酶与含有额外点突变的进化程度更高的蛋白质HG-3.17的结果进行比较，得出了在设计新型酶时应予以考虑的重要信息。对于这种肯普消除酶反应，已证明更高的反应活性与环境中更好的静电预组织有关，这种静电预组织为反应进行创造了更有利的静电势。HG-3的局限性可能与缺乏灵活性、活性位点拟合不佳以及蛋白质静电预组织不足有关，这些因素会减少氧负离子空穴周围的重排。
