Department of Complex Systems, Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224 Warsaw, Poland.
Max-Planck-Institut für Intelligente Systeme, Heisenbergstrasse 3, D-70569 Stuttgart, Germany.
Phys Chem Chem Phys. 2019 Sep 21;21(35):18811-18815. doi: 10.1039/c9cp02842k. Epub 2019 Aug 30.
Recent experiments have reported that diffusion of enzymes can be enhanced in the presence of their substrates. Using a fluctuating dumbbell model of enzymes, it has been argued that such an enhancement can be rationalized by the reduction of the enzyme size and by the suppression of the hydrodynamically coupled conformational fluctuations, induced by binding a substrate or an inhibitor to the enzyme [Nano Lett. 2017, 17, 4415]. Herein, we critically examine these expectations via extensive Brownian dynamics simulations of a similar model. The numerical results show that neither of the two mechanisms can cause an enhancement comparable to that reported experimentally, unless very large, physically counter-intuitive, enzyme deformations are invoked.
最近的实验报告指出，在酶的底物存在的情况下，酶的扩散可以增强。利用酶的波动哑铃模型，有人认为，通过减小酶的大小和抑制结合底物或抑制剂后酶的水动力耦合构象波动，可以合理地解释这种增强[ Nano Lett. 2017, 17, 4415]。在这里，我们通过对类似模型的广泛布朗动力学模拟来严格检验这些预期。数值结果表明，这两种机制都不能引起与实验报告的增强相媲美的增强，除非引入非常大的、违反物理直觉的酶变形。
