Department of Chemistry , Georgetown University , Washington , DC 20057 , United States.
Institute of Materials Science and Department of Civil and Environmental Engineering , The George Washington University , Washington , DC 20052 , United States.
J Phys Chem B. 2018 May 31;122(21):5527-5533. doi: 10.1021/acs.jpcb.7b11838. Epub 2018 Feb 8.
A quasiharmonic analysis (QHA) method is used to compare the potential energy landscapes of dihydrofolate reductase (DHFR) from a piezophile (pressure-loving organism), Moritella profunda (Mp), and a mesophile, Escherichia coli (Ec). The QHA method considers atomic fluctuations of the protein as motions of an atom in a local effective potential created by neighboring atoms and quantitates it in terms of effective force constants, isothermal compressibilities, and thermal expansivities. The analysis indicates that the underlying potential energy surface of MpDHFR is inherently softer than that of EcDHFR. In addition, on picosecond time scales, the energy surfaces become more similar under the growth conditions of Mp and Ec. On these time scales, DHFR behaves as expected; namely, increasing temperature makes the effective energy minimum less steep because thermal fluctuations increase the available volume, whereas increasing pressure steepens it because compression reduces the available volume. Our longer simulations show that, on nanosecond time scales, increasing temperature has a similar effect as on picosecond time scales because thermal fluctuations increase the volume even more on a longer time scale. However, these simulations also indicate that, on nanosecond time scales, pressure makes the local potential less steep, contrary to picosecond time scales. Further examination of the QHA indicates the nanosecond pressure response may originate at picosecond time scales at the exterior of the protein, which suggests that protein-water interactions may be involved. The results may lead to understanding adaptations in enzymes made by piezophiles that enable them to function at higher pressures.
采用准谐分析（QHA）方法比较了嗜压生物摩氏摩根菌（Moritella profunda，Mp）二氢叶酸还原酶（DHFR）和中温生物大肠杆菌（Escherichia coli，Ec）DHFR 的势能景观。QHA 方法将蛋白质的原子波动视为原子在由相邻原子产生的局部有效势能中的运动，并用量子有效力常数、等温压缩率和热膨胀率对其进行量化。分析表明，MpDHFR 的潜在势能表面固有地比 EcDHFR 的柔软。此外，在皮秒时间尺度上，在 Mp 和 Ec 的生长条件下，能量表面变得更加相似。在这些时间尺度上，DHFR 的行为符合预期；即，升高温度会使有效能量最小化变得不那么陡峭，因为热波动会增加可用体积，而升高压力会使它变得陡峭，因为压缩会减少可用体积。我们的更长时间模拟表明，在纳秒时间尺度上，升高温度的效果与皮秒时间尺度相似，因为热波动在更长的时间尺度上会进一步增加体积。然而，这些模拟还表明，在纳秒时间尺度上，压力会使局部势能变得不那么陡峭，与皮秒时间尺度相反。对 QHA 的进一步检查表明，纳秒时间尺度上的压力响应可能起源于蛋白质外部的皮秒时间尺度，这表明蛋白质-水相互作用可能涉及其中。这些结果可能有助于理解嗜压生物酶的适应性，使它们能够在更高的压力下发挥作用。
