The role of high-density and low-density amorphous ice on biomolecules at cryogenic temperatures: a case study with polyalanine.
The role of high-density and low-density amorphous ice on biomolecules at cryogenic temperatures: a case study with polyalanine.
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DOI：
10.1039/d1cp02734d
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发表时间：
2021-09-15
期刊：
影响因子：
--
通讯作者：
Giovambattista N
中科院分区：
文献类型：
--
作者：
Eltareb A;Lopez GE;Giovambattista N
冷冻电子显微镜等实验技术要求在低温 (T ≈ 100 K) 下回收生物样品，且水处于无定形冰态。然而，（大量）水可以存在于 P < 1 GPa 的两种非晶冰中，即低压下的低密度非晶冰（LDA）和高压下的高密度非晶冰（HDA）； HDA 的密度比 LDA 高约 20 – 25%。 1 bar 的快速/切入冷却将样品带入 LDA，而高压冷却 (HPC) 在足够高的压力下产生 HDA。 HDA 也可以通过在低温下等温压缩 LDA 来生产。在这里，我们进行经典的分子动力学模拟来研究 LDA、HDA 和 LDA-HDA 转化对小肽聚丙氨酸的结构和水合的影响。我们遵循的热力学路径对应于 (i) 1 bar 下的快速/切入冷却，(ii) P = 400 MPa 下的 HPC，以及 (iii) T = 80 K 下的压缩/减压循环。过程 (i) 在系统中产生 LDA，而路径 (iii) 则产生 HDA。有趣的是，过程(ii)中产生的无定形冰是中间无定形冰(IA)，其性质介于LDA和HDA之间。值得注意的是，即使水在低密度和高密度液态以及无定形固体 LDA、IA 和 HDA 之间变化，聚丙氨酸的结构变化在所有研究条件（0 – 2000 MPa、80 – 300 K）下都可以忽略不计。描述了 LDA、IA 和 HDA 中玻璃化聚丙氨酸水合的异同。由于所研究的热力学路径适用于生物分子的低温保存，因此我们还研究了聚丙氨酸沿等压和等容加热路径的结构和水合，这可以通过实验进行跟踪以恢复低温保存的样品。加热后，聚丙氨酸的结构实际上保持不变。最后，我们简要讨论了 (a) 使用 HDA 和 IA 作为冷冻保护环境（相对于 LDA），以及 (b) 使用等容加热作为恢复过程（相对于等压加热）的实际优势。
Experimental techniques, such as cryo-electron microscopy, require biological samples to be recovered at cryogenic temperatures (T ≈ 100 K) with water being in an amorphous ice state. However, (bulk) water can exist in two amorphous ices at P < 1 GPa, low-density amorphous (LDA) ice at low pressures and high-density amorphous ice (HDA) at high pressures; HDA is ≈ 20 – 25% denser than LDA. While fast/plunge cooling at 1 bar brings the sample into LDA, high-pressure cooling (HPC), at sufficiently high pressure, produces HDA. HDA can also be produced by isothermal compression of LDA at cryogenic temperatures. Here, we perform classical molecular dynamics simulations to study the effects of LDA, HDA, and the LDA-HDA transformation on the structure and hydration of a small peptide, polyalanine. We follow thermodynamic paths corresponding to (i) fast/plunge cooling at 1 bar, (ii) HPC at P = 400 MPa, and (iii) compression/decompression cycles at T = 80 K. While process (i) produced LDA in the system, path (iii) produces HDA. Interestingly, the amorphous ice produced in process (ii) is an intermediate amorphous ice (IA) with properties that fall in-between those of LDA and HDA. Remarkably, the structural changes in polyalanine are negligible at all conditions studied (0 – 2000 MPa, 80 – 300 K) even when water changes among the low and high-density liquid states as well as the amorphous solids LDA, IA, and HDA. The similarities and differences in the hydration of polyalanine vitrified in LDA, IA, and HDA are described. Since the studied thermodynamic paths are suitable for the cryopreservation of biomolecules, we also study the structure and hydration of polyalanine along isobaric and isochoric heating paths, which can be followed experimentally for the recovery of cryopreserved samples. Upon heating, the structure of polyalanine remains practically unchanged. We conclude with a brief discussion of the practical advantages of (a) using HDA and IA as a cryoprotectant environment (as opposed to LDA), and (b) the use of isochoric heating as a recovery process (as opposed to isobaric heating).
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