在低温下，高密度和低密度非晶冰对生物分子的作用：以多聚丙氨酸为例的研究。

The role of high-density and low-density amorphous ice on biomolecules at cryogenic temperatures: a case study with polyalanine.

机构信息

Department of Physics, Brooklyn College of the City University of New York, Brooklyn, New York 11210, USA.

Ph.D. Program in Physics, The Graduate Center of the City University of New York, New York, NY 10016, USA.

出版信息

Phys Chem Chem Phys. 2021 Sep 15;23(35):19402-19414. doi: 10.1039/d1cp02734d.

DOI:10.1039/d1cp02734d

PMID:34494044

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8491127/

Abstract

Experimental techniques, such as cryo-electron microscopy, require biological samples to be recovered at cryogenic temperatures ( ≈ 100 K) with water being in an amorphous ice state. However, (bulk) water can exist in two amorphous ices at < 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 = 400 MPa, and (iii) compression/decompression cycles at = 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).

摘要

实验技术，如冷冻电子显微镜，要求生物样本在低温（约 100 K）下恢复，此时水处于无定形冰状态。然而，（块状）水在 < 1 GPa 时可以存在于两种无定形冰中，即低压低密度无定形冰（LDA）和高压高密度无定形冰（HDA）；HDA 比 LDA 约 20-25%更密集。当在 1 巴下快速/骤冷时，样品进入 LDA，在足够高的压力下进行高压冷却（HPC），则产生 HDA。在低温下等温压缩 LDA 也可以产生 HDA。在这里，我们进行了经典的分子动力学模拟，以研究 LDA、HDA 以及 LDA-HDA 转变对小肽聚丙氨酸结构和水合作用的影响。我们遵循对应于（i）在 1 巴下快速/骤冷、（ii）在 = 400 MPa 下高压冷却和（iii）在 = 80 K 下压缩/减压循环的热力学路径。虽然过程（i）在系统中产生了 LDA，但过程（iii）产生了 HDA。有趣的是，在过程（ii）中产生的无定形冰是一种中间无定形冰（IA），其性质介于 LDA 和 HDA 之间。值得注意的是，即使在低和高密度液态以及无定形固态 LDA、IA 和 HDA 之间水的变化情况下，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。描述了聚丙氨酸在 LDA、IA 和 HDA 中玻璃化水合的异同。由于所研究的热力学路径适用于生物分子的冷冻保存，我们还研究了沿等压和等容加热路径的聚丙氨酸的结构和水合作用，这些路径可以在实验中用于恢复冷冻保存的样品。在加热时，聚丙氨酸的结构几乎没有变化。最后，我们简要讨论了使用 HDA 和 IA 作为冷冻保护剂环境（而不是 LDA）的实际优势，以及使用等容加热作为恢复过程（而不是等压加热）的实际优势。