Effect of Water Models on Transmembrane Self-Assembled Cyclic Peptide Nanotubes.
Effect of Water Models on Transmembrane Self-Assembled Cyclic Peptide Nanotubes.
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水模型对跨膜自组装环肽纳米管的影响。
DOI：
10.1021/acsnano.1c00155
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发表时间：
2021-04-27
期刊：
影响因子：
17.1
通讯作者：
Garcia-Fandiño R
中科院分区：
文献类型：
--
作者：
Calvelo M;Lynch CI;Granja JR;Sansom MSP;Garcia-Fandiño R
自组装的环肽纳米管插入脂质双层中时可以形成纳米孔，充当离子和/或水可渗透的通道。为了提高这些系统的通用性，可以特异性地设计具有天然和非天然氨基酸的组合的环肽，从而能够控制通道内腔的性质。在这里，两种类型的自组装肽基序的行为，交替α-氨基酸与γ-或δ-氨基环烷羧酸，通过分子动力学（MD）模拟研究。水分子在纳米孔中的行为预计会影响这些通道的性质，因此值得详细研究。MD模拟中常用的一些水模型已经通过它们如何很好地再现散装水的性质进行了验证。然而，目前尚不清楚这些水模型在通道内的纳米约束条件下的行为。四种不同的水模型-TIP 3 P，TIP 4P，TIP 4P/2005，和OPC-的行为进行了评估，在MD模拟不同的组成和直径的自组装环肽纳米管。在这些设计的人工通道中，水分子和离子的动态行为微妙地取决于所使用的水模型。TIP 3 P水分子的运动速度比TIP 4P、TIP 4P/2005和OPC的水分子运动速度快。这种行为在纳米管的填充、孔隙内的水扩散以及肽与水的氢键的数量和稳定性中清楚地观察到。它还表明，水模型的影响，通过纳米管的模拟离子通量，与TIP 3 P产生最大的离子通量。此外，最近的两个模型，TIP 4P/2005和OPC，这是众所周知的再现实验的自扩散系数的散装水相当不错，表现出非常相似的结果在这里研究的纳米约束条件下。由于这些模型都没有被参数化，特别是沃茨限制在肽纳米管，这项研究提供了一个参考点，进一步验证。
Self-assembling cyclic peptide nanotubes can form nanopores when they are inserted in lipid bilayers, acting as ion and/or water permeable channels. In order to improve the versatility of these systems, it is possible to specifically design cyclic peptides with a combination of natural and non-natural amino acids, enabling the control of the nature of the inner cavity of the channels. Here, the behavior of two types of self-assembling peptide motifs, alternating α-amino acids with γ- or δ-aminocycloalkanecarboxylic acids, is studied via molecular dynamics (MD) simulations. The behavior of water molecules in nanopores is expected to affect the properties of these channels and therefore merits detailed examination. A number of water models commonly used in MD simulations have been validated by how well they reproduce bulk water properties. However, it is less clear how these water models behave in the nanoconfined condition inside a channel. The behavior of four different water models—TIP3P, TIP4P, TIP4P/2005, and OPC—are evaluated in MD simulations of self-assembled cyclic peptide nanotubes of distinct composition and diameter. The dynamic behavior of the water molecules and ions in these designed artificial channels depends subtly on the water model used. TIP3P water molecules move faster than those of TIP4P, TIP4P/2005, and OPC. This demeanor is clearly observed in the filling of the nanotube, in water diffusion within the pore, and in the number and stability of hydrogen bonds of the peptides with water. It was also shown that the water model influences the simulated ion flux through the nanotubes, with TIP3P producing the greatest ion flux. Additionally, the two more recent models, TIP4P/2005 and OPC, which are known to reproduce the experimental self-diffusion coefficient of bulk water quite well, exhibit very similar results under the nanoconfined conditions studied here. Because none of these models have been parametrized specifically for waters confined in peptide nanotubes, this study provides a point of reference for further validation.
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影响因子：
2.1
作者：
Alexiadis, Alessio;Kassinos, Stavros
通讯作者：
Kassinos, Stavros
影响因子：
3.3
作者：
Calvelo, Martin;Granja, Juan R.;Garcia-Fandino, Rebeca
通讯作者：
Garcia-Fandino, Rebeca
影响因子：
2.4
作者：
Detcheverry, Francois;Bocquet, Lyderic
通讯作者：
Bocquet, Lyderic
影响因子：
15
作者：
Clark, TD;Buriak, JM;Ghadiri, MR
通讯作者：
Ghadiri, MR
影响因子：
2.8
作者：
Barker, J. A.;Watts, R. O.
通讯作者：
Watts, R. O.