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使用加权系综方法对细胞穿透肽进行自由能分析。

Free Energy Analyses of Cell-Penetrating Peptides Using the Weighted Ensemble Method.

作者信息

Choe Seungho

机构信息

Department of Energy Science & Engineering, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu 42988, Korea.

Energy Science & Engineering Research Center, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu 42988, Korea.

出版信息

Membranes (Basel). 2021 Dec 9;11(12):974. doi: 10.3390/membranes11120974.

DOI:10.3390/membranes11120974
PMID:34940475
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8706838/
Abstract

Cell-penetrating peptides (CPPs) have been widely used for drug-delivery agents; however, it has not been fully understood how they translocate across cell membranes. The Weighted Ensemble (WE) method, one of the most powerful and flexible path sampling techniques, can be helpful to reveal translocation paths and free energy barriers along those paths. Within the WE approach we show how Arg9 (nona-arginine) and Tat interact with a DOPC/DOPG(4:1) model membrane, and we present free energy (or potential mean of forces, PMFs) profiles of penetration, although a translocation across the membrane has not been observed in the current simulations. Two different compositions of lipid molecules were also tried and compared. Our approach can be applied to any CPPs interacting with various model membranes, and it will provide useful information regarding the transport mechanisms of CPPs.

摘要

细胞穿透肽（CPPs）已被广泛用作药物递送剂；然而，它们如何跨细胞膜转运尚未完全清楚。加权系综（WE）方法是最强大、最灵活的路径采样技术之一，有助于揭示转运路径以及沿这些路径的自由能垒。在WE方法中，我们展示了精氨酸9（九聚精氨酸）和Tat如何与DOPC/DOPG（4:1）模型膜相互作用，并给出了穿透的自由能（或平均力势，PMF）分布，尽管在当前模拟中尚未观察到跨膜转运。还尝试并比较了两种不同组成的脂质分子。我们的方法可应用于任何与各种模型膜相互作用的CPPs，并将提供有关CPPs转运机制的有用信息。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3696/8706838/caa91af65835/membranes-11-00974-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3696/8706838/6d7a8dfc3ef8/membranes-11-00974-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3696/8706838/c559ef9c32d8/membranes-11-00974-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3696/8706838/d0e2ce1b0619/membranes-11-00974-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3696/8706838/b22f5ae959df/membranes-11-00974-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3696/8706838/68df01deaa66/membranes-11-00974-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3696/8706838/caa91af65835/membranes-11-00974-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3696/8706838/6d7a8dfc3ef8/membranes-11-00974-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3696/8706838/c559ef9c32d8/membranes-11-00974-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3696/8706838/d0e2ce1b0619/membranes-11-00974-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3696/8706838/b22f5ae959df/membranes-11-00974-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3696/8706838/68df01deaa66/membranes-11-00974-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3696/8706838/caa91af65835/membranes-11-00974-g006.jpg

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引用本文的文献

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Sci Rep. 2023 Jan 20;13(1):1168. doi: 10.1038/s41598-023-28493-4.
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Interaction of Arginine-Rich Cell-Penetrating Peptides with an Artificial Neuronal Membrane.富含精氨酸的细胞穿透肽与人工神经元膜的相互作用。
Cells. 2022 May 13;11(10):1638. doi: 10.3390/cells11101638.

本文引用的文献

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2
Cell-Penetrating Peptides: Correlation between Peptide-Lipid Interaction and Penetration Efficiency.细胞穿透肽：肽-脂质相互作用与穿透效率的相关性。
Chemphyschem. 2021 Mar 3;22(5):493-498. doi: 10.1002/cphc.202000873. Epub 2021 Feb 1.
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A Suite of Tutorials for the WESTPA Rare-Events Sampling Software [Article v1.0].WESTPA稀有事件采样软件教程套件[文章版本1.0]
Living J Comput Mol Sci. 2019;1(2). doi: 10.33011/livecoms.1.2.10607. Epub 2019 Oct 4.
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Internalization mechanisms of cell-penetrating peptides.细胞穿透肽的内化机制
Beilstein J Nanotechnol. 2020 Jan 9;11:101-123. doi: 10.3762/bjnano.11.10. eCollection 2020.
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Interaction of a Polyarginine Peptide with Membranes of Different Mechanical Properties.多精氨酸肽与不同力学性质的膜的相互作用。
Biomolecules. 2019 Oct 18;9(10):625. doi: 10.3390/biom9100625.
6
Elementary processes for the entry of cell-penetrating peptides into lipid bilayer vesicles and bacterial cells.细胞穿透肽进入脂质双分子层囊泡和细菌细胞的基本过程。
Appl Microbiol Biotechnol. 2018 May;102(9):3879-3892. doi: 10.1007/s00253-018-8889-5. Epub 2018 Mar 9.
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Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.用于大型生物分子系统的恒pH分子动力学模拟
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Self-association of a highly charged arginine-rich cell-penetrating peptide.带正电荷的富含精氨酸的细胞穿透肽的自缔合。
Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):11428-11433. doi: 10.1073/pnas.1712078114. Epub 2017 Oct 11.
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