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计算与实验相结合：高效纤维状肽的鉴定

Computation meets experiment: identification of highly efficient fibrillating peptides.

作者信息

Sori Lorenzo, Pizzi Andrea, Bergamaschi Greta, Gori Alessandro, Gautieri Alfonso, Demitri Nicola, Soncini Monica, Metrangolo Pierangelo

机构信息

Laboratory of Supramolecular and BioNano Materials (SupraBioNanoLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano Via Luigi Mancinelli 7 20131 Milan Italy

Istituto di Scienze e Tecnologie Chimiche - National Research Council of Italy (SCITEC-CNR) 20131 Milan Italy.

出版信息

CrystEngComm. 2023 Jul 4;25(32):4503-4510. doi: 10.1039/d3ce00495c. eCollection 2023 Aug 14.

DOI:10.1039/d3ce00495c
PMID:38014394
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10424810/
Abstract

Self-assembling peptides are of huge interest for biological, medical and nanotechnological applications. The enormous chemical variety that is available from the 20 amino acids offers potentially unlimited peptide sequences, but it is currently an issue to predict their supramolecular behavior in a reliable and cheap way. Herein we report a computational method to screen and forecast the aqueous self-assembly propensity of amyloidogenic pentapeptides. This method was found also as an interesting tool to predict peptide crystallinity, which may be of interest for the development of peptide based drugs.

摘要

自组装肽在生物学、医学和纳米技术应用方面具有巨大的研究价值。由20种氨基酸构成的巨大化学多样性提供了潜在无限的肽序列，但目前以可靠且经济的方式预测它们的超分子行为仍是一个问题。在此，我们报告一种计算方法，用于筛选和预测淀粉样五肽的水相自组装倾向。该方法还被发现是预测肽结晶度的一种有趣工具，这对于基于肽的药物开发可能具有重要意义。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1706/10424810/8f37396ad003/d3ce00495c-f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1706/10424810/6a85a3e0da8e/d3ce00495c-f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1706/10424810/dfa88612620c/d3ce00495c-f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1706/10424810/49c089de66c2/d3ce00495c-s1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1706/10424810/48a224f15ff4/d3ce00495c-f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1706/10424810/4cd35d9f9131/d3ce00495c-f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1706/10424810/5f796e409e1c/d3ce00495c-f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1706/10424810/8f37396ad003/d3ce00495c-f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1706/10424810/6a85a3e0da8e/d3ce00495c-f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1706/10424810/dfa88612620c/d3ce00495c-f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1706/10424810/49c089de66c2/d3ce00495c-s1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1706/10424810/48a224f15ff4/d3ce00495c-f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1706/10424810/4cd35d9f9131/d3ce00495c-f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1706/10424810/5f796e409e1c/d3ce00495c-f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1706/10424810/8f37396ad003/d3ce00495c-f6.jpg

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本文引用的文献

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Emergence of Elastic Properties in a Minimalist Resilin-Derived Heptapeptide upon Bromination.溴化作用导致最小化弹性蛋白衍生七肽中弹性性能的出现。
Small. 2022 Aug;18(32):e2200807. doi: 10.1002/smll.202200807. Epub 2022 Jun 20.
2
Fibril Structure Demonstrates the Role of Iodine Labelling on a Pentapeptide Self-Assembly.纤维结构证明了碘标记在五肽自组装中的作用。
Chemistry. 2022 Mar 7;28(14):e202104089. doi: 10.1002/chem.202104089. Epub 2022 Feb 17.
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A hybrid coarse-grained model for structure, solvation and assembly of lipid-like peptides.
一种用于类脂肽结构、溶剂化和组装的混合粗粒度模型。
Phys Chem Chem Phys. 2022 Jan 19;24(3):1553-1568. doi: 10.1039/d1cp04205j.
4
Coarse-grained simulation of the self-assembly of lipid vesicles concomitantly with novel block copolymers with multiple tails.多尾新型嵌段共聚物伴随脂质囊泡自组装的粗粒化模拟。
Soft Matter. 2021 Mar 18;17(10):2753-2764. doi: 10.1039/d0sm01898h.
5
Discovery of Self-Assembling π-Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation.通过主动学习导向的粗粒度分子模拟发现自组装π共轭肽
J Phys Chem B. 2020 May 14;124(19):3873-3891. doi: 10.1021/acs.jpcb.0c00708. Epub 2020 Mar 30.
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: from visualization to analysis, design and prediction.从可视化到分析、设计与预测。
J Appl Crystallogr. 2020 Feb 1;53(Pt 1):226-235. doi: 10.1107/S1600576719014092.
7
Modulating amyloid fibrillation in a minimalist model peptide by intermolecular disulfide chemical reduction.通过分子间二硫键化学还原调节最小模型肽的淀粉样纤维形成。
Phys Chem Chem Phys. 2019 Jun 5;21(22):11916-11923. doi: 10.1039/c9cp01846h.
8
Coarse-Grained Simulations of Peptide Nanoparticle Formation: Role of Local Structure and Nonbonded Interactions.多肽纳米颗粒形成的粗粒化模拟：局部结构和非键相互作用的作用。
J Chem Theory Comput. 2019 Feb 12;15(2):1453-1462. doi: 10.1021/acs.jctc.8b01138. Epub 2019 Jan 30.
9
Guiding principles for peptide nanotechnology through directed discovery.通过定向发现指导肽纳米技术的原则。
Chem Soc Rev. 2018 May 21;47(10):3737-3758. doi: 10.1039/c8cs00177d.
10
Crystallographic insights into the self-assembly of KLVFF amyloid-beta peptides.KLVFF淀粉样β肽自组装的晶体学见解。
Biopolymers. 2017 Nov 27. doi: 10.1002/bip.23088.