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Piskorz T, Perez-Chirinos L, Qiao B, Sasselli IR. Tips and Tricks in the Modeling of Supramolecular Peptide Assemblies. ACS OMEGA 2024; 9:31254-31273. [PMID: 39072142 PMCID: PMC11270692 DOI: 10.1021/acsomega.4c02628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/30/2024]
Abstract
Supramolecular peptide assemblies (SPAs) hold promise as materials for nanotechnology and biomedicine. Although their investigation often entails adapting experimental techniques from their protein counterparts, SPAs are fundamentally distinct from proteins, posing unique challenges for their study. Computational methods have emerged as indispensable tools for gaining deeper insights into SPA structures at the molecular level, surpassing the limitations of experimental techniques, and as screening tools to reduce the experimental search space. However, computational studies have grappled with issues stemming from the absence of standardized procedures and relevant crystal structures. Fundamental disparities between SPAs and protein simulations, such as the absence of experimentally validated initial structures and the importance of the simulation size, number of molecules, and concentration, have compounded these challenges. Understanding the roles of various parameters and the capabilities of different models and simulation setups remains an ongoing endeavor. In this review, we aim to provide readers with guidance on the parameters to consider when conducting SPA simulations, elucidating their potential impact on outcomes and validity.
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Affiliation(s)
| | - Laura Perez-Chirinos
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 182, 20014 Donostia-San Sebastián, Spain
| | - Baofu Qiao
- Department
of Natural Sciences, Baruch College, City
University of New York, New York, New York 10010, United States
| | - Ivan R. Sasselli
- Centro
de Física de Materiales (CFM), CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
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2
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Sasselli IR, Coluzza I. Assessment of the MARTINI 3 Performance for Short Peptide Self-Assembly. J Chem Theory Comput 2024; 20:224-238. [PMID: 38113378 PMCID: PMC10782451 DOI: 10.1021/acs.jctc.3c01015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023]
Abstract
The coarse-grained MARTINI force field, initially developed for membranes, has proven to be an exceptional tool for investigating supramolecular peptide assemblies. Over the years, the force field underwent refinements to enhance accuracy, enabling, for example, the reproduction of protein-ligand interactions and constant pH behavior. However, these protein-focused improvements seem to have compromised its ability to model short peptide self-assembly. In this study, we assess the performance of MARTINI 3 in reproducing peptide self-assembly using the well-established diphenylalanine (FF) as our test case. Unlike its success in version 2.1, FF does not even exhibit aggregation in version 3. By systematically exploring parameters for the aromatic side chains and charged backbone beads, we established a parameter set that effectively reproduces tube formation. Remarkably, these parameter adjustments also replicate the self-assembly of other di- and tripeptides and coassemblies. Furthermore, our analysis uncovers pivotal insights for enhancing the performance of MARTINI in modeling short peptide self-assembly. Specifically, we identify issues stemming from overestimated hydrophilicity arising from charged termini and disruptions in π-stacking interactions due to insufficient planarity in aromatic groups and a discrepancy in intermolecular distances between this and backbone-backbone interactions. This investigation demonstrates that strategic modifications can harness the advancements offered by MARTINI 3 for the realm of short peptide self-assembly.
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Affiliation(s)
- Ivan R. Sasselli
- Centro
de Física de Materiales (CFM), CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research
and Technology Alliance (BRTA), Paseo de Miramón 182, 20014 Donostia-San Sebastián, Spain
| | - Ivan Coluzza
- Ikerbasque,
Basque Foundation for Science, Plaza de Euskadi 5, 48009 Bilbao, Spain
- BCMaterials,
Basque Center for Materials, Applications and Nanostructures, UPV/EHU Science Park, 48940 Leioa, Spain
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3
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Hu T, Xu Y, Xu G. Dipeptide-polysaccharides hydrogels through co-assembly. Food Chem 2023; 422:136272. [PMID: 37141751 DOI: 10.1016/j.foodchem.2023.136272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/27/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023]
Abstract
Self-assembling dipeptide hydrogels are attracting attention in food, materials, and biomedicine. However, there are still limitations such as weak hydrogel properties. Herein, we introduced two types of polysaccharides (Arabic gum and citrus pectin) into an alkyl-chain modified dipeptide (C13-tryptophan-tyrosine (C13-WY)) to generate co-assembled C13-WY-arabic gum and C13-WY-pectin hydrogels. The co-assembled hydrogels exhibited enhanced mechanical properties and stability. The G' value of C13-WY-arabic gum and C13-WY-pectin hydrogels was 3 and 10 times larger than that of C13-WY hydrogel, respectively. The addition of Arabic gum and citrus pectin led to the co-assembly and molecular rearrangement. Moreover, co-assembled hydrogels showed more β-sheet structure and hydrogen bonds. Importantly, the self-/co-assembled hydrogels showed low cytotoxicity. We utilized these hydrogels for the encapsulation of docetaxel and they showed a high embedding rate and slow-release. Our findings provide a novel strategy for the development of stable supramolecular peptide hydrogels with good biocompatibility through simple co-assembly.
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Affiliation(s)
- Tan Hu
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; College of Food Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Wuhan, Hubei 430070, China; Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, China.
| | - Yang Xu
- College of Food Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Wuhan, Hubei 430070, China; Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, China
| | - Gang Xu
- College of Food Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Wuhan, Hubei 430070, China; Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, China
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4
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Co-assembled C13-dipeptide hydrogels by Gallic Acid (CA) and epigallocatechin gallate (EGCG) with antibacterial activity. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.101962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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5
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Hu T, Xu Y, Xu G, Pan S. Sequence-Selected C 13-Dipeptide Self-Assembled Hydrogels for Encapsulation of Lemon Essential Oil with Antibacterial Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:7148-7157. [PMID: 35657010 DOI: 10.1021/acs.jafc.2c02385] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Supramolecular self-assembling peptide hydrogels are attracting attention. The switching of even one amino acid may lead to differences in structure and functions of peptide hydrogels. Herein, we investigate the effect of substitution of a single amino acid residue on the gelation properties of C13-dipeptide hydrogels. We show that four C13-R1Y (C13-VY, C13-FY, C13-WY, and C13-YY) can form hydrogels with drastically tunable rigidity (the G' values were 5.74, 0.16, 27.74, and 67.90 KPa, respectively). Moreover, C13-WY and C13-YY hydrogels with high stability and excellent mechanical properties formed β-sheet nanofiber cross-linked networks. Furthermore, we applied four hydrogels into encapsulation of lemon essential oil (LEO). The peptide hydrogels had a high encapsulation rate and slowly released the LEO. Importantly, the LEO-loaded hydrogels showed enhanced antibacterial activity than free LEO. Our results clearly demonstrate the significance of side-chain interactions in determining hydrogel properties and their potential application in encapsulation for nutrition agents and hydrophobic drugs.
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Affiliation(s)
- Tan Hu
- College of Food Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Wuhan, Hubei 430070, PR China
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
- Hubei Key Laboratory of Fruit & Vegetable Processing & Quality Control (Huazhong Agricultural University), Wuhan, Hubei, 430070, PR China
| | - Yang Xu
- College of Food Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Wuhan, Hubei 430070, PR China
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
- Hubei Key Laboratory of Fruit & Vegetable Processing & Quality Control (Huazhong Agricultural University), Wuhan, Hubei, 430070, PR China
| | - Gang Xu
- College of Food Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Wuhan, Hubei 430070, PR China
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
- Hubei Key Laboratory of Fruit & Vegetable Processing & Quality Control (Huazhong Agricultural University), Wuhan, Hubei, 430070, PR China
| | - Siyi Pan
- College of Food Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Wuhan, Hubei 430070, PR China
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
- Hubei Key Laboratory of Fruit & Vegetable Processing & Quality Control (Huazhong Agricultural University), Wuhan, Hubei, 430070, PR China
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Li L, Xie L, Zheng R, Sun R. Self-Assembly Dipeptide Hydrogel: The Structures and Properties. Front Chem 2021; 9:739791. [PMID: 34540806 PMCID: PMC8440803 DOI: 10.3389/fchem.2021.739791] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/09/2021] [Indexed: 01/20/2023] Open
Abstract
Self-assembly peptide-based hydrogels are well known and popular in biomedical applications due to the fact that they are readily controllable and have biocompatibility properties. A dipeptide is the shortest self-assembling motif of peptides. Due to its small size and simple synthesis method, dipeptide can provide a simple and easy-to-use method to study the mechanism of peptides' self-assembly. This review describes the design and structures of self-assembly linear dipeptide hydrogels. The strategies for preparing the new generation of linear dipeptide hydrogels can be divided into three categories based on the modification site of dipeptide: 1) COOH-terminal and N-terminal modified dipeptide, 2) C-terminal modified dipeptide, and 3) uncapped dipeptide. With a deeper understanding of the relationship between the structures and properties of dipeptides, we believe that dipeptide hydrogels have great potential application in preparing minimal biocompatible materials.
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Affiliation(s)
- Liangchun Li
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Li Xie
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Renlin Zheng
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Rongqin Sun
- School of Materials Science and Engineering, Southwest University of Science and Technology, Mianyang, China
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7
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Scarel M, Marchesan S. Diketopiperazine Gels: New Horizons from the Self-Assembly of Cyclic Dipeptides. Molecules 2021; 26:3376. [PMID: 34204905 PMCID: PMC8199760 DOI: 10.3390/molecules26113376] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/01/2021] [Accepted: 06/01/2021] [Indexed: 02/07/2023] Open
Abstract
Cyclodipeptides (CDPs) or 2,5-diketopiperazines (DKPs) can exert a variety of biological activities and display pronounced resistance against enzymatic hydrolysis as well as a propensity towards self-assembly into gels, relative to the linear-dipeptide counterparts. They have attracted great interest in a variety of fields spanning from functional materials to drug discovery. This concise review will analyze the latest advancements in their synthesis, self-assembly into gels, and their more innovative applications.
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Affiliation(s)
- Marco Scarel
- Chemical and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy;
| | - Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy;
- National Interuniversity Consortium of Materials Science and Technology (INSTM), University of Trieste, 34127 Trieste, Italy
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Chibh S, Mishra J, Kour A, Chauhan VS, Panda JJ. Recent advances in the fabrication and bio-medical applications of self-assembled dipeptide nanostructures. Nanomedicine (Lond) 2021; 16:139-163. [PMID: 33480272 DOI: 10.2217/nnm-2020-0314] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Molecular self-assembly is a widespread natural phenomenon and has inspired several researchers to synthesize a compendium of nano/microstructures with widespread applications. Biomolecules like proteins, peptides and lipids are used as building blocks to fabricate various nanomaterials. Supramolecular peptide self-assembly continue to play a significant role in forming diverse nanostructures with numerous biomedical applications; however, dipeptides offer distinctive supremacy in their ability to self-assemble and produce a variety of nanostructures. Though several reviews have articulated the progress in the field of longer peptides or polymers and their self-assembling behavior, there is a paucity of reviews or literature covering the emerging field of dipeptide-based nanostructures. In this review, our goal is to present the recent advancements in dipeptide-based nanostructures with their potential applications.
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Affiliation(s)
- Sonika Chibh
- Chemical Biology Unit, Institute of Nano Science & Technology, Mohali, Punjab 160062, India
| | - Jibanananda Mishra
- Cell and Molecular Biology Division, AAL Research & Solutions Pvt. Ltd., Panchkula, Haryana 134113, India
| | - Avneet Kour
- Chemical Biology Unit, Institute of Nano Science & Technology, Mohali, Punjab 160062, India
| | - Virander S Chauhan
- International Centre for Genetic Engineering & Biotechnology, New Delhi 110067, India
| | - Jiban J Panda
- Chemical Biology Unit, Institute of Nano Science & Technology, Mohali, Punjab 160062, India
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Hu T, Zhang Z, Euston SR, Geng M, Pan S. Coassembly of C 13-Dipeptides: Gelations from Solutions and Precipitations. Biomacromolecules 2020; 21:5256-5268. [PMID: 33201680 DOI: 10.1021/acs.biomac.0c01325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
C13-dipeptides that did not gel on their own were found to form hydrogels when combined with mixtures (coassembly). At pH = 4.6, by mixing negatively charged C13-WD (C13-WD2- and/or C13-WD-) with C13-KW or C13-YK, where the side chain of K carried positive charge, two composite hydrogels with different mechanical properties were formed. The gels exhibited various fiber structures that would account for their individual functionalities. According to molecular dynamics computer simulations, the composite systems formed spherical micelles through hydrophobic interactions that further aggregate to form gels through electrostatic interactions. The electrostatic repulsions between C13-WD molecules were interfered by insertions of C13-KW or C13-YK molecules, which result in gel formation in the composite systems. The results of computer simulations well explained the experimental observations, which provided new insights into the design and selection strategies for peptide gelators.
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Affiliation(s)
- Tan Hu
- College of Food Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Wuhan, Hubei 430070, PR China.,Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Ministry of Education, Wuhan, Hubei 430070, PR China
| | - Zhuo Zhang
- College of Food Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Wuhan, Hubei 430070, PR China.,Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Ministry of Education, Wuhan, Hubei 430070, PR China
| | - Stephen Robert Euston
- Institute of Mechanical, Process & Energy Engineering School of Engineering & Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K
| | - Mengjie Geng
- College of Food Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Wuhan, Hubei 430070, PR China.,Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Ministry of Education, Wuhan, Hubei 430070, PR China
| | - Siyi Pan
- College of Food Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Wuhan, Hubei 430070, PR China.,Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Ministry of Education, Wuhan, Hubei 430070, PR China
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10
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Das AK, Gavel PK. Low molecular weight self-assembling peptide-based materials for cell culture, antimicrobial, anti-inflammatory, wound healing, anticancer, drug delivery, bioimaging and 3D bioprinting applications. SOFT MATTER 2020; 16:10065-10095. [PMID: 33073836 DOI: 10.1039/d0sm01136c] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this review, we have focused on the design and development of low molecular weight self-assembling peptide-based materials for various applications including cell proliferation, tissue engineering, antibacterial, antifungal, anti-inflammatory, anticancer, wound healing, drug delivery, bioimaging and 3D bioprinting. The first part of the review describes about stimuli and various noncovalent interactions, which are the key components of various self-assembly processes for the construction of organized structures. Subsequently, the chemical functionalization of the peptides has been discussed, which is required for the designing of self-assembling peptide-based soft materials. Various low molecular weight self-assembling peptides have been discussed to explain the important structural features for the construction of defined functional nanostructures. Finally, we have discussed various examples of low molecular weight self-assembling peptide-based materials for cell culture, antimicrobial, anti-inflammatory, anticancer, wound healing, drug delivery, bioimaging and 3D bioprinting applications.
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Affiliation(s)
- Apurba K Das
- Department of Chemistry, Indian Institute of Technology Indore, Indore 453552, India.
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Thomson L, Schweins R, Draper ER, Adams DJ. Creating Transient Gradients in Supramolecular Hydrogels. Macromol Rapid Commun 2020; 41:e2000093. [PMID: 32297369 DOI: 10.1002/marc.202000093] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 12/25/2022]
Abstract
The self-assembly of low molecular weight gelators in water usually produces homogeneous hydrogels. However, homogeneous gels are not always desired. Using a photoacid generator, it is shown how to form gels with a transient gradient in stiffness, proved using cavitation and bulk rheology. Small-angle neutron scattering is used to show that the gels formed by photoacid are the result of the same structures as when using a conventional pH trigger. Patterned gels can also be formed, again with transient differences in stiffness.
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Affiliation(s)
- Lisa Thomson
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, Scotland
| | - Ralf Schweins
- Large Scale Structures Group, Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042 GRENOBLE, Cedex 9, France
| | - Emily R Draper
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, Scotland
| | - Dave J Adams
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, Scotland
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