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Yang X, Ma L, Lu K, Zhao D. Mechanism of Peptide Self-assembly and Its Study in Biomedicine. Protein J 2024; 43:464-476. [PMID: 38676873 DOI: 10.1007/s10930-024-10200-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2024] [Indexed: 04/29/2024]
Abstract
The development of peptide-based materials is one of the most challenging aspects of biomaterials research in recent years. The assembly of peptides is mainly controlled by forces such as hydrogen bonding, hydrophobic interaction, electrostatic interaction, and π-π accumulation. Peptides have unique advantages such as simple structure, easy synthesis, good biocompatibility, non-toxicity, easy modification, etc. These factors make peptides turn into ideal biomedical materials, and they have a broad application prospect in biomedical materials, and thus have received wide attention. In this review, the mechanism and classification of peptide self-assembly and its applications in biomedicine and hydrogels were introduced.
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Affiliation(s)
- Xinyue Yang
- School of Chemistry and Chemical Engineering, Henan University of Technology, Locus Street, High-Tech Industry Development Zone, Zhengzhou, 450001, Henan, China
| | - Li Ma
- School of Chemistry and Chemical Engineering, Henan University of Technology, Locus Street, High-Tech Industry Development Zone, Zhengzhou, 450001, Henan, China
| | - Kui Lu
- School of Chemistry and Chemical Engineering, Henan University of Technology, Locus Street, High-Tech Industry Development Zone, Zhengzhou, 450001, Henan, China
| | - Dongxin Zhao
- School of Chemistry and Chemical Engineering, Henan University of Technology, Locus Street, High-Tech Industry Development Zone, Zhengzhou, 450001, Henan, China.
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Yang Y, Wang X, Dong H. Simulating chemical reactions promoted by self-assembled peptides with catalytic properties. Methods Enzymol 2024; 697:321-343. [PMID: 38816128 DOI: 10.1016/bs.mie.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Peptides that self-assemble exhibit distinct three-dimensional structures and attributes, positioning them as promising candidates for biocatalysts. Exploring their catalytic processes enhances our comprehension of the catalytic actions inherent to self-assembling peptides, laying a theoretical foundation for creating novel biocatalysts. The investigation into the intricate reaction mechanisms of these entities is rendered challenging due to the vast variability in peptide sequences, their aggregated formations, supportive elements, structures of active sites, types of catalytic reactions, and the interplay between these variables. This complexity hampers the elucidation of the linkage between sequence, structure, and catalytic efficiency in self-assembling peptide catalysts. This chapter delves into the latest progress in understanding the mechanisms behind peptide self-assembly, serving as a catalyst in hydrolysis and oxidation reactions, and employing computational analyses. It discusses the establishment of models, selection of computational strategies, and analysis of computational procedures, emphasizing the application of modeling techniques in probing the catalytic mechanisms of peptide self-assemblies. It also looks ahead to the potential future trajectories within this research domain. Despite facing numerous obstacles, a thorough investigation into the structural and catalytic mechanisms of peptide self-assemblies, combined with the ongoing advancement in computational simulations and experimental methodologies, is set to offer valuable theoretical insights for the development of new biocatalysts, thereby significantly advancing the biocatalysis field.
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Affiliation(s)
- Yuqin Yang
- Kuang Yaming Honors School, Nanjing University, Nanjing, P.R. China
| | - Xiaoyu Wang
- Kuang Yaming Honors School, Nanjing University, Nanjing, P.R. China
| | - Hao Dong
- Kuang Yaming Honors School, Nanjing University, Nanjing, P.R. China; State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute for Brain Sciences, Nanjing University, Nanjing, P.R. China.
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Warren JP, Culbert MP, Miles DE, Maude S, Wilcox RK, Beales PA. Controlling the Self-Assembly and Material Properties of β-Sheet Peptide Hydrogels by Modulating Intermolecular Interactions. Gels 2023; 9:441. [PMID: 37367112 DOI: 10.3390/gels9060441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/19/2023] [Accepted: 05/21/2023] [Indexed: 06/28/2023] Open
Abstract
Self-assembling peptides are a promising biomaterial with potential applications in medical devices and drug delivery. In the right combination of conditions, self-assembling peptides can form self-supporting hydrogels. Here, we describe how balancing attractive and repulsive intermolecular forces is critical for successful hydrogel formation. Electrostatic repulsion is tuned by altering the peptide's net charge, and intermolecular attractions are controlled through the degree of hydrogen bonding between specific amino acid residues. We find that an overall net peptide charge of +/-2 is optimal to facilitate the assembly of self-supporting hydrogels. If the net peptide charge is too low then dense aggregates form, while a high molecular charge inhibits the formation of larger structures. At a constant charge, altering the terminal amino acids from glutamine to serine decreases the degree of hydrogen bonding within the assembling network. This tunes the viscoelastic properties of the gel, reducing the elastic modulus by two to three orders of magnitude. Finally, hydrogels could be formed from glutamine-rich, highly charged peptides by mixing the peptides in combinations with a resultant net charge of +/-2. These results illustrate how understanding and controlling self-assembly mechanisms through modulating intermolecular interactions can be exploited to derive a range of structures with tuneable properties.
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Affiliation(s)
- James P Warren
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
- School of Mechanical Engineering, University of Leeds, Leeds LS2 9JT, UK
- Institute of Medical and Biological Engineering, University of Leeds, Leeds LS2 9JT, UK
- Bragg Centre for Materials Research, University of Leeds, Leeds LS2 9JT, UK
| | - Matthew P Culbert
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
- School of Mechanical Engineering, University of Leeds, Leeds LS2 9JT, UK
- Institute of Medical and Biological Engineering, University of Leeds, Leeds LS2 9JT, UK
| | - Danielle E Miles
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
- School of Mechanical Engineering, University of Leeds, Leeds LS2 9JT, UK
- Institute of Medical and Biological Engineering, University of Leeds, Leeds LS2 9JT, UK
| | - Steven Maude
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - Ruth K Wilcox
- School of Mechanical Engineering, University of Leeds, Leeds LS2 9JT, UK
- Institute of Medical and Biological Engineering, University of Leeds, Leeds LS2 9JT, UK
| | - Paul A Beales
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
- Bragg Centre for Materials Research, University of Leeds, Leeds LS2 9JT, UK
- Astbury Centre for Structural Biology, University of Leeds, Leeds LS2 9JT, UK
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de Almeida AR, de Andrade DX, Colherinhas G. Statistical and energetic analysis of hydrogen bonds in short and long peptide nanotapes/nanofibers using molecular dynamics simulations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119308] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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