1
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Kalita M, Yadav K, Archana A, Gopakumar TG, Vasudev PG, Ramapanicker R. Incorporation of phenylcarbonyl groups in the sidechain: A tool to induce ordered assembly of peptides on surfaces. J Pept Sci 2024; 30:e3629. [PMID: 38898708 DOI: 10.1002/psc.3629] [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] [Received: 04/04/2024] [Revised: 05/16/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024]
Abstract
The possibility of introducing various functionalities on peptides with relative ease allows them to be used for molecular applications. However, oligopeptides prepared entirely from proteinogenic amino acids seldom assemble as ordered structures on surfaces. Therefore, sidechain modifications of peptides that can increase the intermolecular interactions without altering the constitution of a given peptide become an attractive route to self-assembling them on surfaces. We find that replacing phenylalanine residues with unusual amino acids that have phenylcarbonyl sidechains in oligopeptides increases the formation of ordered self-assembly on a highly ordered pyrolytic graphite surface. Peptides containing the modified amino acids provided extended long-range ordered assemblies, while the analogous peptides containing phenylalanine residues failed to form long-range assemblies. X-ray crystallographic analysis of the bulk structures of these peptides and the analogous peptides containing phenylalanine residues reveal that such modifications do not alter the secondary structure in crystals. It also reveals that the secondary hydrogen bonding interaction through phenylcarbonyl sidechains facilitates extended growth of the peptides on graphite.
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Affiliation(s)
- Mrinal Kalita
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Khushboo Yadav
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Archana Archana
- Molecular and Structural Biology Department, CSIR - Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | | | - Prema G Vasudev
- Molecular and Structural Biology Department, CSIR - Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Ramesh Ramapanicker
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
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2
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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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3
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Bagchi D, Maity A, Chakraborty A. Metal Ion-Induced Unusual Stability of the Metastable Vesicle-like Intermediates Evolving during the Self-Assembly of Phenylalanine: Prominent Role of Surface Charge Inversion. J Phys Chem Lett 2024; 15:4468-4476. [PMID: 38631022 DOI: 10.1021/acs.jpclett.4c00444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
The underlying mechanism and intermediate formation in the self-assembly of aromatic amino acids, peptides, and proteins remain elusive despite numerous reports. We, for the first time, report that one can stabilize the intermediates by tuning the metal ion-amino acid interaction. Microscopic and spectroscopic investigations of the self-assembly of carboxybenzyl (Z)-protected phenylalanine (ZF) reveal that the bivalent metal ions eventually lead to the formation of fibrillar networks similar to blank ZF whereas the trivalent ions develop vesicle-like intermediates that do not undergo fibrillation for a prolonged time. The time-lapse measurement of surface charge reveals that the surface charge of blank ZF and in the presence of bivalent metal ions changes from a negative value to zero, implying unstable intermediates leading to the fibril network. Strikingly, a prominent charge inversion from an initial negative value to a positive value in the presence of trivalent metal ions imparts unusual stability to the metastable intermediates.
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Affiliation(s)
- Debanjan Bagchi
- Indian Institute of Technology Indore, Department of Chemistry, Indore 453552, Madhya Pradesh, India
| | - Avijit Maity
- Indian Institute of Technology Indore, Department of Chemistry, Indore 453552, Madhya Pradesh, India
| | - Anjan Chakraborty
- Indian Institute of Technology Indore, Department of Chemistry, Indore 453552, Madhya Pradesh, India
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4
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Hooten M, Banerjee A, Dutt M. Multiscale, Multiresolution Coarse-Grained Model via a Hybrid Approach: Solvation, Structure, and Self-Assembly of Aromatic Tripeptides. J Chem Theory Comput 2024; 20:1689-1703. [PMID: 37931005 DOI: 10.1021/acs.jctc.3c00458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Short aromatic peptides have been observed to assemble into diverse nanostructures, including fibers, tubes, and vesicles, using computational techniques. However, the computational studies have employed top-down coarse-grained (CG) models, which are unable to capture the assembly along with the conformation, packing, and organization of the peptides within the aggregates in a manner that is consistent with the all atom (AA) representation of the molecules. In this study, a hybrid structure- and force-based approach is adapted to develop a bottom-up CG force field of triphenylalanine using reference data from AA trajectories. This approach follows a flexible methodology to approximate the chemical complexity of the underlying AA representation with the chosen CG representation. Two CG models are developed with distinct representations of the aromatic side chains. The first uses a simple single-bead representation, while the second uses a three-bead representation to more accurately represent the planarity of the ring. The one-bead model yields nanorods, while the three-bead model results in nanospheres. The role of different chemical groups in the assembly of nanostructures is identified, along with the importance of steric effects on the packing of the peptides within assemblies.
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Affiliation(s)
- Mason Hooten
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Akash Banerjee
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Meenakshi Dutt
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
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5
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Li L, Wu L, Urschbach M, Straßburger D, Liu X, Besenius P, Chen G. Modular Platform of Carbohydrates-modified Supramolecular Polymers Based on Dendritic Peptide Scaffolds. ACS POLYMERS AU 2022; 2:478-485. [PMID: 36536888 PMCID: PMC9756342 DOI: 10.1021/acspolymersau.2c00032] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 06/17/2023]
Abstract
Glycopeptide supramolecular polymers displaying multivalent carbohydrates are particularly suitable for immune-relevant biomaterials, due to the important functions of carbohydrates in mediating cell-cell communication and modulating immune responses. However, the diversity and complexity of carbohydrates limited the generation of glycopeptide supramolecular monomers. Thereby, a modular platform of presenting various carbohydrates, especially more complex oligosaccharides, is highly desirable but remains underexplored. Here, we first prepared the linear amphiphilic glycopeptides that self-assembled into spherical nanoparticles and worm-like nanoparticles. Furthermore, the dendritic glycopeptides that self-assembled into uniform nanorods were designed to generate modular supramolecular polymers with variable functionality, via redesigning the molecular backbone. With various functional oligosaccharide-modified supramolecular polymers, the in vitro studies further indicated that these polymers were not cytotoxic to macrophages, and significantly modulated the production of proinflammatory cytokines. These findings provide a promising platform to develop supramolecular glycopeptide biomaterials with potential applications in immunomodulation and immunotherapy.
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Affiliation(s)
- Long Li
- The
State Key Laboratory of Molecular Engineering of Polymers and Department
of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Libin Wu
- The
State Key Laboratory of Molecular Engineering of Polymers and Department
of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Moritz Urschbach
- Department
of Chemistry, Johannes Gutenberg-University
Mainz, Duesbergweg 10−14, 55128 Mainz, Germany
| | - David Straßburger
- Department
of Chemistry, Johannes Gutenberg-University
Mainz, Duesbergweg 10−14, 55128 Mainz, Germany
| | - Xiaomei Liu
- The
State Key Laboratory of Molecular Engineering of Polymers and Department
of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Pol Besenius
- Department
of Chemistry, Johannes Gutenberg-University
Mainz, Duesbergweg 10−14, 55128 Mainz, Germany
| | - Guosong Chen
- The
State Key Laboratory of Molecular Engineering of Polymers and Department
of Macromolecular Science, Fudan University, Shanghai 200433, China
- Multiscale
Research Institute of Complex Systems, Fudan
University, Shanghai 200433, China
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6
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Adhikary R, Das A. Atomistic Pictures of Self-Assembled Helical Peptide Nanofibers. J Phys Chem B 2022; 126:9476-9492. [PMID: 36350248 DOI: 10.1021/acs.jpcb.2c04484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Spontaneous self-assembly of peptides has been at the forefront of supramolecular chemistry and materials science research over the last two decades. Despite the wealth of information on the morphology of the assembled objects, atomic resolution details of molecular arrangements inside them are largely unknown. In this paper, we investigated non-covalent assemblies of zwitterionic l-phenylalanine tripeptides in water using all-atom explicit-solvent molecular dynamics computer simulations. Our studies produced atomistic pictures of spontaneously assembled nanofibers composed of hundreds of peptide molecules. The dimensions of the nanofibers varied from 10 to 18 nm, with irregular helical twists along the long axes. Previously published experimental data, acquired under similar conditions, provided direct validation of the fibrous morphology and indirect support for the non-trivial helicity observed in our simulations. Quantitative analyses of peptide-water and peptide-peptide interactions revealed heterogeneous local environments of molecules across the nanometer length scales. The combination of electrostatic, hydrogen bonding, van der Waals, and hydrophobic interactions, adopted by a single molecule, was dependent on its relative position inside the fiber. Despite the presence of three hydrophobic phenyl groups, very few molecules were found to be completely shielded from the surrounding water, indicating a subtle role of the hydrophobic effect. Limited conformational flexibility of the tripeptide, along with bare electrostatic interactions, appeared to play a crucial role in the emergence of fibrous morphology of the nanostructures. Our analyses led us to formulate plausible qualitative explanations of the assembly behavior in terms of thermodynamic driving forces and kinetic considerations. We established a clear relationship between details of chemical interactions operating within few molecules and characteristics of the self-assembled states at much longer length scales.
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Affiliation(s)
- Rumela Adhikary
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Avisek Das
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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7
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Bagchi D, Maity A, De SK, Chakraborty A. Metal-Ion-Induced Evolution of Phenylalanine Self-Assembly: Structural Polymorphism of Novel Metastable Intermediates. J Phys Chem Lett 2022; 13:10409-10417. [PMID: 36322139 DOI: 10.1021/acs.jpclett.2c02882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The self-assembly of aromatic amino acids has been widely studied due to their ability to form well-defined amyloid-like fibrillar structures. Herein, for the first time, we report the existence of different metastable intermediate states of diverse morphologies, for example, droplets, spheres, vesicles, flowers, and toroids, that are sequentially formed in aqueous medium during the self-assembly process of phenylalanine in the presence of different divalent (Zn2+, Cd2+, and Hg2+) and trivalent (Al3+, Ga3+, and In3+) metal ions having low pKa values. Due to metal ion-amino acid coordination and strong hydrophobic interaction induced by these metal ions, spherical aggregates are obtained at the initial stage of the structural evolution and further transformed into other intermediate states. Our work may facilitate understanding of the role of metal ions in the amino acid self-assembly process and broaden future applications of the obtained nanostructures in drug delivery, tissue engineering, bioimaging, biocatalysis, and other fields.
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Affiliation(s)
- Debanjan Bagchi
- Indian Institute of Technology Indore, Department of Chemistry, Indore, 453552 Madhya Pradesh, India
| | - Avijit Maity
- Indian Institute of Technology Indore, Department of Chemistry, Indore, 453552 Madhya Pradesh, India
| | - Soumya Kanti De
- Indian Institute of Technology Indore, Department of Chemistry, Indore, 453552 Madhya Pradesh, India
| | - Anjan Chakraborty
- Indian Institute of Technology Indore, Department of Chemistry, Indore, 453552 Madhya Pradesh, India
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8
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NMR and vibrational spectroscopic studies on the structure and self-assembly of Two de novo dipeptides in methanol. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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9
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Diaferia C, Rosa E, Morelli G, Accardo A. Fmoc-Diphenylalanine Hydrogels: Optimization of Preparation Methods and Structural Insights. Pharmaceuticals (Basel) 2022; 15:1048. [PMID: 36145269 PMCID: PMC9505424 DOI: 10.3390/ph15091048] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
Hydrogels (HGs) are tri-dimensional materials with a non-Newtonian flow behaviour formed by networks able to encapsulate high amounts of water or other biological fluids. They can be prepared using both synthetic or natural polymers and their mechanical and functional properties may change according to the preparation method, the solvent, the pH, and to others experimental parameters. Recently, many short and ultra-short peptides have been investigated as building blocks for the formulation of biocompatible hydrogels suitable for different biomedical applications. Due to its simplicity and capability to gel in physiological conditions, Fmoc-FF dipeptide is one of the most studied peptide hydrogelators. Although its identification dates to 15 ago, its behaviour is currently studied because of the observation that the final material obtained is deeply dependent on the preparation method. To collect information about their formulation, here are reported some different strategies adopted until now for the Fmoc-FF HG preparation, noting the changes in the structural arrangement and behaviour in terms of stiffness, matrix porosity, and stability induced by the different formulation strategy on the final material.
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Affiliation(s)
| | | | | | - Antonella Accardo
- Department of Pharmacy and Interuniversity Research Centre on Bioactive Peptides (CIRPeB), University of Naples “Federico II”, Via Montesano 49, 80131 Naples, Italy
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10
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Pérez-Madrigal MM, Gil AM, Casanovas J, Jiménez AI, Macor LP, Alemán C. Self-assembly pathways in a triphenylalanine peptide capped with aromatic groups. Colloids Surf B Biointerfaces 2022; 216:112522. [PMID: 35561635 DOI: 10.1016/j.colsurfb.2022.112522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/22/2022] [Accepted: 04/23/2022] [Indexed: 11/25/2022]
Abstract
Peptide derivatives and, most specifically, their self-assembled supramolecular structures are being considered in the design of novel biofunctional materials. Although the self-assembly of triphenylalanine homopeptides has been found to be more versatile than that of homopeptides containing an even number of residues (i.e. diphenylalanine and tetraphenylalanine), only uncapped triphenylalanine (FFF) and a highly aromatic analog blocked at both the N- and C-termini with fluorenyl-containing groups (Fmoc-FFF-OFm), have been deeply studied before. In this work, we have examined the self-assembly of a triphenylalanine derivative bearing 9-fluorenylmethyloxycarbonyl and benzyl ester end-capping groups at the N- and C-termini, respectively (Fmoc-FFF-OBzl). The antiparallel arrangement clearly dominates in β-sheets formed by Fmoc-FFF-OBzl, whereas the parallel and antiparallel dispositions are almost isoenergetic in Fmoc-FFF-OFm β-sheets and the parallel one is slightly favored for FFF. The effects of both the peptide concentration and the medium on the self-assembly process have been examined considering Fmoc-FFF-OBzl solutions in a wide variety of solvent:co-solvent mixtures. In addition, Fmoc-FFF-OBzl supramolecular structures have been compared to those obtained for FFF and Fmoc-FFF-OFm under identical experimental conditions. The strength of π-π stacking interactions involving the end-capping groups plays a crucial role in the nucleation and growth of supramolecular structures, which determines the resulting morphology. Finally, the influence of a non-invasive external stimulus, ultrasounds, on the nucleation and growth of supramolecular structures has been examined. Overall, FFF-based peptides provide a wide range of supramolecular structures that can be of interest in the biotechnological field.
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Affiliation(s)
- Maria M Pérez-Madrigal
- Departament d'Enginyeria Química (DEQ) and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya (UPC), EEBE, C/ Eduard Maristany 10-14, 08019 Barcelona, Spain.
| | - Ana M Gil
- Departamento de Quimica Organica, Instituto de Sintesis Quimica y Catalisis Homogenea (ISQCH), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Jordi Casanovas
- Departament de Química, Universitat de Lleida, Escola Politècnica Superior, C/ Jaume II no. 69, 25001 Lleida, Spain
| | - Ana I Jiménez
- Departamento de Quimica Organica, Instituto de Sintesis Quimica y Catalisis Homogenea (ISQCH), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Lorena P Macor
- Departament d'Enginyeria Química (DEQ) and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya (UPC), EEBE, C/ Eduard Maristany 10-14, 08019 Barcelona, Spain; IITEMA-CONICET, Departamento de Química, Facultad de Ciencias Exactas Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Agencia Postal Nro. 3, X5804BYA Río Cuarto, Córdoba, Argentina
| | - Carlos Alemán
- Departament d'Enginyeria Química (DEQ) and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya (UPC), EEBE, C/ Eduard Maristany 10-14, 08019 Barcelona, Spain; Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
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11
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Kuhn AJ, Ehlke B, Johnstone TC, Oliver SRJ, Raskatov JA. A crystal-structural study of Pauling-Corey rippled sheets. Chem Sci 2022; 13:671-680. [PMID: 35173931 PMCID: PMC8768883 DOI: 10.1039/d1sc05731f] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/08/2021] [Indexed: 12/20/2022] Open
Abstract
Following the seminal theoretical work on the pleated β-sheet published by Pauling and Corey in 1951, the rippled β-sheet was hypothesized by the same authors in 1953. In the pleated β-sheet the interacting β-strands have the same chirality, whereas in the rippled β-sheet the interacting β-strands are mirror-images. Unlike with the pleated β-sheet that is now common textbook knowledge, the rippled β-sheet has been much slower to evolve. Much of the experimental work on rippled sheets came from groups that study aggregating racemic peptide systems over the course of the past decade. This includes MAX1/DMAX hydrogels (Schneider), L/D-KFE8 aggregating systems (Nilsson), and racemic Amyloid β mixtures (Raskatov). Whether a racemic peptide mixture is “ripple-genic” (i.e., whether it forms a rippled sheet) or “pleat-genic” (i.e., whether it forms a pleated sheet) is likely governed by a complex interplay of thermodynamic and kinetic effects. Structural insights into rippled sheets remain limited to only a very few studies that combined sparse experimental structural constraints with molecular modeling. Crystal structures of rippled sheets are needed so we can rationally design rippled sheet architectures. Here we report a high-resolution crystal structure, in which (l,l,l)-triphenylalanine and (d,d,d)-triphenylalanine form dimeric antiparallel rippled sheets, which pack into herringbone layer structures. The arrangements of the tripeptides and their mirror-images in the individual dimers were in excellent agreement with the theoretical predictions by Pauling and Corey. A subsequent mining of the PDB identified three orphaned rippled sheets among racemic protein crystal structures. Following the seminal theoretical work on the pleated β-sheet published by Pauling and Corey in 1951, the rippled β-sheet was hypothesized by the same authors in 1953.![]()
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Affiliation(s)
- Ariel J Kuhn
- Dept. of Chemistry and Biochemistry, UCSC 1156 High Street Santa Cruz California USA
| | - Beatriz Ehlke
- Dept. of Chemistry and Biochemistry, UCSC 1156 High Street Santa Cruz California USA
| | - Timothy C Johnstone
- Dept. of Chemistry and Biochemistry, UCSC 1156 High Street Santa Cruz California USA
| | - Scott R J Oliver
- Dept. of Chemistry and Biochemistry, UCSC 1156 High Street Santa Cruz California USA
| | - Jevgenij A Raskatov
- Dept. of Chemistry and Biochemistry, UCSC 1156 High Street Santa Cruz California USA
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12
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Bera S, Dong X, Krishnarjuna B, Raab SA, Hales DA, Ji W, Tang Y, Shimon LJ, Ramamoorthy A, Clemmer DE, Wei G, Gazit E. Solid-state packing dictates the unexpected solubility of aromatic peptides. CELL REPORTS. PHYSICAL SCIENCE 2021; 2:100391. [PMID: 33928264 PMCID: PMC8063180 DOI: 10.1016/j.xcrp.2021.100391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/11/2021] [Accepted: 03/12/2021] [Indexed: 05/10/2023]
Abstract
The understanding and prediction of the solubility of biomolecules, even of the simplest ones, reflect an open question and unmet need. Short aromatic tripeptides are among the most highly aggregative biomolecules. However, in marked contrast, Ala-Phe-Ala (AFA) was surprisingly found to be non-aggregative and could be solubilized at millimolar concentrations. Here, aiming to uncover the underlying molecular basis of its high solubility, we explore in detail the solubility, aggregation propensity, and atomic-level structure of the tripeptide. We demonstrate an unexpectedly high water solubility of AFA reaching 672 mM, two orders of magnitude higher than reported previously. The single crystal structure reveals an anti-parallel β sheet conformation devoid of any aromatic interactions. This study provides clear mechanistic insight into the structural basis of solubility and suggests a simple and feasible tool for its estimation, bearing implications for design of peptide drugs, peptides materials, and advancement of peptide nanotechnology.
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Affiliation(s)
- Santu Bera
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Xuewei Dong
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), Fudan University, Shanghai, 200433, People’s Republic of China
| | - Bankala Krishnarjuna
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Shannon A. Raab
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN 47401, USA
| | - David A. Hales
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN 47401, USA
- Department of Chemistry, Hendrix College, Conway, AR 72032, USA
| | - Wei Ji
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Yiming Tang
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), Fudan University, Shanghai, 200433, People’s Republic of China
| | - Linda J.W. Shimon
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - David E. Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN 47401, USA
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), Fudan University, Shanghai, 200433, People’s Republic of China
| | - Ehud Gazit
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
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13
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Diaferia C, Rosa E, Accardo A, Morelli G. Peptide-based hydrogels as delivery systems for doxorubicin. J Pept Sci 2021; 28:e3301. [PMID: 33491262 DOI: 10.1002/psc.3301] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 01/06/2023]
Abstract
Hydrogels (HGs) and nanogels (NGs) have been recently identified as innovative supramolecular materials for many applications in biomedical field such as in tissue engineering, optoelectronic, and local delivery of active pharmaceutical ingredients (APIs). Due to their in vivo biocompatibility, synthetic accessibility, low cost, and tunability, peptides have been used as suitable building blocks for preparation of HGs and NGs formulations. Peptide HGs have shown an outstanding potential to deliver small drugs, protein therapeutics, or diagnostic probes, maintaining the efficacy of their loaded molecules, preventing degradation phenomena, and responding to external physicochemical stimuli. In this review, we discuss the possible use of peptide-based HGs and NGs as vehicles for the delivery of the anticancer drug doxorubicin (Dox). This anthracycline is clinically used for leukemia, stomach, lung, ovarian, breast, and bladder cancer therapy. The loading of Dox into supramolecular systems (liposomes, micelles, hydrogels, and nanogels) allows reducing its cardiotoxicity. According to a primary sequence classification of the constituent peptide, doxorubicin-loaded systems are here classified in short and ultra-short peptide-based HGs, RGD, or RADA-peptide-based HGs and peptide-based NGs.
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Affiliation(s)
- Carlo Diaferia
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Naples, 80134, Italy
| | - Elisabetta Rosa
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Naples, 80134, Italy
| | - Antonella Accardo
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Naples, 80134, Italy
| | - Giancarlo Morelli
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Naples, 80134, Italy
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14
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Mayans E, Alemán C. Revisiting the Self-Assembly of Highly Aromatic Phenylalanine Homopeptides. Molecules 2020; 25:E6037. [PMID: 33419355 PMCID: PMC7766750 DOI: 10.3390/molecules25246037] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/14/2020] [Accepted: 12/18/2020] [Indexed: 02/06/2023] Open
Abstract
Diphenylalanine peptide (FF), which self-assembles into rigid tubular nanostructures, is a very short core recognition motif in Alzheimer's disease β-amyloid (Aβ) polypeptide. Moreover, the ability of the phenylalanine (F or Phe)-homopeptides to self-assemble into ordered nanostructures has been proved. Within this context it was shown that the assembly preferences of this family of compounds is altered by capping both the N- and C-termini using highly aromatic fluorenyl groups (i.e., fluorenyl-9-methoxycarbonyl and 9-fluorenylmethyl ester, named Fmoc and OFm, respectively). In this article the work performed in the field of the effect of the structure and incubation conditions on the morphology and polymorphism of short (from two to four amino acid residues) Phe-homopeptides is reviewed and accompanied by introducing some new results for completing the comparison. Special attention has been paid to the influence of solvent: co-solvent mixture used to solubilize the peptide, the peptide concentration and, in some cases, the temperature. More specifically, uncapped (FF, FFF, and FFFF), N-capped with Fmoc (Fmoc-FF, Fmoc-FFF, and Fmoc-FFFF), C-capped with OFm (FF-OFm), and doubly capped (Fmoc-FF-OFm, Fmoc-FFF-OFm, and Fmoc-FFFF-OFm) Phe-homopeptides have been re-measured. Although many of the experienced assembly conditions have been only revisited as they were previously reported, other experimental conditions have been examined by the first time in this work. In any case, pooling the effect of highly aromatic blocking groups in a single study, using a wide variety of experimental conditions, allows a perspective of how the disappearance of head-to-tail electrostatic interactions and the gradual increase in the amount of π-π stacking interactions, affects the morphology of the assemblies. Future technological applications of Phe-homopeptides can be envisaged by choosing the most appropriate self-assemble structure, defining not only the length of the peptide but also the amount and the position of fluorenyl capping groups.
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Affiliation(s)
| | - Carlos Alemán
- Departament d’Enginyeria Química and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, EEBE, C/Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain;
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15
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Zhu JY, Xu YL, Li Q, Zhang CB, Wang YB, Zhang L, Fu JY, Zhao L. Monitoring the Hierarchical Evolution from a Double-Stranded Helix to a Well-Defined Microscopic Morphology Based on a Turbine-like Aromatic Molecule. ACS OMEGA 2020; 5:16612-16618. [PMID: 32685827 PMCID: PMC7364588 DOI: 10.1021/acsomega.0c01443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
1H-Indazolo[1,2-b]phthalazine-5,10-dione IPDD with an approximate turbine-like spatial structure, primary assembled double-stranded helices at the first level, was predicted by quantum chemical calculations and confirmed by atomic force microscopy. The higher-dimensional hierarchical architectures including fibrils, helical fibers, spherical shells, and porous prismatic structures were observed in sequence by the scanning electron microscopy technique. The final porous prismatic structures sensitive to NH3 vapors have the potential to be applied in gas sensing and absorbing materials.
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Affiliation(s)
- Jun-Yan Zhu
- College
of Chemistry and Chemical Engineering, Henan
University, Kaifeng 475004, China
| | - Ya-Lun Xu
- College
of Chemistry and Chemical Engineering, Henan
University, Kaifeng 475004, China
| | - Qianqian Li
- Institute
of Advanced Synthesis, School of Chemistry and Molecular Engineering,
Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Chuan-Bao Zhang
- College
of Chemistry and Chemical Engineering, Henan
University, Kaifeng 475004, China
| | - Yan-Bo Wang
- College
of Chemistry and Chemical Engineering, Henan
University, Kaifeng 475004, China
| | - Lixiong Zhang
- College
of Chemical Engineering, State Key Laboratory of Materials-Oriented
Chemical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Ji-Ya Fu
- College
of Chemistry and Chemical Engineering, Henan
University, Kaifeng 475004, China
| | - Lili Zhao
- Institute
of Advanced Synthesis, School of Chemistry and Molecular Engineering,
Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
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16
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Gil AM, Casanovas J, Mayans E, Jiménez AI, Puiggalí J, Alemán C. Heterochirality Restricts the Self-Assembly of Phenylalanine Dipeptides Capped with Highly Aromatic Groups. J Phys Chem B 2020; 124:5913-5918. [PMID: 32559085 DOI: 10.1021/acs.jpcb.0c04513] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The influence of stereochemistry on the self-assembly of phenylalanine (Phe) dipeptides bearing aromatic fluorenyl groups at both the N- and C-termini (Fmoc, OFm) has been investigated. For this purpose, Fmoc-d-Phe-l-Phe-OFm and Fmoc-l-Phe-l-Phe-OFm have been examined considering a wide variety of solvents, which differ in dielectric constant and volatility. Results reveal that replacement of l-Phe by d-Phe has a major impact on the self-assembly propensities, restricting drastically the structural diversity and polymorphism shown by the homochiral dipeptide. Thus, the analogous heterochiral dipeptide shows a great propensity to form micro/nanofibers, independently of the environmental conditions. Theoretical calculations revealed that the stability of antiparallel disposition is much higher (a factor of ca. 15) for Fmoc-d-Phe-l-Phe-OFm than that for Fmoc-l-Phe-l-Phe-OFm, which has been attributed to the hydrophobic core formed in the former. Overall, results suggest that control of the backbone chirality is a potent and versatile strategy to drive and finely tune the self-assembly propensities of highly aromatic peptides.
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Affiliation(s)
- Ana M Gil
- Departamento de Quimica Organica, Instituto de Sintesis Quimica y Catalisis Homogenea (ISQCH), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Jordi Casanovas
- Departament de Química, Universitat de Lleida, Escola Politècnica Superior, C/ Jaume II n° 69, E-25001 Lleida, Spain
| | - Enric Mayans
- Departament d'Enginyeria Química and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, EEBE, C/ Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain
| | - Ana I Jiménez
- Departamento de Quimica Organica, Instituto de Sintesis Quimica y Catalisis Homogenea (ISQCH), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Jordi Puiggalí
- Departament d'Enginyeria Química and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, EEBE, C/ Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain
| | - Carlos Alemán
- Departament d'Enginyeria Química and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, EEBE, C/ Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain
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17
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Kim CJ, Park JE, Hu X, Albert SK, Park SJ. Peptide-Driven Shape Control of Low-Dimensional DNA Nanostructures. ACS NANO 2020; 14:2276-2284. [PMID: 31962047 DOI: 10.1021/acsnano.9b09312] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We report the rational design and fabrication of unusual low-dimensional DNA nanostructures through programmable and sequence-specific peptide interactions. Dual-bioactive block copolymers composed of DNA and amino acid-based polymers (DNA-b-poly(amino acid)) were synthesized by coupling oligonucleotides to phenylalanine (Phe)-based polymers. Unlike prototypical DNA block copolymers, which typically form simple spherical micelles, DNA-b-poly(amino acid) assemble into various low-dimensional structures such as nanofibers, ribbons, and sheets through controllable amino acid interactions. Moreover, DNA-b-poly(amino acid) assemblies can undergo protease-induced fiber-to-sheet shape transformations, where the morphology change is dictated by the type of enzymes and amino acid sequences. The peptide-based self-assembly reported here provides a programmable approach to fabricate dynamic DNA assemblies with diverse and unusual low-dimensional structures.
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Affiliation(s)
- Chan-Jin Kim
- Department of Chemistry and Nanoscience , Ewha Womans University , 52 Ewhayeodae-gil, Seodaemun-gu , Seoul 03760 , Korea
| | - Ji-Eun Park
- Department of Chemistry and Nanoscience , Ewha Womans University , 52 Ewhayeodae-gil, Seodaemun-gu , Seoul 03760 , Korea
| | - Xiaole Hu
- Department of Chemistry and Nanoscience , Ewha Womans University , 52 Ewhayeodae-gil, Seodaemun-gu , Seoul 03760 , Korea
| | - Shine K Albert
- Department of Chemistry and Nanoscience , Ewha Womans University , 52 Ewhayeodae-gil, Seodaemun-gu , Seoul 03760 , Korea
| | - So-Jung Park
- Department of Chemistry and Nanoscience , Ewha Womans University , 52 Ewhayeodae-gil, Seodaemun-gu , Seoul 03760 , Korea
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18
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Romanini M, Barrio M, Macovez R, Capaccioli S, Tamarit JL. Mixtures of m-fluoroaniline with apolar aromatic molecules: Phase behaviour, suppression of H-bonded clusters, and local H-bond relaxation dynamics. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111998] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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19
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Datta D, Jana S, Tiwari O. Tubular to spherical mesoscopic self‐assembly of C‐ and N‐termini capped dileucines. Pept Sci (Hoboken) 2019. [DOI: 10.1002/pep2.24134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Dhrubajyoti Datta
- Department of Chemistry, Chemical Biology Unit Indian Institute of Science Education and Research Pune India
| | - Saibal Jana
- Department of Bionano Technology Hanyang University Ansan Republic of Korea
| | - Omshanker Tiwari
- Department of Chemistry, Chemical Biology Unit Indian Institute of Science Education and Research Pune India
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20
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Datta D, Tiwari O, Gupta MK. Self-Assembly of Diphenylalanine-Peptide Nucleic Acid Conjugates. ACS OMEGA 2019; 4:10715-10728. [PMID: 31460170 PMCID: PMC6649282 DOI: 10.1021/acsomega.9b00047] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/07/2019] [Indexed: 05/31/2023]
Abstract
The synthesis and self-assembled nanostructures of a series of nucleopeptides (NPs) derived from the dipeptide Phe-Phe and the peptide nucleic acid unit which are covalently attached through an amide or a triazole linker are described. Depending on the variables such as protecting groups, linkers, and nucleobases, spherical nanoparticles were observed through scanning electron microscopy and high-resolution transmission electron microscopy images, and the porous nature of representative NPs was corroborated by carboxyfluorescein entrapment. Hydrophobic substituents on different sites of NPs and solvents employed for peptide self-assembly played a crucial role for corresponding morphologies. The stability of nanoparticles was also probed under external stimuli such as pH, temperature, and enzymatic hydrolysis using proteolytic enzymes. The semiconducting nature of the NP-modified carbon electrodes suggested their potential use as a new capacitor material.
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21
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Ozawa Y, Sato H, Kayano Y, Yamaki N, Izato YI, Miyake A, Naito A, Kawamura I. Self-assembly of tripeptides into γ-turn nanostructures. Phys Chem Chem Phys 2019; 21:10879-10883. [PMID: 30968092 DOI: 10.1039/c9cp00233b] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Self-assembling phenylalanine-based peptides have garnered interest owing to their potential for creating new functional materials. Here, we designed four diastereomers, l-Phe-l-Phe-l-Phe (FFF), d-Phe-l-Phe-l-Phe (fFF), l-Phe-d-Phe-l-Phe (FfF) and l-Phe-l-Phe-d-Phe (FFf), to analyze the effect of the d-isomer on the self-assembly. Using SEM, TG, VCD, and solid-state NMR measurements, we found that only FFf forms a γ-turn conformation and self-assembles into a nanoplate with higher thermal stability. The supramolecular structure of FFf consists of intra- and intermolecular hydrogen bonds and π-π stackings. From our results, we have discovered that FFf forms a new type of self-assembling γ-turn conformation, clarifying the structural role of a d-amino acid residue in supramolecular formation.
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Affiliation(s)
- Yumi Ozawa
- Graduate School of Engineering, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan.
| | - Hisako Sato
- Department of Chemistry, Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, Japan
| | - Yohei Kayano
- Graduate School of Engineering Science, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Nana Yamaki
- Graduate School of Environment and Information Sciences, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Yu-Ichiro Izato
- Graduate School of Environment and Information Sciences, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Atsumi Miyake
- Institute of Advanced Sciences, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Akira Naito
- Graduate School of Engineering, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan.
| | - Izuru Kawamura
- Graduate School of Engineering, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan. and Graduate School of Engineering Science, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan
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22
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Cui Y, Tao D, Huang X, Lu G, Feng C. Self-Assembled Helical and Twisted Nanostructures of a Preferred Handedness from Achiral π-Conjugated Oligo( p-phenylenevinylene) Derivatives. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:3134-3142. [PMID: 30712352 DOI: 10.1021/acs.langmuir.8b04127] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The formation of chiral nanostructures from the self-assembly of achiral building blocks without external symmetry breaking inducing factors is believed to associate with the origin of chirality. Herein, we reported the synthesis and self-assembly of oligo( p-phenylenevinylene)- b-poly(ethylene glycol) (OPV3- b-PEG17, the subscripts represent the number of repeat unit of each block) in solution. We systematically examined the influence of solvent, heating temperature, and concentration of OPV3- b-PEG17 on the self-assembly of OPV3- b-PEG17 by UV/vis absorption and fluorescence spectrometry, circular dichroism technique, and transmission electron and atomic force microscopy. Interestingly, helical and twisted nanoribbons and nanotubes of a preferred handedness can be formed from achiral OPV3- b-PEG17 in the mixture of water/ethanol (v/v = 1/1) and the solution showed an obvious exciton-coupled bisignated signal, which indicated that symmetry breaking occurred during the formation of these nanostructures without external inducing factors. Our results showed that the occurrence of symmetry breaking is subtle to the experimental factors including solvent, heating temperature, and concentration of OPV3- b-PEG17. The directional π-π stacking along with steric repulsion between PEG domains should be the driving force for the formation of these chiral nanostructures. The occurrence of statistical fluctuations in the initial stage of self-assembly led to an accidental excess of helical or/and twisted structures, that is, symmetry breaking. Subsequently, the autocatalysis effect resulted in the formation of helical or/and twisted nanoribbons with a preferred handedness.
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Affiliation(s)
- Yinan Cui
- Key Laboratory of Synthetic and Self-Assembly Chemistry for Organic Functional Molecules, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences , Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , People's Republic of China
| | - Daliao Tao
- Key Laboratory of Synthetic and Self-Assembly Chemistry for Organic Functional Molecules, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences , Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , People's Republic of China
| | - Xiaoyu Huang
- Key Laboratory of Synthetic and Self-Assembly Chemistry for Organic Functional Molecules, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences , Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , People's Republic of China
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials , Donghua University , 2999 North Renmin Road , Songjiang, Shanghai 201620 , People's Republic of China
| | - Guolin Lu
- Key Laboratory of Synthetic and Self-Assembly Chemistry for Organic Functional Molecules, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences , Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , People's Republic of China
| | - Chun Feng
- Key Laboratory of Synthetic and Self-Assembly Chemistry for Organic Functional Molecules, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences , Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , People's Republic of China
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23
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Casanovas J, Mayans E, Díaz A, Gil AM, Jiménez AI, Cativiela C, Puiggalí J, Alemán C. Amyloid fibrils from organic solutions of an amphiphilic dipeptide. Chem Commun (Camb) 2019; 55:8556-8559. [DOI: 10.1039/c9cc04139g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A diphenylalanine amphiphile blocked at the C-terminus with a fluorenylmethyl ester and stabilized at the N-terminus with a trifluoroacetate forms amyloid fibril networks in organic solvents.
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Affiliation(s)
- Jordi Casanovas
- Departament de Química
- Escola Politècnica Superior, Universitat de Lleida
- Lleida E-25001
- Spain
| | - Enric Mayans
- Departament d’Enginyeria Química and Barcelona Research Center for Multiscale Science and Engineering
- EEBE
- Universitat Politècnica de Catalunya
- 08019 Barcelona
- Spain
| | - Angélica Díaz
- Departament d’Enginyeria Química and Barcelona Research Center for Multiscale Science and Engineering
- EEBE
- Universitat Politècnica de Catalunya
- 08019 Barcelona
- Spain
| | - Ana M. Gil
- Departamento de Quimica Organica
- Instituto de Sintesis Quimica y Catalisis Homogenea (ISQCH)
- CSIC-Universidad de Zaragoza
- 50009 Zaragoza
- Spain
| | - Ana I. Jiménez
- Departamento de Quimica Organica
- Instituto de Sintesis Quimica y Catalisis Homogenea (ISQCH)
- CSIC-Universidad de Zaragoza
- 50009 Zaragoza
- Spain
| | - Carlos Cativiela
- Departamento de Quimica Organica
- Instituto de Sintesis Quimica y Catalisis Homogenea (ISQCH)
- CSIC-Universidad de Zaragoza
- 50009 Zaragoza
- Spain
| | - Jordi Puiggalí
- Departament d’Enginyeria Química and Barcelona Research Center for Multiscale Science and Engineering
- EEBE
- Universitat Politècnica de Catalunya
- 08019 Barcelona
- Spain
| | - Carlos Alemán
- Departament d’Enginyeria Química and Barcelona Research Center for Multiscale Science and Engineering
- EEBE
- Universitat Politècnica de Catalunya
- 08019 Barcelona
- Spain
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24
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Sohora M, Vazdar M, Sović I, Mlinarić-Majerski K, Basarić N. Photocyclization of Tetra- and Pentapeptides Containing Adamantylphthalimide and Phenylalanines: Reaction Efficiency and Diastereoselectivity. J Org Chem 2018; 83:14905-14922. [PMID: 30460849 DOI: 10.1021/acs.joc.8b01785] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A series of tetrapeptides and pentapeptides was synthesized bearing a phthalimide chromophore at the N-terminus. The C-terminus of the peptides was strategically substituted with an amino acid, Phe, Phe(OMe), or Phe(OMe)2 characterized by different oxidation potentials. The photochemical reactivity of the peptides was investigated by preparative irradiation and isolation of photoproducts, as well as with laser flash photolysis. Upon photoexcitation, the peptides undergo photoinduced electron transfer (PET) and decarboxylation, followed by diastereoselective cyclization with the retention of configuration for tetrapeptides or inversion of configuration for pentapeptides. Molecular dynamics (MD) simulations and NOE experiments enabled assignment of the stereochemistry of the cyclic peptides. MD simulations of the linear peptides disclosed conformational reasons for the observed diastereoselectivity, being due to the peptide backbone spatial orientation imposed by the Phe amino acids. The photochemical efficiency for the decarboxylation and cyclization is not dependent on the peptide length, but it depends on the oxidation potential of the amino acid at the C-terminus. The results described herein are particularly important for the rational design of efficient photochemical reactions for the preparation of cyclic peptides with the desired selectivity.
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Affiliation(s)
- Margareta Sohora
- Department of Organic Chemistry and Biochemistry , Rud̵er Bošković Institute , Bijenička cesta 54 , 10000 Zagreb , Croatia
| | - Mario Vazdar
- Department of Organic Chemistry and Biochemistry , Rud̵er Bošković Institute , Bijenička cesta 54 , 10000 Zagreb , Croatia
| | - Irena Sović
- Department of Organic Chemistry and Biochemistry , Rud̵er Bošković Institute , Bijenička cesta 54 , 10000 Zagreb , Croatia
| | - Kata Mlinarić-Majerski
- Department of Organic Chemistry and Biochemistry , Rud̵er Bošković Institute , Bijenička cesta 54 , 10000 Zagreb , Croatia
| | - Nikola Basarić
- Department of Organic Chemistry and Biochemistry , Rud̵er Bošković Institute , Bijenička cesta 54 , 10000 Zagreb , Croatia
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25
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Martí D, Mayans E, Gil AM, Díaz A, Jiménez AI, Yousef I, Keridou I, Cativiela C, Puiggalí J, Alemán C. Amyloid-like Fibrils from a Diphenylalanine Capped with an Aromatic Fluorenyl. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15551-15559. [PMID: 30453736 DOI: 10.1021/acs.langmuir.8b03378] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The self-assembly behavior of a diphenylalanine amphiphile blocked at the C-terminus with a 9-fluorenylmethyl ester and stabilized at the N-terminus with a trifluoroacetate (TFA) anion, TFA·FF-OFm, has been examined. At low peptide concentration (0.5 mg/mL), long amyloid-like fibrils, which come from the fusion of two or more helical ribbons and/or thinner fibrils, organized in bundles or as individual entities are detected. Microbeam synchrotron radiation infrared spectroscopy has shown that TFA·FF-OFm molecules in amyloid-like fibrils arrange, forming antiparallel β-sheets. Alteration of the experimental conditions to prioritize the thermodynamic contribution with respect to the kinetic one in the self-assembly process inhibits the organization of amyloid-like structures in favor of the formation of conventional fibrous structures. On the basis of experimental observations, a structural model where the individual antiparallel β-sheets are oriented in parallel has been proposed for TFA·FF-OFm amyloid-like fibrils.
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Affiliation(s)
- Didac Martí
- Departament d'Enginyeria Química, EEBE , Universitat Politècnica de Catalunya , C/Eduard Maristany, 10-14, Ed. I2 , 08019 Barcelona , Spain
- Barcelona Research Center for Multiscale Science and Engineering , Universitat Politècnica de Catalunya , Eduard Maristany, 10-14 , 08019 Barcelona , Spain
| | - Enric Mayans
- Departament d'Enginyeria Química, EEBE , Universitat Politècnica de Catalunya , C/Eduard Maristany, 10-14, Ed. I2 , 08019 Barcelona , Spain
| | - Ana M Gil
- Departamento de Quimica Organica, Instituto de Sintesis Quimica y Catalisis Homogenea (ISQCH) , CSIC-Universidad de Zaragoza , 50009 Zaragoza , Spain
| | - Angélica Díaz
- Departament d'Enginyeria Química, EEBE , Universitat Politècnica de Catalunya , C/Eduard Maristany, 10-14, Ed. I2 , 08019 Barcelona , Spain
- Barcelona Research Center for Multiscale Science and Engineering , Universitat Politècnica de Catalunya , Eduard Maristany, 10-14 , 08019 Barcelona , Spain
| | - Ana I Jiménez
- Departamento de Quimica Organica, Instituto de Sintesis Quimica y Catalisis Homogenea (ISQCH) , CSIC-Universidad de Zaragoza , 50009 Zaragoza , Spain
| | - Ibraheem Yousef
- ALBA Synchrotron Light Facility , C/de la Llum 2-26, Cerdanyola del Valles , 08290 Barcelona , Spain
| | - Ina Keridou
- Departament d'Enginyeria Química, EEBE , Universitat Politècnica de Catalunya , C/Eduard Maristany, 10-14, Ed. I2 , 08019 Barcelona , Spain
- Barcelona Research Center for Multiscale Science and Engineering , Universitat Politècnica de Catalunya , Eduard Maristany, 10-14 , 08019 Barcelona , Spain
| | - Carlos Cativiela
- Departamento de Quimica Organica, Instituto de Sintesis Quimica y Catalisis Homogenea (ISQCH) , CSIC-Universidad de Zaragoza , 50009 Zaragoza , Spain
| | - Jordi Puiggalí
- Departament d'Enginyeria Química, EEBE , Universitat Politècnica de Catalunya , C/Eduard Maristany, 10-14, Ed. I2 , 08019 Barcelona , Spain
- Barcelona Research Center for Multiscale Science and Engineering , Universitat Politècnica de Catalunya , Eduard Maristany, 10-14 , 08019 Barcelona , Spain
| | - Carlos Alemán
- Departament d'Enginyeria Química, EEBE , Universitat Politècnica de Catalunya , C/Eduard Maristany, 10-14, Ed. I2 , 08019 Barcelona , Spain
- Barcelona Research Center for Multiscale Science and Engineering , Universitat Politècnica de Catalunya , Eduard Maristany, 10-14 , 08019 Barcelona , Spain
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26
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Anderson J, Lake PT, McCullagh M. Initial Aggregation and Ordering Mechanism of Diphenylalanine from Microsecond All-Atom Molecular Dynamics Simulations. J Phys Chem B 2018; 122:12331-12341. [PMID: 30511861 DOI: 10.1021/acs.jpcb.8b10335] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Self-assembled diphenylalanine (FF) nanostructures have recently been demonstrated to be interesting materials for antibacterial and anticancer applications. These applications, among others, seek to take advantage of the high-order and resulting appealing physical properties of FF nanostructures by modifying the peptide in some way to achieve specific functionality. To rationally design modifications to the dipeptide that allow for this behavior, the driving forces of FF self-assembly must be understood. Molecular simulations have been utilized to assess these properties but have yielded conflicting conclusions due to inconsistencies in models chosen as well as the lack of quantitative analyses on the specific driving forces. Here, we present an all-atom explicit solvent molecular dynamics-based study on different length scales of FF aggregation. We utilize a free energy decomposition analysis as well as a dimer cluster analysis to identify the initial aggregation driving force to be FF intermolecular electrostatics, whereas solvent-mediated forces drive crystal growth. These data are consistent with the hypothesis that all hydrophobic dipeptides will have a similar initial aggregation mechanism until a critical aggregate size is reached, at which point crystallization occurs and subsequent crystal growth is dominated by solvent-mediated forces. We demonstrate that this proposed mechanism is testable by infrared spectroscopy focusing on the blueshift of the amide I peak as well as the ordering of the carboxylate peak.
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Affiliation(s)
- Jakob Anderson
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Peter T Lake
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Martin McCullagh
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
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27
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Mayans E, Murase SK, Pérez-Madrigal MM, Cativiela C, Alemán C, Puiggalí J. Hybrid Polypeptide/Polylactide Copolymers with Short Phenylalanine Blocks. MACROMOL CHEM PHYS 2018. [DOI: 10.1002/macp.201800168] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Enric Mayans
- Departament d’Enginyeria Química; EEBE, Universitat Politècnica de Catalunya; c/ Eduard Maristany 10-14, Ed. I2, 08019 Barcelona Spain
- Barcelona Research Center for Multiscale Science and Engineering; Universitat Politècnica de Catalunya; c/ Eduard Maristany 10-14, 08019 Barcelona Spain
| | - Sara K. Murase
- Departament d’Enginyeria Química; EEBE, Universitat Politècnica de Catalunya; c/ Eduard Maristany 10-14, Ed., I2 08019 Barcelona Spain
| | - Maria M. Pérez-Madrigal
- Departament d’Enginyeria Química; EEBE, Universitat Politècnica de Catalunya; c/ Eduard Maristany 10-14, Ed. I2, 08019 Barcelona Spain
- Barcelona Research Center for Multiscale Science and Engineering; Universitat Politècnica de Catalunya; c/ Eduard Maristany 10-14, 08019 Barcelona Spain
| | - Carlos Cativiela
- Departamento de Química Orgánica e Instituto de Síntesis Quimica y Catalisis Homogenea (ISQCH); Universidad de Zaragoza-CSIC; 50009 Zaragoza Spain
| | - Carlos Alemán
- Departament d’Enginyeria Química; EEBE, Universitat Politècnica de Catalunya; c/ Eduard Maristany 10-14, Ed. I2, 08019 Barcelona Spain
- Barcelona Research Center for Multiscale Science and Engineering; Universitat Politècnica de Catalunya; c/ Eduard Maristany 10-14, 08019 Barcelona Spain
| | - Jordi Puiggalí
- Departament d’Enginyeria Química; EEBE, Universitat Politècnica de Catalunya; c/ Eduard Maristany 10-14, Ed. I2, 08019 Barcelona Spain
- Barcelona Research Center for Multiscale Science and Engineering; Universitat Politècnica de Catalunya; c/ Eduard Maristany 10-14, 08019 Barcelona Spain
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28
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Pelin JNBD, Gatto E, Venanzi M, Cavalieri F, Oliveira CLP, Martinho H, Silva ER, Aguilar AM, Souza JS, Alves WA. Hybrid Conjugates Formed between Gold Nanoparticles and an Amyloidogenic Diphenylalanine-Cysteine Peptide. ChemistrySelect 2018. [DOI: 10.1002/slct.201801345] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Juliane N. B. D. Pelin
- Centro de Ciências Naturais e Humanas; Universidade Federal do ABC; 09210-580 Santo André Brazil
| | - Emanuela Gatto
- Department of Chemical Science and Technologies; University of Rome Tor Vergata; Italy
| | - Mariano Venanzi
- Department of Chemical Science and Technologies; University of Rome Tor Vergata; Italy
| | - Francesca Cavalieri
- Department of Chemical and Biomolecular Engineering; The University of Melbourne; Australia
- Department of Chemical Science and Technologies; University of Rome Tor Vergata; Italy
| | | | - Herculano Martinho
- Centro de Ciências Naturais e Humanas; Universidade Federal do ABC; 09210-580 Santo André Brazil
| | - Emerson R. Silva
- Departamento de Biofísica; Universidade Federal de São Paulo; 04023-062 São Paulo Brazil
| | - Andrea M. Aguilar
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas; Universidade Federal de São Paulo; Diadema 09972-270 Brazil
| | - Juliana S. Souza
- Centro de Ciências Naturais e Humanas; Universidade Federal do ABC; 09210-580 Santo André Brazil
| | - Wendel A. Alves
- Centro de Ciências Naturais e Humanas; Universidade Federal do ABC; 09210-580 Santo André Brazil
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29
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Diaferia C, Balasco N, Sibillano T, Ghosh M, Adler-Abramovich L, Giannini C, Vitagliano L, Morelli G, Accardo A. Amyloid-Like Fibrillary Morphology Originated by Tyrosine-Containing Aromatic Hexapeptides. Chemistry 2018; 24:6804-6817. [PMID: 29504716 DOI: 10.1002/chem.201800351] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Indexed: 01/04/2023]
Abstract
Phenylalanine-based nanostructures have attracted the attention of the material science community for their functional properties. These properties strongly depend on the hierarchic organization of the nanostructure that in turn can be finely tuned by punctual chemical modifications of the building blocks. Herein, we investigate how the partial or the complete replacement of the Phe residues in PEG8 -(Phe)6 (PEG8 -F6) with tyrosines to generate PEG8 -(Phe-Tyr)3 (PEG8 -(FY)3) or PEG8 -(Tyr)6 (PEG8 -Y6) affects the structural/functional properties of the nanomaterial formed by the parental compound. Moreover, the effect of the PEG derivatization was evaluated through the characterization of the peptides without the PEG moiety (Tyr)6 (Y6) and (Phe-Tyr)3 ((FY)3). Both PEG8 -Y6 and PEG8 -(FY)3 can self-assemble in water at micromolar concentrations in β-sheet-rich nanostructures. However, WAXS diffraction patterns of these compounds present significant differences. PEG8 -(FY)3 shows a 2D WAXS oriented fiber diffraction profile characterized by the concomitant presence of a 4.7 Å meridional and a 12.5 Å equatorial reflection that are generally associated with cross-β structure. On the other hand, the pattern of PEG8 -Y6 is characterized by the presence of circles typically observed in the presence of PEG crystallization. Molecular modeling and dynamics provide an atomic structural model of the peptide spine of these compounds that is in good agreement with WAXS experimental data. Gelation phenomenon was only detected for PEG8 -(FY)3 above a concentration of 1.0 wt % as confirmed by storage (G'≈100 Pa) and loss (G''≈28 Pa) moduli in rheological studies. The cell viability on CHO cells of this soft hydrogel was certified to be 90 % after 24 hours of incubation.
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Affiliation(s)
- Carlo Diaferia
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II" and DFM Scarl, Via Mezzocannone 16, 80134, Naples, Italy
| | - Nicole Balasco
- Institute of Biostructures and Bioimaging (IBB), CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Teresa Sibillano
- Institute of Crystallography (IC), CNR, Via Amendola 122, 70126, Bari, Italy
| | - Moumita Ghosh
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Cinzia Giannini
- Institute of Crystallography (IC), CNR, Via Amendola 122, 70126, Bari, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging (IBB), CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Giancarlo Morelli
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II" and DFM Scarl, Via Mezzocannone 16, 80134, Naples, Italy
| | - Antonella Accardo
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II" and DFM Scarl, Via Mezzocannone 16, 80134, Naples, Italy
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30
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Datta D, Tiwari O, Ganesh KN. New archetypes in self-assembled Phe-Phe motif induced nanostructures from nucleoside conjugated-diphenylalanines. NANOSCALE 2018; 10:3212-3224. [PMID: 29379926 DOI: 10.1039/c7nr08436f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
During the last two decades, the molecular self-assembly of the short peptide diphenylalanine (Phe-Phe) motif has attracted increasing focus due to its unique morphological structure and utility for potential applications in biomaterial chemistry, sensors and bioelectronics. Due to the ease of their synthetic modifications and a plethora of available experimental tools, the self-assembly of free and protected diphenylalanine scaffolds (H-Phe-Phe-OH, Boc-Phe-Phe-OH and Boc-Phe-Phe-OMe) has unfurled interesting tubular, vesicular or fibrillar morphologies. Developing on this theme, here we attempt to examine the effect of structure and properties (hydrophobic and H-bonding) modifying the functional C-terminus conjugated substituents on Boc-Phe-Phe on its self-assembly process. The consequent self-sorting due to H-bonding, van der Waals force and π-π interactions, generates monodisperse nano-vesicles from these peptides characterized via their SEM, HRTEM, AFM pictures and DLS experiments. The stability of these vesicles to different external stimuli such as pH and temperature, encapsulation of fluorescent probes inside the vesicles and their release by external trigger are reported. The results point to a new direction in the study and applications of the Phe-Phe motif to rationally engineer new functional nano-architectures.
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Affiliation(s)
- Dhrubajyoti Datta
- Department of Chemistry, Chemical Biology Unit, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, India.
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31
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Chan-Seng D, Louwsma J, Lutz JF, Joly S. Synthesis of Macromolecules Containing Phenylalanine and Aliphatic Building Blocks. Macromol Rapid Commun 2018; 39:e1700764. [DOI: 10.1002/marc.201700764] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/13/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Delphine Chan-Seng
- Université de Strasbourg; CNRS; Institut Charles Sadron; F-67000 Strasbourg France
| | - Jeroen Louwsma
- PSA Groupe; Site de Vélizy; Chemin de Gisy 78943 Vélizy-Villacoublay France
| | - Jean-François Lutz
- Université de Strasbourg; CNRS; Institut Charles Sadron; F-67000 Strasbourg France
| | - Stéphane Joly
- PSA Groupe; Site de Vélizy; Chemin de Gisy 78943 Vélizy-Villacoublay France
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