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Avelar S Silva J, Militão Vasconcelos DL, Araújo de Lima R, Cordeiro AJP, Tarso C Freire P. Structural and vibrational analysis of glycyl-L-phenylalanine and phase transition under high-pressure. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 304:123383. [PMID: 37725884 DOI: 10.1016/j.saa.2023.123383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/03/2023] [Accepted: 09/08/2023] [Indexed: 09/21/2023]
Abstract
The structural and vibrational properties of the glycyl-L-phenylalanine dipeptide were investigated using vibrational spectroscopy (Raman and infrared) and first-principle calculations. Raman spectroscopy measurements were performed between 100 and 3200 cm-1 and infrared spectroscopy from 100 and 3200 cm-1 under ambient conditions. The conformational analysis of the zwitterionic form of the dipeptide was performed using the B3LYP functional, the 6-311++ base set and the Polarizable Continuum Model of solvation, determining the lowest energy conformation and assigning the vibrational modes. The effect of pressure on the glycyl-1-phenylalanine crystal was investigated using the Raman spectroscopy between 0.0 and -7.1 GPa in the spectral region of 100 - 3200 cm-1. As a result, conformational changes around 1.0 GPa were observed in the lattice modes and in some internal modes, showing a reorganization of the molecule in the crystal. In the decompression process, it was observed that the conformational change is reversible and the original Raman spectrum is recoverd.
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Affiliation(s)
- José Avelar S Silva
- Departamento de Física, Universidade Federal do Ceará, Caixa Postal 6030, 60021-970, Fortaleza, CE, Brazil.
| | - Daniel L Militão Vasconcelos
- Departamento de Física, Universidade Federal do Ceará, Caixa Postal 6030, 60021-970, Fortaleza, CE, Brazil; Faculdade de Educação Ciências e Letras do Sertão Central, Universidade Estadual do Ceará, CEP 63.902-098 Quixadá, CE, Brazil
| | - Raphaela Araújo de Lima
- Departamento de Física, Universidade Federal do Ceará, Caixa Postal 6030, 60021-970, Fortaleza, CE, Brazil
| | - Adrya J P Cordeiro
- Departamento de Física, Universidade Federal do Ceará, Caixa Postal 6030, 60021-970, Fortaleza, CE, Brazil
| | - Paulo Tarso C Freire
- Departamento de Física, Universidade Federal do Ceará, Caixa Postal 6030, 60021-970, Fortaleza, CE, Brazil.
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2
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The effects of epirubicin-loaded Boc-L-Diphenylalanine peptide nanoparticles on cytotoxicity, genotoxicity, oxidative stress, and apoptosis in non-small cell lung cancer cells. Food Chem Toxicol 2023; 175:113690. [PMID: 36842751 DOI: 10.1016/j.fct.2023.113690] [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: 01/03/2023] [Revised: 02/14/2023] [Accepted: 02/20/2023] [Indexed: 02/26/2023]
Abstract
Peptides, which are important components of the human body, appear in different chemistry applications. Perhaps the most important of these applications is the use of these structures in drug delivery systems due to their biocompatibility properties. Diphenylalanine (FF) peptide-based systems, which are part of the ß-amyloid polypeptide sequence and are known as the smallest dipeptide group, are particularly preferred due to their biocompatible nature, thermal stability, high ionic strength in water in new targeted drug systems. Epirubicin, the epimer of doxorubicin, is utilized in treating lung cancer. The side effects and the applied doses of epirubicin are being tried to be reduced. Therefore, in this study, epirubicin-loaded tert-butyloxycarbonyl protected diphenylalanine (Boc)-FF particles were synthesized and characterized and the effects of these peptides on cytotoxicity, genotoxicity, oxidative stress and apoptosis on non-small cell lung cancer cells (NSCLC) (A549) were evaluated. According to the results of the study, it was determined that epirubicin-loaded Boc-FF dipeptides significantly reduced the viability, oxidative stress, and increased DNA damage and apoptosis in the cells. The study suggests that epirubicin-loaded Boc-FF particles can be used as an alternative drug carrier for NSCLC treatment due to their physiological, chemical, and biological activity.
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Shinde SD, Kulkarni N, Sahu B. Synthesis and Investigation of Backbone Modified Squaramide Dipeptide Self-Assembly. ACS APPLIED BIO MATERIALS 2023; 6:507-518. [PMID: 36716238 DOI: 10.1021/acsabm.2c00803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Dipeptides are minimalistic peptide building blocks that form well ordered structures through molecular self-assembly. The driving forces involved are cooperative noncovalent interactions such as π-π stacking, hydrogen bonding, and ionic as well as hydrophobic interactions. One of the most intriguing self-assembled motifs that has been extensively explored as a low molecular weight hydrogel for drug delivery, tissue engineering, imaging and techtonics, etc. is Phe-Phe (FF). The backbone of the dipeptide is very crucial for extending secondary structures in self-assembly, and any subtle change in the backbone drastically affect the molecular recognitions. The squaramide (SQ) motif has the unique advantage of hydrogen bonding which can promote the self-assembly process. In this work we have integrated the SQ unit into the dipeptide FF backbone to achieve molecular self-assembly. The resulting carbamate protected backbone modified dipeptide (BocFSAF-OH, 10) has exhibited molecular self-assembly with a fibrilar network. It formed a stable hydrogel (with CAC of 0.024 ± 0.0098 wt %) via the solvent switch method and was found to possess excellent enzymatic stability. The dipeptide and the resulting hydrogel were found to be cytocompatible. When integrated with a polysaccharide based biopolymer, e.g. sodium alginate, the resulting matrix exhibited strong hydrogel character. Therefore, the dipeptide hydrogel of 10 may find its applications in a variety of fields including drug delivery and tissue engineering.
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Affiliation(s)
- Suchita Dattatray Shinde
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Neeraj Kulkarni
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Bichismita Sahu
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
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4
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Bellotto O, D'Andrea P, Marchesan S. Nanotubes and water-channels from self-assembling dipeptides. J Mater Chem B 2023. [PMID: 36790014 DOI: 10.1039/d2tb02643k] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Dipeptides are attractive building blocks for biomaterials in light of their inherent biocompatibility, biodegradability, and simplicity of preparation. Since the discovery of diphenylalanine (Phe-Phe) self-assembling ability into nanotubes, research efforts have been devoted towards the identification of other dipeptide sequences capable of forming these interesting nanomorphologies, although design rules towards nanotube formation are still elusive. In this review, we analyze the dipeptide sequences reported thus far for their ability to form nanotubes, which often feature water-filled supramolecular channels as revealed by single-crystal X-ray diffraction, as well as their properties, and their potential biological applications, which span from drug delivery and regenerative medicine, to bioelectronics and bioimaging.
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Affiliation(s)
- Ottavia Bellotto
- Chem. Pharm. Sc. Dept., University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy.
| | - Paola D'Andrea
- Life Sc. Dept., University of Trieste, Via Weiss 2, 34128 Trieste, Italy
| | - Silvia Marchesan
- Chem. Pharm. Sc. Dept., University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy. .,INSTM, Unit of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
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5
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Sahare S, Ghoderao P, Chan Y, Lee SL. Surface supramolecular assemblies tailored by chemical/physical and synergistic stimuli: a scanning tunneling microscopy study. NANOSCALE 2023; 15:1981-2002. [PMID: 36515142 DOI: 10.1039/d2nr05264d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Supramolecular self-assemblies formed by various non-covalent interactions can produce diverse functional networks on solid surfaces. These networks have recently attracted much interest from both fundamental and application points of view. Unlike covalent organic frameworks (COFs), the properties of the assemblies differ from each other depending on the constituent motifs. These various motifs may find diverse applications such as in crystal engineering, surface modification, and molecular electronics. Significantly, these interactions between/among the molecular tectonics are relatively weak and reversible, which makes them responsive to external stimuli. Moreover, for a liquid-solid-interface environment, the dynamic processes are amenable to in situ observation using scanning tunneling microscopy (STM). In the literature, most review articles focus on supramolecular self-assembly interactions. This review summarizes the recent literature in which stimulation sources, including chemical, physical, and their combined stimuli, cooperatively tailor supramolecular assemblies on surfaces. The appropriate design and synthesis of functional molecules that can be integrated on different surfaces permits the use of nanostructured materials and devices for bottom-up nanotechnology. Finally, we discuss synergic effect on materials science.
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Affiliation(s)
- Sanjay Sahare
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China.
- Faculty of Physics, Adam Mickiewicz University, Poznań, 61-614, Poland
| | - Prachi Ghoderao
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China.
| | - Yue Chan
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China.
| | - Shern-Long Lee
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China.
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6
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Water admixture triggers the self-assembly of the glycyl-glycine thin film at the presence of organic vapors. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.129541] [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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7
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Antioxidative, cytotoxic, and antibacterial properties of self-assembled glycine-histidine-based dipeptides with or without silver nanoparticles in bio-inspired film. ARHIV ZA HIGIJENU RADA I TOKSIKOLOGIJU 2022; 73:169-177. [PMID: 35792768 PMCID: PMC9287833 DOI: 10.2478/aiht-2022-73-3658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/01/2022] [Indexed: 12/04/2022]
Abstract
Recent years have seen much attention being given to self-assembly of dipeptide-based structures, especially to self-regulation of dipeptide structures with different amino acid sequences. In this study we investigated the effects of varying solvent environments on the self-assembly of glycine-histidine (Gly-His) dipeptide structures. First we determined the morphological properties of Gly-His films formed in different solvent environments with scanning electron microscopy and then structural properties with Fourier-transform infrared (FTIR) spectroscopy. In addition, we studied the effects of Gly-His films on silver nanoparticle (AgNP) formation and the antioxidant and cytotoxic properties of AgNPs obtained in this way. We also, assessed antibacterial activities of Gly-His films against Gram-negative Escherichia coli and Pseudomonas aeruginosa and Gram-positive Staphylococcus aureus. Silver nanoparticle-decorated Gly-His films were not significantly cytotoxic at concentrations below 2 mg/mL but had antibacterial activity. We therefore believe that AgNP-decorated Gly-His films at concentrations below 2 mg/mL can be used safely against bacteria.
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8
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Sasselli IR, Syrgiannis Z, Sather NA, Palmer LC, Stupp SI. Modeling Interactions within and between Peptide Amphiphile Supramolecular Filaments. J Phys Chem B 2022; 126:650-659. [PMID: 35029997 DOI: 10.1021/acs.jpcb.1c09258] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many peptides are able to self-assemble into one-dimensional (1D) nanostructures, such as cylindrical fibers or ribbons of variable widths, but the relationship between the morphology of 1D objects and their molecular structure is not well understood. Here, we use coarse-grained molecular dynamics (CG-MD) simulations to study the nanostructures formed by self-assembly of different peptide amphiphiles (PAs). The results show that ribbons are hierarchical superstructures formed by laterally assembled cylindrical fibers. Simulations starting from bilayer structures demonstrate the formation of filaments, whereas other simulations starting from filaments indicate varying degrees of interaction among them depending on chemical structure. These interactions are verified by observations using atomic force microscopy of the various systems. The interfilament interactions are predicted to be strongest in supramolecular assemblies that display hydrophilic groups on their surfaces, while those with hydrophobic ones are predicted to interact more weakly as confirmed by viscosity measurements. The simulations also suggest that peptide amphiphiles with hydrophobic termini bend to reduce their interfacial energy with water, which may explain why these systems do not collapse into superstructures of bundled filaments. The simulations suggest that future experiments will need to address mechanistic questions about the self-assembly of these systems into hierarchical structures, namely, the preformation of interactive filaments vs equilibration of large assemblies into superstructures.
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Affiliation(s)
- Ivan R Sasselli
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, 11th Floor, Chicago, Illinois 60611, United States.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Zois Syrgiannis
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, 11th Floor, Chicago, Illinois 60611, United States.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Nicholas A Sather
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, 11th Floor, Chicago, Illinois 60611, United States.,Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States
| | - Liam C Palmer
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, 11th Floor, Chicago, Illinois 60611, United States.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Samuel I Stupp
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, 11th Floor, Chicago, Illinois 60611, United States.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States.,Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States.,Department of Medicine, Northwestern University, 676 N St. Clair, Chicago, Illinois 60611, United States.,Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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9
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Antipin IS, Alfimov MV, Arslanov VV, Burilov VA, Vatsadze SZ, Voloshin YZ, Volcho KP, Gorbatchuk VV, Gorbunova YG, Gromov SP, Dudkin SV, Zaitsev SY, Zakharova LY, Ziganshin MA, Zolotukhina AV, Kalinina MA, Karakhanov EA, Kashapov RR, Koifman OI, Konovalov AI, Korenev VS, Maksimov AL, Mamardashvili NZ, Mamardashvili GM, Martynov AG, Mustafina AR, Nugmanov RI, Ovsyannikov AS, Padnya PL, Potapov AS, Selektor SL, Sokolov MN, Solovieva SE, Stoikov II, Stuzhin PA, Suslov EV, Ushakov EN, Fedin VP, Fedorenko SV, Fedorova OA, Fedorov YV, Chvalun SN, Tsivadze AY, Shtykov SN, Shurpik DN, Shcherbina MA, Yakimova LS. Functional supramolecular systems: design and applications. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr5011] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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10
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Tan T, Guo Z, Wang Y, Ji Y, Hu J, Zhang Y. Gelation of a Pentapeptide in Alcohols. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:8961-8970. [PMID: 34297581 DOI: 10.1021/acs.langmuir.1c00841] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Properties of solvents such as polarity and H-bond-forming ability are critical for the formation of an organogel and have a significant impact on the gel behavior, as solvents are the majority of organogel systems. However, so far, there is still a lack of systematic studies regarding the effects of molecular structures of solvents on the characteristics of organogels. Motivated by revealing such a relationship, in this paper, we studied the morphologies of assemblies, gelation behaviors, and secondary structures of a pentapeptide termed EAF-5 in a wide variety of alcohols. The side chains and lengths of carbon chains of the solvent molecules were found to play a critical role in the self-assembly and gelation of EAF-5. EAF-5 was capable of self-assembling into fibers and entangling into a network in alcohols including ethanol, propanol, butanol, n-pentanol, and n-hexanol, which further immobilized the corresponding alcohols to form gels. In these organogels, increasing β-sheet secondary structures of the peptides were formed by introducing side chains and extending the length of primary alcohol molecules. We hypothesized that alcohol molecules with extended lengths and side chains reduced the gelator-solvent interactions and promoted the gelator-gelator interactions, resulting in the self-assembly of EAF-5 into fibril structures and development of gels. These findings provide a new sight into the interactions between gelators and solvents and are helpful for designing peptide-based organogelators.
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Affiliation(s)
- Tingyuan Tan
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Guo
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yujiao Wang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuwen Ji
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Hu
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Yi Zhang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
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11
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Erdoğan H. Cation-based approach to morphological diversity of diphenylalanine dipeptide structures. SOFT MATTER 2021; 17:5221-5230. [PMID: 33949599 DOI: 10.1039/d1sm00083g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Different approaches are taken in order to examine the spontaneous arrangement processes of dipeptide structures. One of these approaches is to examine the effects of common cations on dipeptide structures' self-assembly processes. In this study, the effects of Al3+, Cu2+, Pb2+, Hg2+, Mg2+, Zn2+, Cd2+, Fe2+ and Ni2+ cations on the self-assembly processes of diphenylalanine (FF) dipeptide molecules were investigated. A detailed examination was made of the self-assembly of FF dipeptides in the presence of Hg2+, and a spherical architecture structure was shown. The morphological diversity resulting from the effects of Hg2+ cations at different concentrations on FF dipeptides was explained using Scanning Electron Microscopy (SEM), X-ray Diffraction, (XRD), and Fourier Transform Infrared Spectroscopy (FTIR) techniques. It is thought that this work will contribute to the indexing of the effects of toxic species such as Hg2+ on dipeptides, which are the smallest peptide units obtained. We think that the examination of FF dipeptides in the structures of amyloid plaques, which are thought to affect neurological disorders such as Alzheimer's and Parkinson's, will prompt further studies.
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Affiliation(s)
- Hakan Erdoğan
- University of Health Sciences Turkey, Gülhane Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 06018 Ankara, Turkey.
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12
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Islas‐Trejo E, Avila‐Montiel C, Tlahuext H, Lechuga‐Islas VD, Tapia‐Benavides AR, Tlahuextl M. The Effects of pH on the Supramolecular Structure of Amino Amides. ChemistrySelect 2021. [DOI: 10.1002/slct.202100579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Eltonh Islas‐Trejo
- Chemistry Department Universidad Autónoma del Estado de Hidalgo Pachuca-Tulancingo, 4.5, M de la Reforma Hgo 42184 México
| | - Concepción Avila‐Montiel
- Chemistry Department Universidad Autónoma del Estado de Hidalgo Pachuca-Tulancingo, 4.5, M de la Reforma Hgo 42184 México
| | - Hugo Tlahuext
- Centro de Investigaciones Químicas Universidad Autónoma del Estado de Morelos Avenida Universidad 1001 Cuernavaca Mor 62100 México
| | - Víctor D. Lechuga‐Islas
- Chemistry Department Universidad Autónoma del Estado de Hidalgo Pachuca-Tulancingo, 4.5, M de la Reforma Hgo 42184 México
| | - Antonio R. Tapia‐Benavides
- Chemistry Department Universidad Autónoma del Estado de Hidalgo Pachuca-Tulancingo, 4.5, M de la Reforma Hgo 42184 México
| | - Margarita Tlahuextl
- Chemistry Department Universidad Autónoma del Estado de Hidalgo Pachuca-Tulancingo, 4.5, M de la Reforma Hgo 42184 México
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13
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To T, Sakamoto Y, Sadakane K, Matsugami M, Takamuku T. Aggregation of the Dipeptide Leu-Gly in Alcohol-Water Binary Solvents Elucidated from the Solvation Structure for Each Moiety. J Phys Chem B 2021; 125:240-252. [PMID: 33395527 DOI: 10.1021/acs.jpcb.0c08809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The aggregation of a dipeptide, l-leucine-glycine (Leu-Gly), at 100 mmol dm-3 has been observed in 1,1,1,3,3,3-hexafluoroisopropanol (HFIP)-water and 2-propanol (2-PrOH)-water solvents at various alcohol mole fractions, xA, using the dynamic light scattering technique and molecular dynamics (MD) simulations. Leu-Gly was dissolved into the HFIP solvents at the concentration over the entire xA range, while the dipeptide was not dissolved in the 2-PrOH solvents above xA = 0.6. Interestingly, the MD snapshots showed different shapes of Leu-Gly aggregates in the HFIP and 2-PrOH solvents. A linear-shaped aggregate forms in the former; in contrast, a spherical-shaped aggregate is generated in the latter. The solvation structure of each moiety of Leu-Gly in the HFIP and 2-PrOH solvents was observed using experimental and theoretical techniques,1H and 13C NMR, IR, and 19F-1H HOESY measurements and MD simulations. These results gave us the reasons for the different shapes of Leu-Gly aggregates in both solvents. In the HFIP solvents, most of the moieties of the dipeptide are easily solvated by HFIP. This induces the elongated structure of Leu-Gly, leading to the electrostatic interaction between the N- (NH3+ group) and C- (COO- group) terminals of dipeptide molecules. On the other hand, in the 2-PrOH solvents, water molecules that initially solvate the moieties of Leu-Gly, such as the N- and C-terminals and the peptide linkage, are not easily eliminated even as the xA is close to 0.6. The water molecules can bridge such moieties of Leu-Gly to form spherical-shaped aggregates. The diffusion coefficients of Leu-Gly in both alcohol-water binary solvents were experimentally determined by NMR DOSY to estimate the geometries of the aggregates in the solvents. The sizes of Leu-Gly aggregates obtained by DOSY for both solvent systems were consistent with those estimated from the MD snapshots.
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Affiliation(s)
- Takahiro To
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Honjo-machi, Saga 840-8502, Japan
| | - Yusuke Sakamoto
- Faculty of Science and Engineering, Saga University, Honjo-machi, Saga 840-8502, Japan
| | - Koichiro Sadakane
- Faculty of Life and Medical Sciences, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe, Kyoto 610-0394, Japan
| | - Masaru Matsugami
- Faculty of Liberal Arts, National Institute of Technology (KOSEN), Kumamoto College, 2659-2 Suya, Koshi, Kumamoto 861-1102, Japan
| | - Toshiyuki Takamuku
- Faculty of Science and Engineering, Saga University, Honjo-machi, Saga 840-8502, Japan
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14
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Tan T, Shen Z, Wang Y, Guo Z, Hu J, Zhang Y. Self-assembly of pentapeptides in ethanol to develop organogels. SOFT MATTER 2020; 16:10567-10573. [PMID: 33079116 DOI: 10.1039/d0sm01303j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Organogels have a wide variety of applications in the fields of chemistry, electricity, biomedicine and environmental engineering, which call for robust strategies for designing and developing novel organogelators. Here, we reported a pentapeptide, ECAYF, which was capable of forming a self-healing ethanol gel exhibiting viscoelastic and solid-like properties. The ethanol gel of ECAYF was stable for at least several months, suggesting strong non-covalent interactions between ethanol and the peptide in the gel. In the ethanol gel, self-assembled peptide fibrils were found to immobilize the ethanol molecules for gelation. Results also suggested that the EAF-5 peptide adopted H-bonding β-sheet secondary structures, which further assembled into fibrils. Meanwhile, the self-assembly of the ECAYF peptide in mixtures of differently fractioned ethanol and H2O was observed, which clearly indicated that ethanol promoted the assembly of ECAYF in the solutions. These findings are helpful in understanding the roles of organic solvents as well as the complicated interactions between the solvent and gelator molecules in gelation.
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Affiliation(s)
- Tingyuan Tan
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.
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15
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Gupta S, Singh I, Sharma AK, Kumar P. Ultrashort Peptide Self-Assembly: Front-Runners to Transport Drug and Gene Cargos. Front Bioeng Biotechnol 2020; 8:504. [PMID: 32548101 PMCID: PMC7273840 DOI: 10.3389/fbioe.2020.00504] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/29/2020] [Indexed: 12/18/2022] Open
Abstract
The translational therapies to promote interaction between cell and signal come with stringent eligibility criteria. The chemically defined, hierarchically organized, and simpler yet blessed with robust intermolecular association, the peptides, are privileged to make the cut-off for sensing the cell-signal for biologics delivery and tissue engineering. The signature service and insoluble network formation of the peptide self-assemblies as hydrogels have drawn a spell of research activity among the scientists all around the globe in the past decades. The therapeutic peptide market players are anticipating promising growth opportunities due to the ample technological advancements in this field. The presence of the other organic moieties, enzyme substrates and well-established protecting groups like Fmoc and Boc etc., bring the best of both worlds. Since the large sequences of peptides severely limit the purification and their isolation, this article reviews the account of last 5 years' efforts on novel approaches for formulation and development of single molecule amino acids, ultra-short peptide self-assemblies (di- and tri- peptides only) and their derivatives as drug/gene carriers and tissue-engineering systems.
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Affiliation(s)
- Seema Gupta
- Chemistry Department, Acharya Narendra Dev College, University of Delhi, New Delhi, India
| | - Indu Singh
- Chemistry Department, Acharya Narendra Dev College, University of Delhi, New Delhi, India
- Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Ashwani K. Sharma
- Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Pradeep Kumar
- Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
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16
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Pappas CG, Wijerathne N, Sahoo JK, Jain A, Kroiss D, Sasselli IR, Pina AS, Lampel A, Ulijn RV. Spontaneous Aminolytic Cyclization and Self‐Assembly of Dipeptide Methyl Esters in Water. CHEMSYSTEMSCHEM 2020. [DOI: 10.1002/syst.202000013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Charalampos G. Pappas
- Department of Pure and Applied Chemistry, Technology and Innovative CentreUniversity of Strathclyde Glasgow G1 1RD UK
- Advanced Science Research Center (ASRC) at theCity University of New York (CUNY) 85 St Nicholas Terrace New York 10031 USA
| | - Nadeesha Wijerathne
- Advanced Science Research Center (ASRC) at theCity University of New York (CUNY) 85 St Nicholas Terrace New York 10031 USA
- Hunter CollegeDepartment of Chemistry CUNY 695 Park Avenue New York 10065 USA
- Ph.D. Program in Chemistry, TheGraduate Center of the City University of New York New York NY, 10016 USA
| | - Jugal Kishore Sahoo
- Department of Pure and Applied Chemistry, Technology and Innovative CentreUniversity of Strathclyde Glasgow G1 1RD UK
| | - Ankit Jain
- Advanced Science Research Center (ASRC) at theCity University of New York (CUNY) 85 St Nicholas Terrace New York 10031 USA
| | - Daniela Kroiss
- Advanced Science Research Center (ASRC) at theCity University of New York (CUNY) 85 St Nicholas Terrace New York 10031 USA
- Ph.D. Program in Biochemistry, TheGraduate Center of the City University of New York New York NY, 10016 USA
| | - Ivan R. Sasselli
- Department of Pure and Applied Chemistry, Technology and Innovative CentreUniversity of Strathclyde Glasgow G1 1RD UK
| | - Ana Sofia Pina
- Advanced Science Research Center (ASRC) at theCity University of New York (CUNY) 85 St Nicholas Terrace New York 10031 USA
| | - Ayala Lampel
- Advanced Science Research Center (ASRC) at theCity University of New York (CUNY) 85 St Nicholas Terrace New York 10031 USA
| | - Rein V. Ulijn
- Advanced Science Research Center (ASRC) at theCity University of New York (CUNY) 85 St Nicholas Terrace New York 10031 USA
- Hunter CollegeDepartment of Chemistry CUNY 695 Park Avenue New York 10065 USA
- Ph.D. Program in Chemistry, TheGraduate Center of the City University of New York New York NY, 10016 USA
- Ph.D. Program in Biochemistry, TheGraduate Center of the City University of New York New York NY, 10016 USA
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17
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Banerjee P, Pyne A, Sarkar N. Understanding the Self-Assembling Behavior of Biological Building Block Molecules: A Spectroscopic and Microscopic Approach. J Phys Chem B 2020; 124:2065-2080. [PMID: 32081003 DOI: 10.1021/acs.jpcb.9b09123] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
"Mother nature" utilizes molecular self-assembly as an efficient tool to design several fascinating supramolecular architectures from simple building blocks like amino acids, peptides, and nucleobases. The self-assembling behavior of various biologically important molecules, morphological outcomes, molecular mechanism of association, and finally their applications in the real world draw broad interest from chemical and biological point of views. In this present Feature Article, the amyloid hypothesis is extended to include nonproteinaceous single metabolites that invoke a new paradigm for the pathology of inborn metabolic disorders. In this scenario, we dedicate this paper to understanding the morphological consequences and mechanistic insight of the self-assembly of some important amino acids (e.g., l-phenylalanine, l-tyrosine, glycine, etc.) and nucleobases (adenine and eight uracil moiety derivatives). Using proper spectroscopic and microscopic tools, distinct assembling mechanisms of different amino acids and nucleobases have been established. Again, lanthanides, polyphenolic compounds such as crown ethers, and a worldwide drink, beer, are elegantly employed as inhibitors of the resulting fibrillar aggregated structures. As a consequence, this study will cover literally a vast region in the self-assembling outcomes of single biologically important molecules, and therefore, we expect that a detailed understanding of such morphological outcomes using spectroscopic and microscopic approaches may open a new paradigm in this burgeoning field.
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Affiliation(s)
- Pavel Banerjee
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302 WB, India
| | - Arghajit Pyne
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302 WB, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302 WB, India
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18
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Dutta R, Sil S, Kundu S, Nandi S, Sarkar N. Multi-stimuli responsive fabrication of supramolecular assemblies using ionic self-assembly approach. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.04.138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Xiong Q, Jiang Y, Cai X, Yang F, Li Z, Han W. Conformation Dependence of Diphenylalanine Self-Assembly Structures and Dynamics: Insights from Hybrid-Resolution Simulations. ACS NANO 2019; 13:4455-4468. [PMID: 30869864 DOI: 10.1021/acsnano.8b09741] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The molecular design of peptide-assembled nanostructures relies on extensive knowledge pertaining to the relationship between conformational features of peptide constituents and their behavior regarding self-assembly, and characterizing the conformational details of peptides during their self-assembly is experimentally challenging. Here, we demonstrate that a hybrid-resolution modeling method can be employed to investigate the role that conformation plays during the assembly of terminally capped diphenylalanines (FF) through microsecond simulations of hundreds or thousands of peptides. Our simulations discovered tubular or vesicular nanostructures that were consistent with experimental observation while reproducing critical self-assembly concentration and secondary structure contents in the assemblies that were measured in our experiments. The atomic details provided by our method allowed us to uncover diverse FF conformations and conformation dependence of assembled nanostructures. We found that the assembled morphologies and the molecular packing of FFs in the observed assemblies are linked closely with side-chain angle and peptide bond orientation, respectively. Of various conformations accessible to soluble FFs, only a select few are compatible with the assembled morphologies in water. A conformation resembling a FF crystal, in particular, became predominant due to its ability to permit highly ordered and energetically favorable FF packing in aqueous assemblies. Strikingly, several conformations incompatible with the assemblies arose transiently as intermediates, facilitating key steps of the assembly process. The molecular rationale behind the role of these intermediate conformations were further explained. Collectively, the structural details reported here advance the understanding of the FF self-assembly mechanism, and our method shows promise for studying peptide-assembled nanostructures and their rational design.
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Affiliation(s)
- Qinsi Xiong
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen 518055 , China
| | - Yixiang Jiang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen 518055 , China
| | - Xiang Cai
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen 518055 , China
| | - Fadeng Yang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen 518055 , China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen 518055 , China
| | - Wei Han
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen 518055 , China
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20
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Kundu N, Banik D, Sarkar N. Self-Assembly of Amphiphiles into Vesicles and Fibrils: Investigation of Structure and Dynamics Using Spectroscopy and Microscopy Techniques. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:11637-11654. [PMID: 29544249 DOI: 10.1021/acs.langmuir.7b04355] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Amphiphiles are a class of molecules which are known to assemble into a variety of nanostructures. The understanding and applications of self-assembled systems are based on what has been learned from biology. Among the vast number of self-assemblies, in this article, we have described the formation, characterization, and dynamics of two important biologically inspired assemblies: vesicles and fibrils. Vesicles, which can be classified into several categories depending on the sizes and components, are of great interest due to their potential applications in drug delivery and as nanoscale reactors. The structure and dynamics of vesicles can also mimic the complex geometry of the cell membrane. On the other hand, the self-assembly of proteins, peptides, and even single amino acids leads to a number of degenerative disorders. Thus, a complete understanding of these self-assembled systems is necessary. In this article, we discuss recent work on vesicular aggregates composed of phospholipids, fatty acids, and ionic as well as nonionic surfactants and single amino acid-based fibrils such as phenylalanine and tyrosine. Beside the characterization, we also emphasize the excited-state dynamics inside the aggregates for a proper understanding of the organization, reactivity, and heterogeneity of the aggregates.
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Affiliation(s)
- Niloy Kundu
- Department of Chemistry , Indian Institute of Technology , Kharagpur 721302 , WB India
| | - Debasis Banik
- Department of Chemistry , Indian Institute of Technology , Kharagpur 721302 , WB India
| | - Nilmoni Sarkar
- Department of Chemistry , Indian Institute of Technology , Kharagpur 721302 , WB India
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21
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Lampel A, Ulijn RV, Tuttle T. Guiding principles for peptide nanotechnology through directed discovery. Chem Soc Rev 2018; 47:3737-3758. [PMID: 29748676 DOI: 10.1039/c8cs00177d] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Life's diverse molecular functions are largely based on only a small number of highly conserved building blocks - the twenty canonical amino acids. These building blocks are chemically simple, but when they are organized in three-dimensional structures of tremendous complexity, new properties emerge. This review explores recent efforts in the directed discovery of functional nanoscale systems and materials based on these same amino acids, but that are not guided by copying or editing biological systems. The review summarises insights obtained using three complementary approaches of searching the sequence space to explore sequence-structure relationships for assembly, reactivity and complexation, namely: (i) strategic editing of short peptide sequences; (ii) computational approaches to predicting and comparing assembly behaviours; (iii) dynamic peptide libraries that explore the free energy landscape. These approaches give rise to guiding principles on controlling order/disorder, complexation and reactivity by peptide sequence design.
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Affiliation(s)
- A Lampel
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), New York, NY, USA.
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22
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Clarke DE, Parmenter CDJ, Scherman OA. Tunable Pentapeptide Self-Assembled β-Sheet Hydrogels. Angew Chem Int Ed Engl 2018; 57:7709-7713. [PMID: 29603545 PMCID: PMC6055752 DOI: 10.1002/anie.201801001] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Indexed: 01/13/2023]
Abstract
Oligopeptide‐based supramolecular hydrogels hold promise in a range of applications. The gelation of these systems is hard to control, with minor alterations in the peptide sequence significantly influencing the self‐assembly process. We explored three pentapeptide sequences with different charge distributions and discovered that they formed robust, pH‐responsive hydrogels. By altering the concentration and charge distribution of the peptide sequence, the stiffness of the hydrogels could be tuned across two orders of magnitude (2–200 kPa). Also, through reassembly of the β‐sheet interactions the hydrogels could self‐heal and they demonstrated shear‐thin behavior. Using spectroscopic and cryo‐imaging techniques, we investigated the relationship between peptide sequence and molecular structure, and how these influence the mechanical properties of the hydrogel. These pentapeptide hydrogels with tunable morphology and mechanical properties have promise in tissue engineering, injectable delivery vectors, and 3D printing applications.
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Affiliation(s)
- David E Clarke
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Christopher D J Parmenter
- Nottingham Nanoscale and Microscale Research Centre, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Oren A Scherman
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
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23
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Clarke DE, Parmenter CDJ, Scherman OA. Tunable Pentapeptide Self-Assembled β-Sheet Hydrogels. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- David E. Clarke
- Melville Laboratory for Polymer Synthesis; Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Christopher D. J. Parmenter
- Nottingham Nanoscale and Microscale Research Centre; University of Nottingham; University Park Nottingham NG7 2RD UK
| | - Oren A. Scherman
- Melville Laboratory for Polymer Synthesis; Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
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24
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Safaryan S, Slabov V, Kopyl S, Romanyuk K, Bdikin I, Vasilev S, Zelenovskiy P, Shur VY, Uslamin EA, Pidko EA, Vinogradov AV, Kholkin AL. Diphenylalanine-Based Microribbons for Piezoelectric Applications via Inkjet Printing. ACS APPLIED MATERIALS & INTERFACES 2018; 10:10543-10551. [PMID: 29498259 DOI: 10.1021/acsami.7b19668] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Peptide-based nanostructures are very promising for nanotechnological applications because of their excellent self-assembly properties, biological and chemical flexibility, and unique multifunctional performance. However, one of the limiting factors for the integration of peptide assemblies into functional devices is poor control of their alignment and other geometrical parameters required for device fabrication. In this work, we report a novel method for the controlled deposition of one of the representative self-assembled peptides-diphenylalanine (FF)-using a commercial inkjet printer. The initial FF solution, which has been shown to readily self-assemble into different structures such as nano- and microtubes and microrods, was modified to be used as an efficient ink for the printing of aligned FF-based structures. Furthermore, during the development of the suitable ink, we were able to produce a novel type of FF conformation with high piezoelectric response and excellent stability. By using this method, ribbonlike microcrystals based on FF could be formed and precisely patterned on different surfaces. Possible mechanisms of structure formation and piezoelectric effect in printed microribbons are discussed along with the possible applications.
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Affiliation(s)
- Sofia Safaryan
- Laboratory of Solution Chemistry of Advanced Materials and Technologies , ITMO University , St. Petersburg 197101 , Russian Federation
| | - Vladislav Slabov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies , ITMO University , St. Petersburg 197101 , Russian Federation
| | - Svitlana Kopyl
- Department of Physics & CICECO-Aveiro Institute of Materials , University of Aveiro , 3810-193 Aveiro , Portugal
| | - Konstantin Romanyuk
- Department of Physics & CICECO-Aveiro Institute of Materials , University of Aveiro , 3810-193 Aveiro , Portugal
- School of Natural Sciences and Mathematics , Ural Federal University , Ekaterinburg 620000 , Russian Federation
| | - Igor Bdikin
- Department of Mechanical Engineering & TEMA- Centre for Mechanical Technology and Automation , University of Aveiro , 3810-193 Aveiro , Portugal
| | - Semen Vasilev
- School of Natural Sciences and Mathematics , Ural Federal University , Ekaterinburg 620000 , Russian Federation
| | - Pavel Zelenovskiy
- School of Natural Sciences and Mathematics , Ural Federal University , Ekaterinburg 620000 , Russian Federation
| | - Vladimir Ya Shur
- School of Natural Sciences and Mathematics , Ural Federal University , Ekaterinburg 620000 , Russian Federation
| | - Evgeny A Uslamin
- Inorganic Materials Chemistry Group , Eindhoven University of Technology , PO Box 513, Eindhoven 5600 MB , The Netherlands
| | - Evgeny A Pidko
- Laboratory of Solution Chemistry of Advanced Materials and Technologies , ITMO University , St. Petersburg 197101 , Russian Federation
- Inorganic Materials Chemistry Group , Eindhoven University of Technology , PO Box 513, Eindhoven 5600 MB , The Netherlands
| | - Alexander V Vinogradov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies , ITMO University , St. Petersburg 197101 , Russian Federation
| | - Andrei L Kholkin
- Department of Physics & CICECO-Aveiro Institute of Materials , University of Aveiro , 3810-193 Aveiro , Portugal
- School of Natural Sciences and Mathematics , Ural Federal University , Ekaterinburg 620000 , Russian Federation
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25
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Sasselli IR, Moreira IP, Ulijn RV, Tuttle T. Molecular dynamics simulations reveal disruptive self-assembly in dynamic peptide libraries. Org Biomol Chem 2018; 15:6541-6547. [PMID: 28745772 DOI: 10.1039/c7ob01268c] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
There is significant interest in the use of unmodified self-assembling peptides as building blocks for functional, supramolecular biomaterials. Recently, dynamic peptide libraries (DPLs) have been proposed to select self-assembling materials from dynamically exchanging mixtures of dipeptide inputs in the presence of a nonspecific protease enzyme, where peptide sequences are selected and amplified based on their self-assembling tendencies. It was shown that the results of the DPL of mixed sequences (e.g. starting from a mixture of dileucine, L2, and diphenylalanine, F2) did not give the same outcome as the separate L2 and F2 libraries (which give rise to the formation of F6 and L6), implying that interactions between these sequences could disrupt the self-assembly. In this study, coarse grained molecular dynamics (CG-MD) simulations are used to understand the DPL results for F2, L2 and mixed libraries. CG-MD simulations demonstrate that interactions between precursors can cause the low formation yield of hexapeptides in the mixtures of dipeptides and show that this ability to disrupt is influenced by the concentration of the different species in the DPL. The disrupting self-assembly effect between the species in the DPL is an important effect to take into account in dynamic combinatorial chemistry as it affects the possible discovery of new materials. This work shows that combined computational and experimental screening can be used complementarily and in combination providing a powerful means to discover new supramolecular peptide nanostructures.
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Affiliation(s)
- I R Sasselli
- Department of Pure & Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK.
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26
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Subbalakshmi C, Basak P, Nagaraj R. Self-assembly of t-butyloxycarbonyl protected dipeptide methyl esters composed of leucine, isoleucine, and valine into highly organized structures from alcohol and aqueous alcohol mixtures. Biopolymers 2017; 108. [DOI: 10.1002/bip.23033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 05/05/2017] [Accepted: 05/26/2017] [Indexed: 01/13/2023]
Affiliation(s)
- Chivukula Subbalakshmi
- CSIR-Centre for Cellular and Molecular Biology; Uppal Road; Hyderabad Telangana 500007 India
| | - Pratyay Basak
- Nanomaterials Laboratory, Inorganic & Physical Chemistry Division; CSIR-Indian Institute of Chemical Technology, Uppal Road; Hyderabad Telangana 500007 India
| | - Ramakrishnan Nagaraj
- CSIR-Centre for Cellular and Molecular Biology; Uppal Road; Hyderabad Telangana 500007 India
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27
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Cao M, Lu S, Zhao W, Deng L, Wang M, Wang J, Zhou P, Wang D, Xu H, Lu JR. Peptide Self-Assembled Nanostructures with Distinct Morphologies and Properties Fabricated by Molecular Design. ACS APPLIED MATERIALS & INTERFACES 2017; 9:39174-39184. [PMID: 29067798 DOI: 10.1021/acsami.7b11681] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Six surfactant-like peptides with the same amino acid composition but different primary sequences are designed, including G3A3V3I3K3, K3I3V3A3G3, I3V3A3G3K3, K3G3A3V3I3, V3G3I3A3K3, and K3A3I3G3V3. These peptides form antiparallel β-sheets during self-assembly. Because the constituent residues have different side chain size and hydrophobicity, sequence changes adjust group distribution and hydrophobicity on the two sides of a given β-sheet. This consequently tunes the binding energy of the side-to-side pairing conformations and leads to different self-assembled structures. G3A3V3I3K3 and K3I3V3A3G3 form short nanorods with diameters of 8.5 ± 1.0 nm and lengths <150 nm. I3V3A3G3K3 and K3G3A3V3I3 form nanosheets with heights of 4.0 ± 0.5 nm and limited lengths and widths. V3G3I3A3K3 and K3A3I3G3V3 form long fibrils with diameters of 7.0 ± 1.0 nm and lengths of micrometer scale. These nanostructures exhibit different capacity in encapsulating insoluble hydrophobic drug molecules and delivering them into the cells. The nanosheets of I3V3A3G3K3 and K3G3A3V3I3 can encapsulate both nile red and doxorubicin molecules to an extent of up to 17-23% in mole ratio. Moreover, the shape and size of the nanostructures affect the drug delivery into cells greatly, with the nanosheets and short rods exhibiting higher efficiency than the long fibrils. The study provides new insights into programmed peptide self-assembly toward specific functionalities.
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Affiliation(s)
- Meiwen Cao
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Sha Lu
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Wenjing Zhao
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Li Deng
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Meng Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Jiqian Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Peng Zhou
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Dong Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Hai Xu
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Jian R Lu
- Biological Physics Laboratory, School of Physics and Astronomy, University of Manchester , Schuster Building, Oxford Road, Manchester M13 9PL, U.K
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28
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Banik D, Banerjee P, Sabeehuddin G, Sarkar N. Effects of a common worldwide drink (Beer) on l-Phenylalanine and l-Tyrosine fibrillar assemblies. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.08.066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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29
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Banik D, Kundu S, Banerjee P, Dutta R, Sarkar N. Investigation of Fibril Forming Mechanisms of l-Phenylalanine and l-Tyrosine: Microscopic Insight toward Phenylketonuria and Tyrosinemia Type II. J Phys Chem B 2017; 121:1533-1543. [DOI: 10.1021/acs.jpcb.6b12220] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Debasis Banik
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Sangita Kundu
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Pavel Banerjee
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Rupam Dutta
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
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30
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Ziganshin MA, Safiullina AS, Ziganshina SA, Gerasimov AV, Gorbatchuk VV. Non-zeolitic properties of the dipeptide l-leucyl–l-leucine as a result of the specific nanostructure formation. Phys Chem Chem Phys 2017; 19:13788-13797. [DOI: 10.1039/c7cp01393k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Non-zeolitic sorption properties of l-leucyl–l-leucine which results from a specific self-organization of the dipeptide into different micro- and nanostructures may be used for the separation of mixtures of organic compounds.
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Affiliation(s)
- Marat A. Ziganshin
- A. M. Butlerov Institute of Chemistry
- Kazan Federal University
- Kazan, 420008
- Russia
| | - Aisylu S. Safiullina
- A. M. Butlerov Institute of Chemistry
- Kazan Federal University
- Kazan, 420008
- Russia
| | - Sufia A. Ziganshina
- Kazan Zavoisky Physical-Technical Institute of the Kazan Scientific Center of the Russian Academy of Sciences
- Kazan, 420029
- Russia
| | | | - Valery V. Gorbatchuk
- A. M. Butlerov Institute of Chemistry
- Kazan Federal University
- Kazan, 420008
- Russia
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31
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Abul-Haija YM, Scott GG, Sahoo JK, Tuttle T, Ulijn RV. Cooperative, ion-sensitive co-assembly of tripeptide hydrogels. Chem Commun (Camb) 2017; 53:9562-9565. [DOI: 10.1039/c7cc04796g] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Computational simulations and experimental validation of cooperative co-assembly of structural and functional tripeptides shows selective hydrogel formation in response to complexation with copper.
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Affiliation(s)
- Yousef M. Abul-Haija
- WestCHEM/Department of Pure and Applied Chemistry
- University of Strathclyde
- Glasgow G1 1XL
- UK
- WestCHEM/School of Chemistry
| | - Gary G. Scott
- WestCHEM/Department of Pure and Applied Chemistry
- University of Strathclyde
- Glasgow G1 1XL
- UK
| | - Jugal Kishore Sahoo
- WestCHEM/Department of Pure and Applied Chemistry
- University of Strathclyde
- Glasgow G1 1XL
- UK
| | - Tell Tuttle
- WestCHEM/Department of Pure and Applied Chemistry
- University of Strathclyde
- Glasgow G1 1XL
- UK
| | - Rein V. Ulijn
- WestCHEM/Department of Pure and Applied Chemistry
- University of Strathclyde
- Glasgow G1 1XL
- UK
- Advanced Science Research Center (ASRC) at the Graduate Center of the City University of New York (CUNY)
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32
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Pappas CG, Shafi R, Sasselli IR, Siccardi H, Wang T, Narang V, Abzalimov R, Wijerathne N, Ulijn RV. Dynamic peptide libraries for the discovery of supramolecular nanomaterials. NATURE NANOTECHNOLOGY 2016; 11:960-967. [PMID: 27694850 DOI: 10.1038/nnano.2016.169] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 08/11/2016] [Indexed: 06/06/2023]
Abstract
Sequence-specific polymers, such as oligonucleotides and peptides, can be used as building blocks for functional supramolecular nanomaterials. The design and selection of suitable self-assembling sequences is, however, challenging because of the vast combinatorial space available. Here we report a methodology that allows the peptide sequence space to be searched for self-assembling structures. In this approach, unprotected homo- and heterodipeptides (including aromatic, aliphatic, polar and charged amino acids) are subjected to continuous enzymatic condensation, hydrolysis and sequence exchange to create a dynamic combinatorial peptide library. The free-energy change associated with the assembly process itself gives rise to selective amplification of self-assembling candidates. By changing the environmental conditions during the selection process, different sequences and consequent nanoscale morphologies are selected.
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Affiliation(s)
- Charalampos G Pappas
- Advanced Science Research Center (ASRC), City University of New York, 85 St Nicholas Terrace, New York 10031, USA
- WestCHEM/Department of Pure &Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - Ramim Shafi
- Advanced Science Research Center (ASRC), City University of New York, 85 St Nicholas Terrace, New York 10031, USA
| | - Ivan R Sasselli
- WestCHEM/Department of Pure &Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - Henry Siccardi
- Advanced Science Research Center (ASRC), City University of New York, 85 St Nicholas Terrace, New York 10031, USA
| | - Tong Wang
- Imaging Facility of CUNY ASRC, 85 St Nicholas Terrace, New York 10031, USA
| | - Vishal Narang
- Advanced Science Research Center (ASRC), City University of New York, 85 St Nicholas Terrace, New York 10031, USA
| | - Rinat Abzalimov
- Advanced Science Research Center (ASRC), City University of New York, 85 St Nicholas Terrace, New York 10031, USA
| | - Nadeesha Wijerathne
- Advanced Science Research Center (ASRC), City University of New York, 85 St Nicholas Terrace, New York 10031, USA
- Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, New York 10065, USA
- The Graduate Center of the City University of New York, New York 10016, USA
| | - Rein V Ulijn
- Advanced Science Research Center (ASRC), City University of New York, 85 St Nicholas Terrace, New York 10031, USA
- WestCHEM/Department of Pure &Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK
- Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, New York 10065, USA
- The Graduate Center of the City University of New York, New York 10016, USA
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33
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Banik D, Dutta R, Banerjee P, Kundu S, Sarkar N. Inhibition of Fibrillar Assemblies of l-Phenylalanine by Crown Ethers: A Potential Approach toward Phenylketonuria. J Phys Chem B 2016; 120:7662-70. [DOI: 10.1021/acs.jpcb.6b05209] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Debasis Banik
- Department
of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Rupam Dutta
- Department
of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Pavel Banerjee
- Department
of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Sangita Kundu
- Department
of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Nilmoni Sarkar
- Department
of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
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34
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Mazzier D, Carraro F, Crisma M, Rancan M, Toniolo C, Moretto A. A terminally protected dipeptide: from crystal structure and self-assembly, through co-assembly with carbon-based materials, to a ternary catalyst for reduction chemistry in water. SOFT MATTER 2016; 12:238-245. [PMID: 26463728 DOI: 10.1039/c5sm02189h] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A terminally protected, hydrophobic dipeptide Boc-L-Cys(Me)-L-Leu-OMe (1) was synthesized and its 3D-structure was determined by single crystal X-ray diffraction analysis. This peptide is able to hierarchically self-assemble in a variety of superstructures, including hollow rods, ranging from the nano- to the macroscale, and organogels. In addition, 1 is able to drive fullerene (C60) or multiwalled carbon nanotubes (MWCNTs) in an organogel by co-assembling with them. A hybrid 1-C60–MWCNT organogel was prepared and converted (through a high vacuum-drying process) into a robust, high-volume, water insoluble, solid material where C60 is well dispersed over the entire superstructure. This ternary material was successfully tested as a catalyst for: (i) the reduction reaction of water-soluble azo compounds mediated by NaBH4 and UV-light with an overall performance remarkably better than that provided by C60 alone, and (ii) the NaBH4-mediated reduction of benzoic acid to benzyl alcohol. Our results suggest that the self-assembly properties of 1 might be related to the occurrence in its single crystal structure of a sixfold screw axis, a feature shared by most of the linear peptides known so far to give rise to nanotubes.
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Affiliation(s)
- Daniela Mazzier
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.
| | - Francesco Carraro
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.
| | - Marco Crisma
- Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Marzio Rancan
- Institute for Energetics and Interphases, CNR, 35131 Padova, Italy
| | - Claudio Toniolo
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy. and Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Alessandro Moretto
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy. and Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
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35
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Conte MP, Singh N, Sasselli IR, Escuder B, Ulijn RV. Metastable hydrogels from aromatic dipeptides. Chem Commun (Camb) 2016; 52:13889-13892. [DOI: 10.1039/c6cc05821c] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The dipeptides FF and FF-NH2 form metastable hydrogels upon sonication. The hydrogels show instantaneous syneresis upon mechanical contact.
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Affiliation(s)
- M. P. Conte
- WestCHEM/Department of Pure & Applied Chemistry
- University of Strathclyde
- Glasgow
- UK
| | - N. Singh
- Departament de Química Inorgànica i Orgànica
- Universitat Jaume I
- 12071 Castelló
- Spain
| | - I. R. Sasselli
- WestCHEM/Department of Pure & Applied Chemistry
- University of Strathclyde
- Glasgow
- UK
| | - B. Escuder
- Departament de Química Inorgànica i Orgànica
- Universitat Jaume I
- 12071 Castelló
- Spain
| | - R. V. Ulijn
- WestCHEM/Department of Pure & Applied Chemistry
- University of Strathclyde
- Glasgow
- UK
- Advanced Science Research Center (ASRC) and Hunter College
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36
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Liang Z, Wang Y, Wang W, Han X, Chen JF, Xue C, Zhao H. Structural Correspondence of the Oriented Attachment Growth Mechanism of Crystals of the Pharmaceutical Dirithromycin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:13802-13812. [PMID: 26632998 DOI: 10.1021/acs.langmuir.5b02901] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The oriented attachment (OA) mechanism is promising for designing novel nanomaterials, yet an intensive understanding of the relationship between the crystal structure and attachment orientation is still lacking. In this work, we report layered hexagonal crystals of the pharmaceutical dirithromycin (DIR) containing multiple layers fabricated via a solvothermal method for a certain period of time at 40 °C. These elongated hexagonal crystals experience an OA that is preferentially on the face (001) of the initial crystals to assemble the final crystals into layered stacks. Through agreement with molecular modeling calculations, we predicted the final crystal growth morphology and confirmed the favored attachment surface based on the energy change ΔE following an OA event. These simulation results at the molecular level yielded good agreement with the crystal growth experiments. This study demonstrates the critical importance of combining experiments with a computational approach to understand the intrinsic molecular details of the OA growth mechanism of other compounds and to design nanomaterials with a desirable morphology and physical and chemical properties.
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Affiliation(s)
- Zuozhong Liang
- State Key Laboratory of Organic-Inorganic Composites, ‡Research Center of the Ministry of Education for High Gravity Engineering and Technology, and §Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology , Beijing 100029, China
| | - Yuan Wang
- State Key Laboratory of Organic-Inorganic Composites, ‡Research Center of the Ministry of Education for High Gravity Engineering and Technology, and §Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology , Beijing 100029, China
| | - Wei Wang
- State Key Laboratory of Organic-Inorganic Composites, ‡Research Center of the Ministry of Education for High Gravity Engineering and Technology, and §Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology , Beijing 100029, China
| | - Xianglong Han
- State Key Laboratory of Organic-Inorganic Composites, ‡Research Center of the Ministry of Education for High Gravity Engineering and Technology, and §Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology , Beijing 100029, China
| | - Jian-Feng Chen
- State Key Laboratory of Organic-Inorganic Composites, ‡Research Center of the Ministry of Education for High Gravity Engineering and Technology, and §Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology , Beijing 100029, China
| | - Chunyu Xue
- State Key Laboratory of Organic-Inorganic Composites, ‡Research Center of the Ministry of Education for High Gravity Engineering and Technology, and §Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology , Beijing 100029, China
| | - Hong Zhao
- State Key Laboratory of Organic-Inorganic Composites, ‡Research Center of the Ministry of Education for High Gravity Engineering and Technology, and §Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology , Beijing 100029, China
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