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Identification of heterochirality-mediated stereochemical interactions in peptide architectures. Colloids Surf B Biointerfaces 2023; 224:113200. [PMID: 36774824 DOI: 10.1016/j.colsurfb.2023.113200] [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: 10/22/2022] [Revised: 01/26/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023]
Abstract
In this work, we illustrate a strategy for constructing heterochiral peptide architectures with distinct structural, mechanical and thermal characteristics. A series of nanotube structures based on diphenylalanine (FF) and its chiral derivatives were examined. Pronounced effects relating to heterochirality on mechanostability and thermal stability can be identified. The homochiral peptide FF and its enantiomer ff formed nanotubes with high thermal and mechanical stabilities (Young's modulus: 20.3 ± 5.9 GPa for FF and 21.2 ± 4.7 GPa for ff). In contrast, heterochiral nanotubes formed by Ff and fF manifest superstructures along the axial direction with differed thermal and mechanical strength (Young's modulus: 7.3 ± 2.4 GPa for Ff and 8.3 ± 2.1 GPa for fF). Combining their single-crystal XRD structure and in silico results, it was demonstrated that the spatial orientations of aromatic moieties were subtly changed by heterochirality of peptide building blocks, which led to intramolecular face-to-face interactions. As the result, both intermolecular axial and interchannel interactions in heterochiral nanotubes were weakened as reflected in the strikingly deteriorated mechanical and thermal stabilities. Conversely, two aromatic side chains of the homochiral peptides were staggered and formed interdigitated steric zippers, which served as strong glues that secured the robustness of nanotubes in both axial and radial orientation. Furthermore, the generality of the heterochiral-mediated stereochemical effects was demonstrated in other "FF class" dipeptides, including fluorinated Ff, FW and FL. Our results unequivocally revealed the relationship between amino acid chirality, peptide molecule packing, and physical stabilities of "FF class" dipeptide self-assembled materials and provide valuable molecular insights into chirality-mediated stereochemical interactions in determining the properties of peptide architectures.
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2
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Almohammed S, Kanoun MB, Goumri‐Said S, Alam MW, Fularz A, Alnaim A, Rice JH, Rodriguez BJ. Thermally‐controlled spherical peptide gel architectures prepared using the
pH
switch method. Pept Sci (Hoboken) 2023. [DOI: 10.1002/pep2.24304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Affiliation(s)
- Sawsan Almohammed
- School of Physics University College Dublin Dublin Ireland
- Conway Institute of Biomolecular and Biomedical Research University College Dublin Dublin Ireland
| | | | - Souraya Goumri‐Said
- Physics Department, College of Science and General Studies Alfaisal University Riyadh Saudi Arabia
| | - Mir Waqas Alam
- Department of Physics, College of Science King Faisal University Al‐Ahsa Saudi Arabia
| | - Agata Fularz
- School of Physics University College Dublin Dublin Ireland
| | - Abdullah Alnaim
- Department of Physics, College of Science King Faisal University Al‐Ahsa Saudi Arabia
| | - James H. Rice
- School of Physics University College Dublin Dublin Ireland
| | - Brian J. Rodriguez
- School of Physics University College Dublin Dublin Ireland
- Conway Institute of Biomolecular and Biomedical Research University College Dublin Dublin Ireland
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3
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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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4
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Carlini L, Chiarinelli J, Mattioli G, Castrovilli MC, Valentini V, De Stefanis A, Bauer EM, Bolognesi P, Avaldi L. Insights into the Thermally Activated Cyclization Mechanism in a Linear Phenylalanine-Alanine Dipeptide. J Phys Chem B 2022; 126:2968-2978. [PMID: 35438499 PMCID: PMC9059117 DOI: 10.1021/acs.jpcb.1c10736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/31/2022] [Indexed: 11/29/2022]
Abstract
Dipeptides, the prototype peptides, exist in both linear (l-) and cyclo (c-) structures. Since the first mass spectrometry experiments, it has been observed that some l-structures may turn into the cyclo ones, likely via a temperature-induced process. In this work, combining several different experimental techniques (mass spectrometry, infrared and Raman spectroscopy, and thermogravimetric analysis) with tight-binding and ab initio simulations, we provide evidence that, in the case of l-phenylalanyl-l-alanine, an irreversible cyclization mechanism, catalyzed by water and driven by temperature, occurs in the condensed phase. This process can be considered as a very efficient strategy to improve dipeptide stability by turning the comparatively fragile linear structure into the robust and more stable cyclic one. This mechanism may have played a role in prebiotic chemistry and can be further exploited in the preparation of nanomaterials and drugs.
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Affiliation(s)
- Laura Carlini
- CNR-Istituto di Struttura
della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo
Scalo 00015, Italy
| | - Jacopo Chiarinelli
- CNR-Istituto di Struttura
della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo
Scalo 00015, Italy
| | - Giuseppe Mattioli
- CNR-Istituto di Struttura
della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo
Scalo 00015, Italy
| | - Mattea Carmen Castrovilli
- CNR-Istituto di Struttura
della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo
Scalo 00015, Italy
| | - Veronica Valentini
- CNR-Istituto di Struttura
della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo
Scalo 00015, Italy
| | - Adriana De Stefanis
- CNR-Istituto di Struttura
della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo
Scalo 00015, Italy
| | - Elvira Maria Bauer
- CNR-Istituto di Struttura
della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo
Scalo 00015, Italy
| | - Paola Bolognesi
- CNR-Istituto di Struttura
della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo
Scalo 00015, Italy
| | - Lorenzo Avaldi
- CNR-Istituto di Struttura
della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo
Scalo 00015, Italy
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5
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Poonia BK, Sidhu A, Sharma AB. Cyclo(l-proline-l-serine) Dipeptide Suppresses Seed Borne Fungal Pathogens of Rice: Altered Cellular Membrane Integrity of Fungal Hyphae and Seed Quality Benefits. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:2160-2168. [PMID: 35142498 DOI: 10.1021/acs.jafc.1c07659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Five proline-containing diketopiperazines (Pro-DKPs) produced by antagonistic microorganisms as secondary metabolites were selected and synthesized under laboratory conditions. Out of five synthesized Pro-DKPs, cyclo(l-Pro-l-Ser) (DKP-6) revealed the best inhibition of fungal pathogens (Fusarium verticillioides and Fusarium fujikuroi) of rice under in vitro conditions with effective doses lower than standard fungicide carbendazim. DKP-6 induced stress on the fungal cell membrane integrity, which was revealed by calcofluor white and propidium iodide assays, endorsed by ultra-microscopic details and soluble protein leakage assays. In vivo seed treatment of infested rice seeds with DKP-6 at 2000 μg/mL for 10 h of seed treatment inflicted best reduction in seed rot and seedling blight with respect to control and carbendazim. Significant enhancement in seedling quality parameters were also observed. The work presented the strong influence of cyclo(l-Pro-l-Ser) as a mycocidal seed treatment agent better than synthetic toxic fungicides for rice.
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Affiliation(s)
| | - Anjali Sidhu
- Department of Soil Science, Punjab Agricultural University, Ludhiana 141004, India
| | - Anju Bala Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana 141004, India
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6
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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: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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7
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Scarel M, Marchesan S. Diketopiperazine Gels: New Horizons from the Self-Assembly of Cyclic Dipeptides. Molecules 2021; 26:3376. [PMID: 34204905 PMCID: PMC8199760 DOI: 10.3390/molecules26113376] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/01/2021] [Accepted: 06/01/2021] [Indexed: 02/07/2023] Open
Abstract
Cyclodipeptides (CDPs) or 2,5-diketopiperazines (DKPs) can exert a variety of biological activities and display pronounced resistance against enzymatic hydrolysis as well as a propensity towards self-assembly into gels, relative to the linear-dipeptide counterparts. They have attracted great interest in a variety of fields spanning from functional materials to drug discovery. This concise review will analyze the latest advancements in their synthesis, self-assembly into gels, and their more innovative applications.
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Affiliation(s)
- Marco Scarel
- Chemical and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy;
| | - Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy;
- National Interuniversity Consortium of Materials Science and Technology (INSTM), University of Trieste, 34127 Trieste, Italy
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Chen Y, Tao K, Ji W, Makam P, Rencus-Lazar S, Gazit E. Self-Assembly of Cyclic Dipeptides: Platforms for Functional Materials. Protein Pept Lett 2021; 27:688-697. [PMID: 32048950 DOI: 10.2174/0929866527666200212123542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/29/2019] [Accepted: 12/09/2019] [Indexed: 11/22/2022]
Abstract
Supramolecular self-assembled functional materials comprised of cyclic dipeptide building blocks have excellent prospects for biotechnology applications due to their exceptional structural rigidity, morphological flexibility, ease of preparation and modification. Although the pharmacological uses of many natural cyclic dipeptides have been studied in detail, relatively little is reported on the engineering of these supramolecular architectures for the fabrication of functional materials. In this review, we discuss the progress in the design, synthesis, and characterization of cyclic dipeptide supramolecular nanomaterials over the past few decades, highlighting applications in biotechnology and optoelectronics engineering.
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Affiliation(s)
- Yu Chen
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Kai Tao
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Wei Ji
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Pandeeswar Makam
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sigal Rencus-Lazar
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
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9
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Zhao K, Xing R, Yan X. Cyclic dipeptides: Biological activities and self‐assembled materials. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24202] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Kaili Zhao
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering, Chinese Academy of Sciences Beijing China
- School of Chemical Engineering University of Chinese Academy of Sciences Beijing China
| | - Ruirui Xing
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering, Chinese Academy of Sciences Beijing China
- School of Chemical Engineering University of Chinese Academy of Sciences Beijing China
| | - Xuehai Yan
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering, Chinese Academy of Sciences Beijing China
- School of Chemical Engineering University of Chinese Academy of Sciences Beijing China
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10
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Kleinsmann AJ, Nachtsheim BJ. A minimalistic hydrolase based on co-assembled cyclic dipeptides. Org Biomol Chem 2020; 18:102-107. [PMID: 31799587 DOI: 10.1039/c9ob02198a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The self-assembly of small peptides into larger aggregates is an important process for the fundamental understanding of abiogenesis. In this article we demonstrate that blends of cyclic dipeptides (2,5-diketopiperazines - DKPs) bearing either histidine or cysteine in combination with a lipophilic amino acid form highly stable aggregates in aqueous solution with esterase-like activity. We demonstrate that the catalytic activity is based on an intermolecular cooperative behavior between histidine and cysteine. A high control of the molecular arrangement of the peptide assemblies was gained by C-H-π interactions between Phe and Leu or Val sidechains, resulting in a significant increase in catalytic activity. These interactions were strongly supported by Hartree-Fock calculations and finally confirmed via1H-NMR HRMAS NOE spectroscopy.
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Affiliation(s)
- Alexander J Kleinsmann
- Institut für Organische Chemie Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
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