1
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Nakatani T, Koga A, Goto S, Inoue M, Shigedomi K, Seki K, Araki K, Taira J, Kodama H, Osada S. Importance of isoleucine residue in ion channel formation ability of 11-residue peptaibols. Bioorg Med Chem 2024; 110:117839. [PMID: 39029438 DOI: 10.1016/j.bmc.2024.117839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024]
Abstract
Peptaibols are a class of short peptides, typically 7 to 20 amino acids long, characterized by noncanonical amino acid residues such as aminoisobutyric acid (Aib). Although the helix length is shorter than the membrane thickness, the 11-residue peptaibol trichorovin-XII (TV-XII) can form ion channels in membranes. Assuming that a higher proportion of isoleucine (Ile) relative to leucine (Leu) residues is crucial for maintaining the ion channel activity of TV-XII, peptide analogs of TV-XII with varying Ile content were designed, synthesized, and evaluated. The secondary structure of all derivatives under hydrophobic conditions was confirmed by CD measurement as an α-helix-like β-bend ribbon spiral structure. The most stable ion channel activity was found in compound 4a with maximum Ile. Furthermore, the C-terminal Ile analog showed greater ion channel activity compared to the Leu analog. This suggests that the choice between Leu and Ile can influence the expression of ion channel activity, which will be crucial for the de novo designed functional peptides.
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Affiliation(s)
- Taiki Nakatani
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | - Ami Koga
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | - Shogo Goto
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | - Marina Inoue
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | - Keita Shigedomi
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | - Kiyohiko Seki
- Department of Applied Biochemistry and Food Science, Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | - Kaoru Araki
- Health Care Center, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | - Junichi Taira
- Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka 820-8502, Japan
| | - Hiroaki Kodama
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | - Satoshi Osada
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, 1 Honjo-machi, Saga 840-8502, Japan.
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2
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Tyagi C, Marik T, Szekeres A, Vágvölgyi C, Kredics L, Ötvös F. Modeling the Effect on a Novel Fungal Peptaibol Placed in an All-Atom Bacterial Membrane Mimicking System via Accelerated Molecular Dynamics Simulations. Life (Basel) 2023; 13:2288. [PMID: 38137889 PMCID: PMC10744397 DOI: 10.3390/life13122288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
We previously reported on a novel peptaibol, named Tripleurin XIIc (TPN), an 18-residue long sequence produced by the fungus Trichoderma pleuroti. We elucidated its 3D structure via classical and accelerated molecular dynamics simulation (aMD) methods and reported the folding dynamics of TPN in water and chloroform solvents. Peptaibols, in general, are insoluble in water, as they are amphipathic and may prefer hydrophobic environments like transmembrane regions. In this study, we attempted to use aMD simulations to model an all-atom bacterial membrane system while placing a TPN molecule in its vicinity. The results highlighted that TPN was able to introduce some disorder into the membrane and caused lipid clustering. It could also enter the transmembrane region from the water-bilayer interface. The structural dynamics of TPN in the transmembrane region revealed a single energetically stable conformation similar to the one obtained from water and chloroform solvent simulations reported by us previously. However, this linear structure was found to be at the local energy minimum (stable) in water but at a metastable intermediate state (higher energy) in chloroform. Therefore, it could be said that the water solvent can be successfully used for folding simulations of peptaibols.
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Affiliation(s)
- Chetna Tyagi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (T.M.); (A.S.); (C.V.); (L.K.)
| | - Tamás Marik
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (T.M.); (A.S.); (C.V.); (L.K.)
| | - András Szekeres
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (T.M.); (A.S.); (C.V.); (L.K.)
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (T.M.); (A.S.); (C.V.); (L.K.)
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (T.M.); (A.S.); (C.V.); (L.K.)
| | - Ferenc Ötvös
- Institute of Biochemistry, Biological Research Centre, Temesvári krt. 62, H-6726 Szeged, Hungary;
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3
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Niu X, Thaochan N, Hu Q. Diversity of Linear Non-Ribosomal Peptide in Biocontrol Fungi. J Fungi (Basel) 2020; 6:E61. [PMID: 32408496 PMCID: PMC7345191 DOI: 10.3390/jof6020061] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/27/2020] [Accepted: 05/09/2020] [Indexed: 12/16/2022] Open
Abstract
Biocontrol fungi (BFs) play a key role in regulation of pest populations. BFs produce multiple non-ribosomal peptides (NRPs) and other secondary metabolites that interact with pests, plants and microorganisms. NRPs-including linear and cyclic peptides (L-NRPs and C-NRPs)-are small peptides frequently containing special amino acids and other organic acids. They are biosynthesized in fungi through non-ribosomal peptide synthases (NRPSs). Compared with C-NRPs, L-NRPs have simpler structures, with only a linear chain and biosynthesis without cyclization. BFs mainly include entomopathogenic and mycoparasitic fungi, that are used to control insect pests and phytopathogens in fields, respectively. NRPs play an important role of in the interactions of BFs with insects or phytopathogens. On the other hand, the residues of NRPs may contaminate food through BFs activities in the environment. In recent decades, C-NRPs in BFs have been thoroughly reviewed. However, L-NRPs are rarely investigated. In order to better understand the species and potential problems of L-NRPs in BFs, this review lists the L-NRPs from entomopathogenic and mycoparasitic fungi, summarizes their sources, structures, activities and biosynthesis, and details risks and utilization prospects.
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Affiliation(s)
- Xiaoyan Niu
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China;
| | - Narit Thaochan
- Pest Management Biotechnology and Plant Physiology Laboratory, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand;
| | - Qiongbo Hu
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China;
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4
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Chen CH, Melo MC, Berglund N, Khan A, de la Fuente-Nunez C, Ulmschneider JP, Ulmschneider MB. Understanding and modelling the interactions of peptides with membranes: from partitioning to self-assembly. Curr Opin Struct Biol 2020; 61:160-166. [PMID: 32006812 DOI: 10.1016/j.sbi.2019.12.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/27/2019] [Accepted: 12/28/2019] [Indexed: 12/14/2022]
Abstract
Atomic detail simulations are starting to reveal how flexible polypeptides interact with fluid lipid bilayers. These insights are transforming our understanding of one of the fundamental processes in biology: membrane protein folding and assembly. Advanced molecular dynamics (MD) simulation techniques enable accurate prediction of protein structure, folding pathways and assembly in microsecond-timescales. Such simulations show how membrane-active peptides self-assemble in cell membranes, revealing their binding, folding, insertion, and aggregation, while at the same time providing atomic resolution details of peptide-lipid interactions. Essential to the impact of simulations are experimental approaches that enable calibration and validation of the computational models and techniques. In this review, we summarize the current development of applying unbiased atomic detail MD simulations and the relation to experimental techniques, to study peptide folding and provide our perspective of the field.
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Affiliation(s)
- Charles H Chen
- Department of Chemistry, King's College London, London, UK
| | - Marcelo Cr Melo
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nils Berglund
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Ayesha Khan
- College of Medicine and Health, University of Exeter, Exeter, UK
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
| | - Jakob P Ulmschneider
- Institute of Natural Sciences and School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China.
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5
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Marik T, Tyagi C, Balázs D, Urbán P, Szepesi Á, Bakacsy L, Endre G, Rakk D, Szekeres A, Andersson MA, Salonen H, Druzhinina IS, Vágvölgyi C, Kredics L. Structural Diversity and Bioactivities of Peptaibol Compounds From the Longibrachiatum Clade of the Filamentous Fungal Genus Trichoderma. Front Microbiol 2019; 10:1434. [PMID: 31293557 PMCID: PMC6606783 DOI: 10.3389/fmicb.2019.01434] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/06/2019] [Indexed: 01/18/2023] Open
Abstract
This study examined the structural diversity and bioactivity of peptaibol compounds produced by species from the phylogenetically separated Longibrachiatum Clade of the filamentous fungal genus Trichoderma, which contains several biotechnologically, agriculturally and clinically important species. HPLC-ESI-MS investigations of crude extracts from 17 species of the Longibrachiatum Clade (T. aethiopicum, T. andinense, T. capillare, T. citrinoviride, T. effusum, T. flagellatum, T. ghanense, T. konilangbra, T. longibrachiatum, T. novae-zelandiae, T. pinnatum, T. parareesei, T. pseudokoningii, T. reesei, T. saturnisporum, T. sinensis, and T. orientale) revealed several new and recurrent 20-residue peptaibols related to trichobrachins, paracelsins, suzukacillins, saturnisporins, trichoaureocins, trichocellins, longibrachins, hyporientalins, trichokonins, trilongins, metanicins, trichosporins, gliodeliquescins, alamethicins and hypophellins, as well as eight 19-residue sequences from a new subfamily of peptaibols named brevicelsins. Non-ribosomal peptide synthetase genes were mined from the available genome sequences of the Longibrachiatum Clade. Their annotation and product prediction were performed in silico and revealed full agreement in 11 out of 20 positions regarding the amino acids predicted based on the signature sequences and the detected amino acids incorporated. Molecular dynamics simulations were performed for structural characterization of four selected peptaibol sequences: paracelsins B, H and their 19-residue counterparts brevicelsins I and IV. Loss of position R6 in brevicelsins resulted in smaller helical structures with higher atomic fluctuation for every residue than the structures formed by paracelsins. We observed the formation of highly bent, almost hairpin-like, helical structures throughout the trajectory, along with linear conformation. Bioactivity tests were performed on the purified peptaibol extract of T. reesei on clinically and phytopathologically important filamentous fungi, mammalian cells, and Arabidopsis thaliana seedlings. Porcine kidney cells and boar spermatozoa proved to be sensitive to the purified peptaibol extract. Peptaibol concentrations ≥0.3 mg ml-1 deterred the growth of A. thaliana. However, negative effects to plants were not detected at concentrations below 0.1 mg ml-1, which could still inhibit plant pathogenic filamentous fungi, suggesting that those peptaibols reported here may have applications for plant protection.
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Affiliation(s)
- Tamás Marik
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Chetna Tyagi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Dóra Balázs
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Péter Urbán
- Department of General and Environmental Microbiology, Faculty of Sciences, and Szentágothai Research Center, University of Pécs, Pécs, Hungary
| | - Ágnes Szepesi
- Department of Plant Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - László Bakacsy
- Department of Plant Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Gábor Endre
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Dávid Rakk
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - András Szekeres
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | | | - Heidi Salonen
- Department of Civil Engineering, Aalto University, Espoo, Finland
| | - Irina S. Druzhinina
- Research Area Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
- Jiangsu Provincial Key Laboratory of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
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6
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Grage SL, Kara S, Bordessa A, Doan V, Rizzolo F, Putzu M, Kubař T, Papini AM, Chaume G, Brigaud T, Afonin S, Ulrich AS. Orthogonal 19 F-Labeling for Solid-State NMR Spectroscopy Reveals the Conformation and Orientation of Short Peptaibols in Membranes. Chemistry 2018; 24:4328-4335. [PMID: 29323432 DOI: 10.1002/chem.201704307] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Indexed: 11/10/2022]
Abstract
Peptaibols are promising drug candidates in view of their interference with cellular membranes. Knowledge of their lipid interactions and membrane-bound structure is needed to understand their activity and should be, in principle, accessible by solid-state NMR spectroscopy. However, their unusual amino acid composition and noncanonical conformations make it very challenging to find suitable labels for NMR spectroscopy. Particularly in the case of short sequences, new strategies are required to maximize the structural information that can be obtained from each label. Herein, l-3-(trifluoromethyl)bicyclopent[1.1.1]-1-ylglycine, (R)- and (S)-trifluoromethylalanine, and 15 N-backbone labels, each probing a different direction in the molecule, have been combined to elucidate the conformation and membrane alignment of harzianin HK-VI. For the short sequence of 11 amino acids, 12 orientational constraints have been obtained by using 19 F and 15 N NMR spectroscopy. This strategy revealed a β-bend ribbon structure, which becomes realigned in the membrane from a surface-parallel state towards a membrane-spanning state, with increasing positive spontaneous curvature of the lipids.
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Affiliation(s)
- Stephan L Grage
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021, Karlsruhe, Germany
| | - Sezgin Kara
- Institute of Organic Chemistry (IOC), KIT, Fritz-Haber Weg 6, 76131, Karlsruhe, Germany
| | - Andrea Bordessa
- Laboratoire de Chimie Biologique (LCB), EA4505, Platform PeptLab@UCP, Université de Cergy-Pontoise, 5 Mail Gay-Lussac, Neuville sur Oise, 95000, Cergy-Pontoise cedex, France
| | - Véronique Doan
- Laboratoire de Chimie Biologique (LCB), EA4505, Platform PeptLab@UCP, Université de Cergy-Pontoise, 5 Mail Gay-Lussac, Neuville sur Oise, 95000, Cergy-Pontoise cedex, France
| | - Fabio Rizzolo
- Laboratoire de Chimie Biologique (LCB), EA4505, Platform PeptLab@UCP, Université de Cergy-Pontoise, 5 Mail Gay-Lussac, Neuville sur Oise, 95000, Cergy-Pontoise cedex, France.,French-Italian Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology (PeptLab), Department of Chemistry "Ugo Schiff", CNR-IBB, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Marina Putzu
- Institute of Physical Chemistry (IPC), Center for Functional Nanostructures (CFN), KIT, 76131, Karlsruhe, Germany
| | - Tomáš Kubař
- Institute of Physical Chemistry (IPC), Center for Functional Nanostructures (CFN), KIT, 76131, Karlsruhe, Germany
| | - Anna Maria Papini
- Laboratoire de Chimie Biologique (LCB), EA4505, Platform PeptLab@UCP, Université de Cergy-Pontoise, 5 Mail Gay-Lussac, Neuville sur Oise, 95000, Cergy-Pontoise cedex, France.,French-Italian Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology (PeptLab), Department of Chemistry "Ugo Schiff", CNR-IBB, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Grégory Chaume
- Laboratoire de Chimie Biologique (LCB), EA4505, Platform PeptLab@UCP, Université de Cergy-Pontoise, 5 Mail Gay-Lussac, Neuville sur Oise, 95000, Cergy-Pontoise cedex, France
| | - Thierry Brigaud
- Laboratoire de Chimie Biologique (LCB), EA4505, Platform PeptLab@UCP, Université de Cergy-Pontoise, 5 Mail Gay-Lussac, Neuville sur Oise, 95000, Cergy-Pontoise cedex, France
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021, Karlsruhe, Germany
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021, Karlsruhe, Germany.,Institute of Organic Chemistry (IOC), KIT, Fritz-Haber Weg 6, 76131, Karlsruhe, Germany
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7
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Castro TG, Micaêlo NM, Melle-Franco M. Modeling the secondary structures of the peptaibols antiamoebin I and zervamicin II modified with D-amino acids and proline analogues. J Mol Model 2017; 23:313. [DOI: 10.1007/s00894-017-3479-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/19/2017] [Indexed: 11/29/2022]
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