1
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Roseli RB, Huang YH, Henriques ST, Kaas Q, Craik DJ. Molecular dynamics simulations support a preference of cyclotide kalata B1 for phosphatidylethanolamine phospholipids. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184268. [PMID: 38191035 DOI: 10.1016/j.bbamem.2023.184268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 01/10/2024]
Abstract
Kalata B1 (kB1), a naturally occurring cyclotide has been shown experimentally to bind lipid membranes that contain phosphatidylethanolamine (PE) phospholipids. Here, molecular dynamics simulations were used to explore its interaction with two phospholipids, palmitoyloleoylphosphatidylethanolamine (POPE), palmitoyloleoylphosphatidylcholine (POPC), and a heterogeneous membrane comprising POPC/POPE (90:10), to understand the basis for the selectivity of kB1 towards PE phospholipids. The simulations showed that in the presence of only 10 % POPE lipid, kB1 forms a stable binding complex with membrane bilayers. An ionic interaction between the E7 carboxylate group of kB1 and the ammonium group of PE headgroups consistently initiates binding of kB1 to the membrane. Additionally, stable noncovalent interactions such as hydrogen bonding (E7, T8, V10, G11, T13 and N15), cation-π (W23), and CH-π (W23) interactions between specific residues of kB1 and the lipid membrane play an important role in stabilizing the binding. These findings are consistent with a structure-activity relationship study on kB1 where lysine mutagenesis on the bioactive and hydrophobic faces of the peptide abolished membrane-dependent bioactivities. In summary, our simulations suggest the importance of residue E7 (in the bioactive face) in enabling kB1 to recognize and bind selectively to PE-containing phospholipids bilayers through ionic and hydrogen bonding interactions, and of W23 (in the hydrophobic face) for the association and insertion of kB1 into the lipid bilayer through cation-π and CH-π interactions. Overall, this work enhances our understanding of the molecular basis of the membrane binding and bioactivity of this prototypic cyclotide.
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Affiliation(s)
- Ras Baizureen Roseli
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sónia Troeira Henriques
- School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia.
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2
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Sharma A, Butool B, Sahu P, Mishra R, Mohanty A. In Silico Analysis of Natural Plant-Derived Cyclotides with Antifungal Activity against Pathogenic Fungi. Protein Pept Lett 2024; 31:247-260. [PMID: 38445693 DOI: 10.2174/0109298665295545240223114346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUND Fungal infections in plants, animals, and humans are widespread across the world. Limited classes of antifungal drugs to treat fungal infections and loss of drug efficacy due to rapidly evolving fungal strains pose a challenge in the agriculture and health sectors. Hence, the search for a new class of antifungal agents is imperative. Cyclotides are cyclic plant peptides with multiple bioactivities, including antifungal activity. They have six conserved cysteine residues forming three disulfide linkages (CI-CIV, CII-CV, CIII-CVI) that establish a Cyclic Cystine Knot (CCK) structure, making them extremely resistant to chemical, enzymatic, and thermal attacks. AIM This in silico analysis of natural, plant-derived cyclotides aimed to assess the parameters that can assist and hasten the process of selecting the cyclotides with potent antifungal activity and prioritize them for in vivo/ in vitro experiments. OBJECTIVE The objective of this study was to conduct in silico studies to compare the physicochemical parameters, sequence diversity, surface structures, and membrane-cyclotide interactions of experimentally screened (from literature survey) potent (MIC ≤ 20 μM) and non-potent (MIC > 20 μM) cyclotides for antifungal activity. METHODOLOGY Cyclotide sequences assessed for antifungal activity were retrieved from the database (Cybase). Various online and offline tools were used for sequence-based studies, such as physicochemical parameters, sequence diversity, and neighbor-joining trees. Structure-based studies involving surface structure analysis and membrane-cyclotide interaction were also carried out. All investigations were conducted in silico. RESULTS Physicochemical parameter values, viz. isoelectric point, net charge, and the number of basic amino acids, were significantly higher in potent cyclotides compared to non-potent cyclotides. The surface structure of potent cyclotides showed a larger hydrophobic patch with a higher number of hydrophobic amino acids. Furthermore, the membrane-cyclotide interaction studies of potent cyclotides revealed lower transfer free energy (ΔG transfer) and higher penetration depth into fungal membranes, indicating higher binding stability and membrane-disruption ability. CONCLUSION These in silico studies can be applied for rapidly identifying putatively potent antifungal cyclotides for in vivo and in vitro experiments, which will ultimately be relevant in the agriculture and pharmaceutical sectors.
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Affiliation(s)
- Akshita Sharma
- Department of Botany, Gargi College, University of Delhi, Delhi, India
| | - Bisma Butool
- Department of Botany, Gargi College, University of Delhi, Delhi, India
| | - Pallavi Sahu
- Department of Botany, Gargi College, University of Delhi, Delhi, India
| | - Reema Mishra
- Department of Botany, Gargi College, University of Delhi, Delhi, India
| | - Aparajita Mohanty
- Department of Botany, Gargi College, University of Delhi, Delhi, India
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3
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Panina IS, Balandin SV, Tsarev AV, Chugunov AO, Tagaev AA, Finkina EI, Antoshina DV, Sheremeteva EV, Paramonov AS, Rickmeyer J, Bierbaum G, Efremov RG, Shenkarev ZO, Ovchinnikova TV. Specific Binding of the α-Component of the Lantibiotic Lichenicidin to the Peptidoglycan Precursor Lipid II Predetermines Its Antimicrobial Activity. Int J Mol Sci 2023; 24:ijms24021332. [PMID: 36674846 PMCID: PMC9863751 DOI: 10.3390/ijms24021332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/21/2022] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
To date, a number of lantibiotics have been shown to use lipid II-a highly conserved peptidoglycan precursor in the cytoplasmic membrane of bacteria-as their molecular target. The α-component (Lchα) of the two-component lantibiotic lichenicidin, previously isolated from the Bacillus licheniformis VK21 strain, seems to contain two putative lipid II binding sites in its N-terminal and C-terminal domains. Using NMR spectroscopy in DPC micelles, we obtained convincing evidence that the C-terminal mersacidin-like site is involved in the interaction with lipid II. These data were confirmed by the MD simulations. The contact area of lipid II includes pyrophosphate and disaccharide residues along with the first isoprene units of bactoprenol. MD also showed the potential for the formation of a stable N-terminal nisin-like complex; however, the conditions necessary for its implementation in vitro remain unknown. Overall, our results clarify the picture of two component lantibiotics mechanism of antimicrobial action.
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Affiliation(s)
- Irina S. Panina
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Sergey V. Balandin
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Correspondence: ; Tel.: +7-495-335-0900
| | - Andrey V. Tsarev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Anton O. Chugunov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Andrey A. Tagaev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Ekaterina I. Finkina
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Daria V. Antoshina
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Elvira V. Sheremeteva
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Alexander S. Paramonov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Jasmin Rickmeyer
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, 53117 Bonn, Germany
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, 53117 Bonn, Germany
| | - Roman G. Efremov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Department of Applied Mathematics, National Research University Higher School of Economics, 101000 Moscow, Russia
| | - Zakhar O. Shenkarev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Tatiana V. Ovchinnikova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Department of Bioorganic Chemistry, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
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4
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Aqueous Self-assembly of Extracted Cyclotides from Viola odorata into Novel Stable Supramolecular Structures. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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5
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Mehta L, Shambhawi, Kumar S, Mohanty A. In silico Analysis of Native Cyclotides with Antibacterial Activity against Gram-negative Bacteria. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822060096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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Du Q, Huang YH, Wang CK, Kaas Q, Craik DJ. Mutagenesis of bracelet cyclotide hyen D reveals functionally and structurally critical residues for membrane binding and cytotoxicity. J Biol Chem 2022; 298:101822. [PMID: 35283188 PMCID: PMC9006653 DOI: 10.1016/j.jbc.2022.101822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/19/2022] [Accepted: 02/21/2022] [Indexed: 11/05/2022] Open
Abstract
Cyclotides have a wide range of bioactivities relevant for agricultural and pharmaceutical applications. This large family of naturally occurring macrocyclic peptides is divided into three subfamilies, with the bracelet subfamily being the largest and comprising the most potent cyclotides reported to date. However, attempts to harness the natural bioactivities of bracelet cyclotides and engineer-optimized analogs have been hindered by a lack of understanding of the structural and functional role of their constituent residues, which has been challenging because bracelet cyclotides are difficult to produce synthetically. We recently established a facile strategy to make the I11L mutant of cyclotide hyen D that is as active as the parent peptide, enabling the subsequent production of a series of variants. In the current study, we report an alanine mutagenesis structure-activity study of [I11L] hyen D to probe the role of individual residues on peptide folding using analytical chromatography, on molecular function using surface plasmon resonance, and on therapeutic potential using cytotoxicity assays. We found that Glu-6 and Thr-15 are critical for maintaining the structure of bracelet cyclotides and that hydrophobic residues in loops 2 and 3 are essential for membrane binding and cytotoxic activity, findings that are distinct from the structural and functional characteristics determined for other cyclotide subfamilies. In conclusion, this is the first report of a mutagenesis scan conducted on a bracelet cyclotide, offering insights into their function and supporting future efforts to engineer bracelet cyclotides for biotechnological applications.
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Affiliation(s)
- Qingdan Du
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, Australia.
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, Australia.
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7
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Spatial structure and oligomerization of viscotoxin A3 in detergent micelles: Implication for mechanisms of ion channel formation and membrane lysis. Biochem Biophys Res Commun 2021; 585:22-28. [PMID: 34781057 DOI: 10.1016/j.bbrc.2021.11.022] [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: 10/06/2021] [Accepted: 11/03/2021] [Indexed: 11/22/2022]
Abstract
Thionins are the family of small (∼5 kDa) cationic cysteine-rich peptides involved in the immune response in plants. Viscotoxin A3 (VtA3) is the thionin from mistletoe (Viscum album) demonstrating antimicrobial and cytotoxic activity against cancer cells in vitro. VtA3 (charge +6) interacts with the membranes containing anionic lipids and forms cation-selective ion channels. Here we studied the VtA3 structure in membrane-mimicking media by NMR spectroscopy. Spatial structure of VtA3, consisting of a helical hairpin and a short β-sheet, was stable and did not undergo significant changes during micelle binding. VtA3 molecule bound with high affinity to the surface of zwitterionic dodecylphosphocholine (DPC) micelle by hydrophobic patch in the helical hairpin. Oligomerization of VtA3 was observed in the anionic micelles of sodium dodecylsulphate (SDS). No direct contacts between the peptide molecules were observed and the possible interfaces of detergent-assisted oligomerization were revealed. The data obtained suggest that the VtA3 membrane activity, depending on the concentration, obeys the 'toroidal' pore model or the 'carpet' mechanism. The model of the membrane disrupting complex, which explains the ion channel formation in the partially anionic membranes, was proposed.
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8
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van den Broek K, Epple M, Kersten LS, Kuhn H, Zielesny A. Quantitative Estimation of Cyclotide-Induced Bilayer Membrane Disruption by Lipid Extraction with Mesoscopic Simulation. J Chem Inf Model 2021; 61:3027-3040. [PMID: 34008405 DOI: 10.1021/acs.jcim.1c00332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclotide-induced membrane disruption is studied at the microsecond timescale by dissipative particle dynamics to quantitatively estimate a kinetic rate constant for membrane lipid extraction with a ″sandwich″ interaction model where two bilayer membranes enclose a cyclotide/water compartment. The obtained bioactivity trends for cyclotides Kalata B1, Cycloviolacin O2, and selected mutants with different membrane types are in agreement with experimental findings: For all membranes investigated, Cycloviolacin O2 shows a higher lipid extraction activity than Kalata B1. The presence of cholesterol leads to a decreased cyclotide activity compared to cholesterol-free membranes. Phosphoethanolamine-rich membranes exhibit an increased membrane disruption. A cyclotide's ″hydrophobic patch″ surface area is important for its bioactivity. A replacement of or with charged amino acid residues may lead to super-mutants with above-native activity but without simple charge-activity patterns. Cyclotide mixtures show linearly additive bioactivities without significant sub- or over-additive effects. The proposed method can be applied as a fast and easy-to-use tool for exploring structure-activity relationships of cyclotide/membrane systems: With the open software provided, the rate constant of a single cyclotide/membrane system can be determined in about 1 day by a scientific end-user without programming skills.
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Affiliation(s)
- Karina van den Broek
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, 45141 Essen, Germany.,Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, 45665 Recklinghausen, Germany
| | - Matthias Epple
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, 45141 Essen, Germany
| | - Lisa Sophie Kersten
- Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, 45665 Recklinghausen, Germany
| | - Hubert Kuhn
- CAM-D Technologies GmbH, 42697 Solingen, Germany
| | - Achim Zielesny
- Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, 45665 Recklinghausen, Germany
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9
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Grover T, Mishra R, Gulati P, Mohanty A. An insight into biological activities of native cyclotides for potential applications in agriculture and pharmaceutics. Peptides 2021; 135:170430. [PMID: 33096195 DOI: 10.1016/j.peptides.2020.170430] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 10/06/2020] [Accepted: 10/12/2020] [Indexed: 02/08/2023]
Abstract
Cyclotides are plant-derived mini-proteins of 28 - 37 amino acids. They have a characteristic head-to-tail cyclic backbone and three disulfide cross-linkages formed by six highly conserved cysteine residues, creating a unique knotted ring structure, known as a cyclic cystine knot (CCK) motif. The CCK topology confers immense stability to cyclotides with resistance to thermal and enzymatic degradation. Native cyclotides are of interest due to their multiple biological activities with several potential applications in agricultural (e.g. biopesticides, antifungal) and pharmaceutical (e.g. anti-HIV, cytotoxic to tumor cells) sectors. The most recent application of insecticidal activity of cyclotides is the commercially available biopesticidal spray known as 'Sero X' for cotton crops. Cyclotides have a general mode of action and their potency of bioactivity is determined through their binding ability, pore formation and disruption of the target biological membranes. Keeping in view the important potential applications of biological activities of cyclotides and the lack of an extensive and analytical compilation of bioactive cyclotides, the present review systematically describes eight major biological activities of the native cyclotides from four angiosperm families viz. Fabaceae, Poaceae, Rubiaceae, Violaceae. The bioactivities of 94 cytotoxic, 57 antibacterial, 44 hemolytic, 25 antifungal, 21 anti-HIV, 20 nematocidal, 10 insecticidal and 5 molluscicidal cyclotides have been comprehensively elaborated. Further, their distribution in angiosperm families, mode of action and future prospects have also been discussed.
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Affiliation(s)
- Tripti Grover
- Bioinformatics Infrastructure Facility, Gargi College, University of Delhi, India
| | - Reema Mishra
- Department of Botany, Gargi College, University of Delhi, India
| | - Pooja Gulati
- Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Aparajita Mohanty
- Bioinformatics Infrastructure Facility, Gargi College, University of Delhi, India.
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10
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Panteleev PV, Tsarev AV, Safronova VN, Reznikova OV, Bolosov IA, Sychev SV, Shenkarev ZO, Ovchinnikova TV. Structure Elucidation and Functional Studies of a Novel β-hairpin Antimicrobial Peptide from the Marine Polychaeta Capitella teleta. Mar Drugs 2020; 18:md18120620. [PMID: 33291782 PMCID: PMC7761999 DOI: 10.3390/md18120620] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/27/2020] [Accepted: 12/02/2020] [Indexed: 12/21/2022] Open
Abstract
Endogenous antimicrobial peptides (AMPs) are evolutionary ancient molecular factors of innate immunity that play a key role in host defense. Among the most active and stable under physiological conditions AMPs are the peptides of animal origin that adopt a β-hairpin conformation stabilized by disulfide bridges. In this study, a novel BRICHOS-domain related AMP from the marine polychaeta Capitella teleta, named capitellacin, was produced as the recombinant analogue and investigated. The mature capitellacin exhibits high homology with the known β-hairpin AMP family—tachyplesins and polyphemusins from the horseshoe crabs. The β-hairpin structure of the recombinant capitellacin was proved by CD and NMR spectroscopy. In aqueous solution the peptide exists as monomeric right-handed twisted β-hairpin and its structure does not reveal significant amphipathicity. Moreover, the peptide retains this conformation in membrane environment and incorporates into lipid bilayer. Capitellacin exhibits a strong antimicrobial activity in vitro against a wide panel of bacteria including extensively drug-resistant strains. In contrast to other known β-hairpin AMPs, this peptide acts apparently via non-lytic mechanism at concentrations inhibiting bacterial growth. The molecular mechanism of the peptide antimicrobial action does not seem to be related to the inhibition of bacterial translation therefore other molecular targets may be assumed. The reduced cytotoxicity against human cells and high antibacterial cell selectivity as compared to tachyplesin-1 make it an attractive candidate compound for an anti-infective drug design.
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Affiliation(s)
- Pavel V. Panteleev
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow, Russia; (P.V.P.); (A.V.T.); (V.N.S.); (O.V.R.); (I.A.B.); (S.V.S.); (Z.O.S.)
| | - Andrey V. Tsarev
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow, Russia; (P.V.P.); (A.V.T.); (V.N.S.); (O.V.R.); (I.A.B.); (S.V.S.); (Z.O.S.)
| | - Victoria N. Safronova
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow, Russia; (P.V.P.); (A.V.T.); (V.N.S.); (O.V.R.); (I.A.B.); (S.V.S.); (Z.O.S.)
| | - Olesia V. Reznikova
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow, Russia; (P.V.P.); (A.V.T.); (V.N.S.); (O.V.R.); (I.A.B.); (S.V.S.); (Z.O.S.)
| | - Ilia A. Bolosov
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow, Russia; (P.V.P.); (A.V.T.); (V.N.S.); (O.V.R.); (I.A.B.); (S.V.S.); (Z.O.S.)
| | - Sergei V. Sychev
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow, Russia; (P.V.P.); (A.V.T.); (V.N.S.); (O.V.R.); (I.A.B.); (S.V.S.); (Z.O.S.)
| | - Zakhar O. Shenkarev
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow, Russia; (P.V.P.); (A.V.T.); (V.N.S.); (O.V.R.); (I.A.B.); (S.V.S.); (Z.O.S.)
| | - Tatiana V. Ovchinnikova
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow, Russia; (P.V.P.); (A.V.T.); (V.N.S.); (O.V.R.); (I.A.B.); (S.V.S.); (Z.O.S.)
- Department of Biotechnology, I.M. Sechenov First Moscow State Medical University, Trubetskaya str., 8–2, 119991 Moscow, Russia
- Correspondence: ; Tel.: +7-495-336-44-44
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11
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Handley TNG, Wang CK, Harvey PJ, Lawrence N, Craik DJ. Cyclotide Structures Revealed by NMR, with a Little Help from X‐ray Crystallography. Chembiochem 2020; 21:3463-3475. [DOI: 10.1002/cbic.202000315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/08/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Thomas N. G. Handley
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Conan K. Wang
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Peta J. Harvey
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Nicole Lawrence
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - David J. Craik
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
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12
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Muratspahić E, Koehbach J, Gruber CW, Craik DJ. Harnessing cyclotides to design and develop novel peptide GPCR ligands. RSC Chem Biol 2020; 1:177-191. [PMID: 34458757 PMCID: PMC8341132 DOI: 10.1039/d0cb00062k] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/10/2020] [Indexed: 12/13/2022] Open
Abstract
Cyclotides are plant-derived cyclic, disulfide-rich peptides with a unique cyclic cystine knot topology that confers them with remarkable structural stability and resistance to proteolytic degradation. Recently, cyclotides have emerged as promising scaffold molecules for designing peptide-based therapeutics. Here, we provide examples of how engineering cyclotides using molecular grafting may lead to the development of novel peptide ligands of G protein-coupled receptors (GPCRs), today's most exploited drug targets. Integrating bioactive epitopes into stable cyclotide scaffolds can lead to improved pharmacokinetics and oral activity as well as selectivity and high enzymatic stability. We also discuss and highlight the importance of engineered cyclotides as novel tools to study GPCR signaling.
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Affiliation(s)
- Edin Muratspahić
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna Austria
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane Queensland 4072 Australia
| | - Johannes Koehbach
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane Queensland 4072 Australia
| | - Christian W Gruber
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna Austria
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane Queensland 4072 Australia
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13
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Abstract
This Review explores the class of plant-derived macrocyclic peptides called cyclotides. We include an account of their discovery, characterization, and distribution in the plant kingdom as well as a detailed analysis of their sequences and structures, biosynthesis and chemical synthesis, biological functions, and applications. These macrocyclic peptides are around 30 amino acids in size and are characterized by their head-to-tail cyclic backbone and cystine knot motif, which render them to be exceptionally stable, with resistance to thermal or enzymatic degradation. Routes to their chemical synthesis have been developed over the past two decades, and this capability has facilitated a wide range of mutagenesis and structure-activity relationship studies. In turn, these studies have both led to an increased understanding of their mechanisms of action as well as facilitated a range of applications in agriculture and medicine, as ecofriendly crop protection agents, and as drug leads or scaffolds for pharmaceutical design. Our overall objective in this Review is to provide readers with a comprehensive overview of cyclotides that we hope will stimulate further work on this fascinating family of peptides.
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Affiliation(s)
- Simon J de Veer
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Meng-Wei Kan
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
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14
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Huang YH, Du Q, Craik DJ. Cyclotides: Disulfide-rich peptide toxins in plants. Toxicon 2019; 172:33-44. [DOI: 10.1016/j.toxicon.2019.10.244] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/30/2019] [Accepted: 10/30/2019] [Indexed: 12/27/2022]
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15
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A model for hydrophobic protrusions on peripheral membrane proteins. PLoS Comput Biol 2018; 14:e1006325. [PMID: 30048443 PMCID: PMC6080788 DOI: 10.1371/journal.pcbi.1006325] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 08/07/2018] [Accepted: 06/24/2018] [Indexed: 11/19/2022] Open
Abstract
With remarkable spatial and temporal specificities, peripheral membrane proteins bind to biological membranes. They do this without compromising solubility of the protein, and their binding sites are not easily distinguished. Prototypical peripheral membrane binding sites display a combination of patches of basic and hydrophobic amino acids that are also frequently present on other protein surfaces. The purpose of this contribution is to identify simple but essential components for membrane binding, through structural criteria that distinguish exposed hydrophobes at membrane binding sites from those that are frequently found on any protein surface. We formulate the concepts of protruding hydrophobes and co-insertability and have analysed more than 300 families of proteins that are classified as peripheral membrane binders. We find that this structural motif strongly discriminates the surfaces of membrane-binding and non-binding proteins. Our model constitutes a novel formulation of a structural pattern for membrane recognition and emphasizes the importance of subtle structural properties of hydrophobic membrane binding sites. Peripheral membrane proteins bind cellular membranes transiently, and are otherwise soluble proteins. As the interaction between proteins and membranes happens at cellular interfaces they are naturally involved in important interfacial processes such as recognition, signaling and trafficking. Commonly their binding sites are also soluble, and their binding mechanisms poorly understood. This complicates the elaboration of conceptual and quantitative models for peripheral membrane binding and makes binding site prediction difficult. It is therefore of great interest to discover traits that are common between these binding sites and that distinguishes them from other protein surfaces. In this work we identify simple and general structural features that facilitate membrane recognition by soluble proteins. We show that these motifs are highly over-represented on peripheral membrane proteins.
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16
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Henderson JM, Waring AJ, Separovic F, Lee KYC. Antimicrobial Peptides Share a Common Interaction Driven by Membrane Line Tension Reduction. Biophys J 2017; 111:2176-2189. [PMID: 27851941 DOI: 10.1016/j.bpj.2016.10.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/30/2016] [Accepted: 10/05/2016] [Indexed: 12/30/2022] Open
Abstract
Antimicrobial peptides (AMPs) are a class of host-defense molecules that neutralize a broad range of pathogens. Their membrane-permeabilizing behavior has been commonly attributed to the formation of pores; however, with the continuing discovery of AMPs, many are uncharacterized and their exact mechanism remains unknown. Using atomic force microscopy, we previously characterized the disruption of model membranes by protegrin-1 (PG-1), a cationic AMP from pig leukocytes. When incubated with zwitterionic membranes of dimyristoylphosphocholine, PG-1 first induced edge instability at low concentrations, then porous defects at intermediate concentrations, and finally worm-like micelle structures at high concentrations. These rich structural changes suggested that pore formation constitutes only an intermediate state along the route of PG-1's membrane disruption process. The formation of these structures could be best understood by using a mesophase framework of a binary mixture of lipids and peptides, where PG-1 acts as a line-active agent in lowering interfacial bilayer tensions. We have proposed that rather than being static pore formers, AMPs share a common ability to lower interfacial tensions that promote membrane transformations. In a study of 13 different AMPs, we found that peptide line-active behavior was not driven by the overall charge, and instead was correlated with their adoption of imperfect secondary structures. These peptide structures commonly positioned charged residues near the membrane interface to promote deformation favorable for their incorporation into the membrane. Uniquely, the data showed that barrel-stave-forming peptides such as alamethicin are not line-active, and that the seemingly disparate models of toroidal pores and carpet activity are actually related. We speculate that this interplay between peptide structure and the distribution of polar residues in relation to the membrane governs AMP line activity in general and represents a novel, to our knowledge, avenue for the rational design of new drugs.
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Affiliation(s)
- J Michael Henderson
- Department of Chemistry, The University of Chicago, Chicago, Illinois; Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois; The James Frank Institute, The University of Chicago, Chicago, Illinois
| | - Alan J Waring
- Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California; Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Frances Separovic
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Ka Yee C Lee
- Department of Chemistry, The University of Chicago, Chicago, Illinois; Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois; The James Frank Institute, The University of Chicago, Chicago, Illinois.
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17
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Grage SL, Sani MA, Cheneval O, Henriques ST, Schalck C, Heinzmann R, Mylne JS, Mykhailiuk PK, Afonin S, Komarov IV, Separovic F, Craik DJ, Ulrich AS. Orientation and Location of the Cyclotide Kalata B1 in Lipid Bilayers Revealed by Solid-State NMR. Biophys J 2017; 112:630-642. [PMID: 28256223 PMCID: PMC5340158 DOI: 10.1016/j.bpj.2016.12.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 12/23/2016] [Accepted: 12/29/2016] [Indexed: 02/04/2023] Open
Abstract
Cyclotides are ultra-stable cyclic disulfide-rich peptides from plants. Their biophysical effects and medically interesting activities are related to their membrane-binding properties, with particularly high affinity for phosphatidylethanolamine lipids. In this study we were interested in understanding the molecular details of cyclotide-membrane interactions, specifically with regard to the spatial orientation of the cyclotide kalata B1 from Oldenlandia affinis when embedded in a lipid bilayer. Our experimental approach was based on the use of solid-state 19F-NMR of oriented bilayers in conjunction with the conformationally restricted amino acid L-3-(trifluoromethyl)bicyclopent-[1.1.1]-1-ylglycine as an orientation-sensitive 19F-NMR probe. Its rigid connection to the kalata B1 backbone scaffold, together with the well-defined structure of the cyclotide, allowed us to calculate the protein alignment in the membrane directly from the orientation-sensitive 19F-NMR signal. The hydrophobic and polar residues on the surface of kalata B1 form well-separated patches, endowing this cyclotide with a pronounced amphipathicity. The peptide orientation, as determined by NMR, showed that this amphipathic structure matches the polar/apolar interface of the lipid bilayer very well. A location in the amphiphilic headgroup region of the bilayer was supported by 15N-NMR of uniformly labeled protein, and confirmed using solid-state 31P- and 2H-NMR. 31P-NMR relaxation data indicated a change in lipid headgroup dynamics induced by kalata B1. Changes in the 2H-NMR order parameter profile of the acyl chains suggest membrane thinning, as typically observed for amphiphilic peptides embedded near the polar/apolar bilayer interface. Furthermore, from the 19F-NMR analysis two important charged residues, E7 and R28, were found to be positioned equatorially. The observed location thus would be favorable for the postulated binding of E7 to phosphatidylethanolamine lipid headgroups. Furthermore, it may be speculated that this pair of side chains could promote oligomerization of kalata B1 through electrostatic intermolecular contacts via their complementary charges.
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Affiliation(s)
- Stephan L Grage
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Marc-Antoine Sani
- School of Chemistry, Bio21 Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Olivier Cheneval
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Sónia Troeira Henriques
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Constantin Schalck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Ralf Heinzmann
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Joshua S Mylne
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Pavel K Mykhailiuk
- Chemistry Department, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine; Enamine Ltd., Kyiv, Ukraine
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Igor V Komarov
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Frances Separovic
- School of Chemistry, Bio21 Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany; Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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18
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Cunha NBD, Barbosa AEADD, de Almeida RG, Porto WF, Maximiano MR, Álvares LCS, Munhoz CBR, Eugênio CUO, Viana AAB, Franco OL, Dias SC. Cloning and characterization of novel cyclotides genes from South American plants. Biopolymers 2017; 106:784-795. [PMID: 27554590 DOI: 10.1002/bip.22938] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 08/10/2016] [Accepted: 08/21/2016] [Indexed: 01/06/2023]
Abstract
Cyclotides are multifunctional plant cyclic peptides containing 28-37 amino acid residues and a pattern of three disulfide bridges, forming a motif known as the cyclic cystine knot. Due to their high biotechnological potential, the sequencing and characterization of cyclotide genes are crucial not only for cloning and establishing heterologous expression strategies, but also to understand local plant evolution in the context of host-pathogen relationships. Here, two species from the Brazilian Cerrado, Palicourea rigida (Rubiaceae) and Pombalia lanata (A.St.-Hil.) Paula-Souza (Violaceae), were used for cloning and characterizing novel cyclotide genes. Using 3' and 5' RACE PCR and sequencing, two full cDNAs, named parigidin-br2 (P. rigida) and hyla-br1 (P. lanata), were isolated and shown to have similar genetic structures to other cyclotides. Both contained the conserved ER-signal domain, N-terminal prodomain, mature cyclotide domain and a C-terminal region. Genomic sequencing of parigidin-br2 revealed two different gene copies: one intronless allele and one presenting a rare 131-bp intron. In contrast, genomic sequencing of hyla-br1 revealed an intronless gene-a common characteristic of members of the Violaceae family. Parigidin-br2 5' and 3' UTRs showed the presence of 12 putative candidate sites for binding of regulatory proteins, suggesting that the flanking and intronic regions of the parigidin-br2 gene must play important roles in transcriptional rates and in the regulation of temporal and spatial gene expression. The high degree of genetic similarity and structural organization among the cyclotide genes isolated in the present study from the Brazilian Cerrado and other well-characterized plant cyclotides may contribute to a better understanding of cyclotide evolution.
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Affiliation(s)
- Nicolau Brito da Cunha
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | | | - Renato Goulart de Almeida
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - William Farias Porto
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - Mariana Rocha Maximiano
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - Luana Cristina Silva Álvares
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - Cassia Beatriz Rodrigues Munhoz
- Departamento de Botânica, Instituto de Ciências Biológicas. Bloco D. Universidade de Brasília. Campus Darcy Ribeiro 70904-970, Asa Norte. Brasília, DF, Brazil
| | - Chesterton Ulysses Orlando Eugênio
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - Antônio Américo Barbosa Viana
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - Octavio Luiz Franco
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil.,S-Inova Biotech, Pós Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Simoni Campos Dias
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
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19
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Troeira Henriques S, Craik DJ. Cyclotide Structure and Function: The Role of Membrane Binding and Permeation. Biochemistry 2017; 56:669-682. [DOI: 10.1021/acs.biochem.6b01212] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sónia Troeira Henriques
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072 QLD, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072 QLD, Australia
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20
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Gao X, Stanger K, Kaluarachchi H, Maurer T, Ciepla P, Chalouni C, Franke Y, Hannoush RN. Cellular uptake of a cystine-knot peptide and modulation of its intracellular trafficking. Sci Rep 2016; 6:35179. [PMID: 27734922 PMCID: PMC5062073 DOI: 10.1038/srep35179] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/26/2016] [Indexed: 11/09/2022] Open
Abstract
Cyclotides or cyclic cystine-knot peptides have emerged as a promising class of pharmacological ligands that modulate protein function. Interestingly, very few cyclotides have been shown to enter into cells. Yet, it remains unknown whether backbone cyclization is required for their cellular internalization. In this report, we studied the cellular behavior of EETI-II, a model acyclic cystine-knot peptide. Even though synthetic methods have been used to generate EETI-II, recombinant methods that allow efficient large scale biosynthesis of EETI-II have been lagging. Here, we describe a novel protocol for recombinant generation of folded EETI-II in high yields and to near homogeneity. We also uncover that EETI-II is efficiently uptaken via an active endocytic pathway to early endosomes in mammalian cells, eventually accumulating in late endosomes and lysosomes. Notably, co-incubation with a cell-penetrating peptide enhanced the cellular uptake and altered the trafficking of EETI-II, leading to its evasion of lysosomes. Our results demonstrate the feasibility of modulating the subcellular distribution and intracellular targeting of cystine-knot peptides, and hence enable future exploration of their utility in drug discovery and delivery.
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Affiliation(s)
- Xinxin Gao
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California
| | - Karen Stanger
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California
| | - Harini Kaluarachchi
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California
| | - Till Maurer
- Department of Structural Biology, Genentech, South San Francisco, California
| | - Paulina Ciepla
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California
| | - Cecile Chalouni
- Department of Pathology, Genentech, South San Francisco, California
| | - Yvonne Franke
- Department of Structural Biology, Genentech, South San Francisco, California
| | - Rami N Hannoush
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California
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21
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Rosengren KJ, Daly NL, Harvey PJ, Craik DJ. The self-association of the cyclotide kalata B2 in solution is guided by hydrophobic interactions. Biopolymers 2016; 100:453-60. [PMID: 23893463 DOI: 10.1002/bip.22269] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 04/17/2013] [Accepted: 04/19/2013] [Indexed: 01/28/2023]
Abstract
The cyclotides are a family of small head-to-tail cyclic plant defense proteins. In addition to their cyclic backbone, cyclotides comprise three disulfide bonds in a knotted arrangement, resulting in a highly cross-braced structure that provides exceptional chemical and proteolytic stability. A number of bioactivities have been associated with cyclotides, including insecticidal, antimicrobial, anti-viral and cytotoxic, and these activities are related to an ability to target and disrupt biological membranes. Kalata B2 and to a lesser extent kalata B1, isolated from Oldenlandia affinis, self-associate to tetramers and octamers in aqueous buffers, and this oligomerization has been suggested to be relevant for their ability to form pores in membranes. Here we demonstrate by solution NMR spectroscopy analysis that the oligomerization of kalata B2 is concentration dependent and that it involves the packing of hydrophobic residues normally exposed on the surface of kalata B2 into a multimeric hydrophobic core. Interestingly, the hydrophobic surface that is "quenched" has previously been shown to be responsible for the ability of kalata B2 to insert into membranes. Thus, it seems unlikely that the oligomers observed in aqueous solution are related to any multimeric state present in a membrane environment, and responsible for the formation of pores. The ability to self-associate might alternatively provide a mechanism for preventing self-toxicity when stored at high concentrations in intracellular compartments.
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Affiliation(s)
- K Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
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22
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Mohanram H, Bhattacharjya S. 'Lollipop'-shaped helical structure of a hybrid antimicrobial peptide of temporin B-lipopolysaccharide binding motif and mapping cationic residues in antibacterial activity. Biochim Biophys Acta Gen Subj 2016; 1860:1362-72. [PMID: 27015761 DOI: 10.1016/j.bbagen.2016.03.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 03/08/2016] [Accepted: 03/20/2016] [Indexed: 12/17/2022]
Abstract
BACKGROUND Temporins are attractive templates for the development of antibiotics. However, many temporins are inactive against Gram-negative bacteria. Previously, we demonstrated conjugation of a lipopolysaccharide binding motif peptide to temporins yielded hybrid non-haemolytic AMPs that killed several Gram-negative bacteria. METHODS We carried out a systematic Ala replacement of individual cationic and polar amino acid residues of LG21, a hybrid AMP consisted of temporin B (TB) and LPS binding motif. These Ala containing analogs of LG21 were examined for antibacterial activity, cell membrane permeabilization and liposome leakage assays using optical spectroscopic methods. Atomic resolution structure of LG21 was determined in zwitterionic dodecyl phosphocholine (DPC) micelles by NMR spectroscopy. RESULTS Cationic residues in the LPS binding motif of LG21 were critical for bactericidal and membrane permeabilization. Detergent bound structure of LG21 revealed helical conformation containing extensive sidechain/sidechain packing including cation/π interactions in the LPS binding motif. The helical structure of LG21 resembled a 'lollipop' like shape that was sustained by a compacted bulky aromatic/cationic head with a comparatively thinner 'stick' at the N-terminal region. The 'head' of the structure could be localized into micelle-water interfacial region whereas the 'stick' region may be inserted into the hydrophobic core of micelle. CONCLUSIONS The LPS binding motif of LG21 played dominant roles in broad spectrum activity and the 3-D structure provided plausible mechanistic insights for permeabilization of bacterial membrane. GENERAL SIGNIFICANCE Hybrid AMPs containing LPS binding motif could be useful for the structure based development of broad spectrum antibiotics.
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Affiliation(s)
- Harini Mohanram
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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23
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Strömstedt AA, Kristiansen PE, Gunasekera S, Grob N, Skjeldal L, Göransson U. Selective membrane disruption by the cyclotide kalata B7: complex ions and essential functional groups in the phosphatidylethanolamine binding pocket. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1317-27. [PMID: 26878982 DOI: 10.1016/j.bbamem.2016.02.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 02/10/2016] [Accepted: 02/11/2016] [Indexed: 01/17/2023]
Abstract
The cyclic cystine knot plant peptides called cyclotides are active against a wide variety of organisms. This is primarily achieved through membrane binding and disruption, in part deriving from a high affinity for phosphatidylethanolamine (PE) lipids. Some cyclotides, such as kalata B7 (kB7), form complexes with divalent cations in a pocket associated with the tyrosine residue at position 15 (Tyr15). In the current work we explore the effect of cations on membrane leakage caused by cyclotides kB1, kB2 and kB7, and we identify a functional group that is essential for PE selectivity. The presence of PE-lipids in liposomes increased the membrane permeabilizing potency of the cyclotides, with the potency of kB7 increasing by as much as 740-fold. The divalent cations Mn(2+), Mg(2+) and Ca(2+) had no apparent effect on PE selectivity. However, amino acid substitutions in kB7 proved that Tyr15 is crucial for PE-selective membrane permeabilization on various liposome systems. Although the tertiary structure of kB7 was maintained, as reflected by the NMR solution structure, mutating Tyr into Ser at position 15 resulted in substantially reduced PE selectivity. Ala substitution at the same position produced a similar reduction in PE selectivity, while substitution with Phe maintained high selectivity. We conclude that the phenyl ring in Tyr15 is critical for the high PE selectivity of kB7. Our results suggest that PE-binding and divalent cation coordination occur in the same pocket without adverse effects of competitive binding for the phospholipid.
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Affiliation(s)
- Adam A Strömstedt
- Department of Medicinal Chemistry, Division of Pharmacognosy, Uppsala University, Box 574, SE 75123 Uppsala, Sweden
| | - Per Eugen Kristiansen
- Department of Molecular Biosciences, University of Oslo, Box 1041, 0316 Oslo, Norway
| | - Sunithi Gunasekera
- Department of Medicinal Chemistry, Division of Pharmacognosy, Uppsala University, Box 574, SE 75123 Uppsala, Sweden
| | - Nathalie Grob
- Department of Medicinal Chemistry, Division of Pharmacognosy, Uppsala University, Box 574, SE 75123 Uppsala, Sweden
| | - Lars Skjeldal
- Department of Chemistry, Biochemistry and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Ulf Göransson
- Department of Medicinal Chemistry, Division of Pharmacognosy, Uppsala University, Box 574, SE 75123 Uppsala, Sweden
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24
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Ravipati AS, Henriques ST, Poth AG, Kaas Q, Wang CK, Colgrave ML, Craik DJ. Lysine-rich Cyclotides: A New Subclass of Circular Knotted Proteins from Violaceae. ACS Chem Biol 2015; 10:2491-500. [PMID: 26322745 DOI: 10.1021/acschembio.5b00454] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclotides are macrocyclic proteins produced by plants for host defense. Although they occur sparsely in other plant families, cyclotides have been detected in every Violaceae plant species so far screened. Many of the Violaceae species examined until now have been from closely related geographical regions or habitats. To test the hypothesis that cyclotides are ubiquitous in this family, two geographically isolated (and critically endangered) species of Australasian Violaceae, namely Melicytus chathamicus and M. latifolius, were examined. Surprisingly, we discovered a suite of cyclotides possessing novel sequence features, including a lysine-rich nature, distinguishing them from "conventional" cyclotides and suggesting that they might have different physiological activities in plants to those reported to date. The newly discovered cyclotides were found to bind to lipid membranes and were cytotoxic against cancer cell lines but had low toxicity against red blood cells, which is advantageous for potential therapeutic applications. This suite of novel Lys-rich cyclotides emphasizes the broad diversity of cyclotides in Violaceae species.
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Affiliation(s)
- Anjaneya S. Ravipati
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sónia Troeira Henriques
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Aaron G. Poth
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Quentin Kaas
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Conan K. Wang
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Michelle L. Colgrave
- Commonwealth Scientific and Industrial Research Organization, Agriculture Flagship, St. Lucia, Queensland 4067, Australia
| | - David J. Craik
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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25
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Tam JP, Wang S, Wong KH, Tan WL. Antimicrobial Peptides from Plants. Pharmaceuticals (Basel) 2015; 8:711-57. [PMID: 26580629 PMCID: PMC4695807 DOI: 10.3390/ph8040711] [Citation(s) in RCA: 276] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 08/06/2015] [Accepted: 09/01/2015] [Indexed: 12/25/2022] Open
Abstract
Plant antimicrobial peptides (AMPs) have evolved differently from AMPs from other life forms. They are generally rich in cysteine residues which form multiple disulfides. In turn, the disulfides cross-braced plant AMPs as cystine-rich peptides to confer them with extraordinary high chemical, thermal and proteolytic stability. The cystine-rich or commonly known as cysteine-rich peptides (CRPs) of plant AMPs are classified into families based on their sequence similarity, cysteine motifs that determine their distinctive disulfide bond patterns and tertiary structure fold. Cystine-rich plant AMP families include thionins, defensins, hevein-like peptides, knottin-type peptides (linear and cyclic), lipid transfer proteins, α-hairpinin and snakins family. In addition, there are AMPs which are rich in other amino acids. The ability of plant AMPs to organize into specific families with conserved structural folds that enable sequence variation of non-Cys residues encased in the same scaffold within a particular family to play multiple functions. Furthermore, the ability of plant AMPs to tolerate hypervariable sequences using a conserved scaffold provides diversity to recognize different targets by varying the sequence of the non-cysteine residues. These properties bode well for developing plant AMPs as potential therapeutics and for protection of crops through transgenic methods. This review provides an overview of the major families of plant AMPs, including their structures, functions, and putative mechanisms.
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Affiliation(s)
- James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Shujing Wang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Ka H Wong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Wei Liang Tan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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26
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Truszkowski A, van den Broek K, Kuhn H, Zielesny A, Epple M. Mesoscopic Simulation of Phospholipid Membranes, Peptides, and Proteins with Molecular Fragment Dynamics. J Chem Inf Model 2015; 55:983-97. [DOI: 10.1021/ci5006096] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Andreas Truszkowski
- Inorganic
Chemistry and Center for Nanointegration Duisburg−Essen (CENIDE), University of Duisburg−Essen, 45141 Essen, Germany
- Institute
for Bioinformatics and Cheminformatics, Westphalian University of Applied Sciences, 45665 Recklinghausen, Germany
| | - Karina van den Broek
- Department
of Pharmacy−Center for Drug Research, Ludwig-Maximilians University Munich, 80539 Munich, Germany
| | - Hubert Kuhn
- Inorganic
Chemistry and Center for Nanointegration Duisburg−Essen (CENIDE), University of Duisburg−Essen, 45141 Essen, Germany
- CAM-D Technologies, 45127 Essen, Germany
| | - Achim Zielesny
- Institute
for Bioinformatics and Cheminformatics, Westphalian University of Applied Sciences, 45665 Recklinghausen, Germany
| | - Matthias Epple
- Inorganic
Chemistry and Center for Nanointegration Duisburg−Essen (CENIDE), University of Duisburg−Essen, 45141 Essen, Germany
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27
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Nawae W, Hannongbua S, Ruengjitchatchawalya M. Dynamic scenario of membrane binding process of kalata b1. PLoS One 2014; 9:e114473. [PMID: 25473840 PMCID: PMC4256454 DOI: 10.1371/journal.pone.0114473] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 11/11/2014] [Indexed: 11/18/2022] Open
Abstract
Kalata B1 (kB1), a cyclotide that has been used in medical applications, displays cytotoxicity related to membrane binding and oligomerization. Our molecular dynamics simulation results demonstrate that Trp19 in loop 5 of both monomeric and tetrameric kB1 is a key residue for initial anchoring in the membrane binding process. This residue also facilitates the formation of kB1 tetramers. Additionally, we elucidate that kB1 preferentially binds to the membrane interfacial zone and is unable to penetrate into the membrane. In particular, significant roles of amino acid residues in loop 5 and loop 6 on the localization of kB1 to this membrane-water interface zone are found. This study reveals the roles of amino acid residues in the bioactivity of kB1, which is information that can be useful for designing new therapeutic cyclotides with less toxicity.
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Affiliation(s)
- Wanapinun Nawae
- Biological Engineering Program, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Thung Khru, Bangkok, Thailand
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Marasri Ruengjitchatchawalya
- Bioinformatics and Systems Biology program, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bang Khun Thian, Bangkok, Thailand; Biotechnology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bang Khun Thian, Bangkok, Thailand
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28
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Manzo G, Casu M, Rinaldi AC, Montaldo NP, Luganini A, Gribaudo G, Scorciapino MA. Folded structure and insertion depth of the frog-skin antimicrobial Peptide esculentin-1b(1-18) in the presence of differently charged membrane-mimicking micelles. JOURNAL OF NATURAL PRODUCTS 2014; 77:2410-2417. [PMID: 25337981 DOI: 10.1021/np5004406] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Antimicrobial peptides (AMPs) are effectors of the innate immunity of most organisms. Their role in the defense against pathogen attack and their high selectivity for bacterial cells make them attractive for the development of a new class of antimicrobial drugs. The N-terminal fragment of the frog-skin peptide esculentin-1b (Esc(1-18)) has shown broad-spectrum antimicrobial activity. Similarly to most cationic AMPs, it is supposed to act by binding to and damaging the negatively charged plasma membrane of bacteria. Differently from many other AMPs, Esc(1-18) activity is preserved in biological fluids such as serum. In this work, a structural investigation was performed through NMR spectroscopy. The 3D structure was obtained in the presence of either zwitterionic or negatively charged micelles as membrane models for eukaryotic and prokaryotic membranes, respectively. Esc(1-18) showed a higher affinity for and deeper insertion into the latter and adopted an amphipathic helical structure characterized by a kink at the residue G8. These findings were confirmed by measuring penetration into lipid monolayers. The presence of negatively charged lipids in the bilayer appears to be necessary for Esc(1-18) to bind, to fold in the right three-dimensional structure, and, ultimately, to exert its biological role as an AMP.
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Affiliation(s)
- Giorgia Manzo
- Department of Chemical and Geological Sciences and ‡Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria , I-09042 Monserrato (CA), Italy
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29
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Wang CK, Northfield SE, Swedberg JE, Harvey PJ, Mathiowetz AM, Price DA, Liras S, Craik DJ. Translational diffusion of cyclic peptides measured using pulsed-field gradient NMR. J Phys Chem B 2014; 118:11129-36. [PMID: 25184622 DOI: 10.1021/jp506678f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Cyclic peptides are increasingly being recognized as valuable templates for drug discovery or design. To facilitate efforts in the structural characterization of cyclic peptides, we explore the use of pulse-field gradient experiments as a convenient and noninvasive approach for characterizing their diffusion properties in solution. We present diffusion coefficient measurements of five cyclic peptides, including dichC, SFTI-1, cVc1.1, kB1, and kB2. These peptides range in size from six to 29 amino acids and have various therapeutically interesting activities. We explore the use of internal standards, such as dioxane and acetonitrile, to evaluate the hydrodynamic radius from the diffusion coefficient, and show that 2,2-dimethyl-2-silapentane-5-sulfonic acid, a commonly used chemical shift reference, can be used as an internal standard to avoid spectral overlap issues and simplify data analysis. The experimentally measured hydrodynamic radii correlate with increasing molecular weight and in silico predictions. We further applied diffusion measurements to characterize the self-association of kB2 and showed that it forms oligomers in a concentration-dependent manner, which may be relevant to its mechanism of action. Diffusion coefficient measurements appear to have broad utility in cyclic peptide structural biology, allowing for the rapid characterization of their molecular shape in solution.
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Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland 4072, Australia
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30
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Troeira Henriques S, Huang YH, Chaousis S, Wang CK, Craik DJ. Anticancer and toxic properties of cyclotides are dependent on phosphatidylethanolamine phospholipid targeting. Chembiochem 2014; 15:1956-65. [PMID: 25099014 DOI: 10.1002/cbic.201402144] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Indexed: 11/11/2022]
Abstract
Cyclotides, ultrastable disulfide-rich cyclic peptides, can be engineered to bind and inhibit specific cancer targets. In addition, some cyclotides are toxic to cancer cells, though not much is known about their mechanisms of action. Here we delineated the potential mode of action of cyclotides towards cancer cells. A novel set of analogues of kalata B1 (the prototypic cyclotide) and kalata B2 and cycloviolacin O2 were examined for their membrane-binding affinity and selectivity towards cancer cells. By using solution-state NMR, surface plasmon resonance, flow cytometry and bioassays we show that cyclotides are toxic against cancer and non-cancerous cells and their toxicity correlates with their ability to target and disrupt lipid bilayers that contain phosphatidylethanolamine phospholipids. Our results suggest that the potential of cyclotides as anticancer therapeutics might best be realised by combining their amenability to epitope engineering with their ability to bind cancer cell membranes.
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Affiliation(s)
- Sónia Troeira Henriques
- The University of Queensland, Institute for Molecular Bioscience, Carmody Road, St. Lucia, Brisbane, QLD 4072 (Australia).
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31
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Burman R, Gunasekera S, Strömstedt AA, Göransson U. Chemistry and biology of cyclotides: circular plant peptides outside the box. JOURNAL OF NATURAL PRODUCTS 2014; 77:724-36. [PMID: 24527877 DOI: 10.1021/np401055j] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Cyclotides stand out as the largest family of circular proteins of plant origin hitherto known, with more than 280 sequences isolated at peptide level and many more predicted from gene sequences. Their unusual stability resulting from the signature cyclic cystine knot (CCK) motif has triggered a broad interest in these molecules for potential therapeutic and agricultural applications. Since the time of the first cyclotide discovery, our laboratory in Uppsala has been engaged in cyclotide discovery as well as the development of protocols to isolate and characterize these seamless peptides. We have also developed methods to chemically synthesize cyclotides by Fmoc-SPPS, which are useful in protein grafting applications. In this review, experience in cyclotide research over two decades and the recent literature related to their structures, synthesis, and folding as well the recent proof-of-concept findings on their use as "epitope" stabilizing scaffolds are summarized.
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Affiliation(s)
- Robert Burman
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University , Biomedical Centre, Box 574, SE-751 23 Uppsala, Sweden
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32
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Defining the membrane disruption mechanism of kalata B1 via coarse-grained molecular dynamics simulations. Sci Rep 2014; 4:3933. [PMID: 24492660 PMCID: PMC3910381 DOI: 10.1038/srep03933] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 01/13/2014] [Indexed: 11/08/2022] Open
Abstract
Kalata B1 has been demonstrated to have bioactivity relating to membrane disruption. In this study, we conducted coarse-grained molecular dynamics simulations to gain further insight into kB1 bioactivity. The simulations were performed at various concentrations of kB1 to capture the overall progression of its activity. Two configurations of kB1 oligomers, termed tower-like and wall-like clusters, were detected. The conjugation between the wall-like oligomers resulted in the formation of a ring-like hollow in the kB1 cluster on the membrane surface. Our results indicated that the molecules of kB1 were trapped at the membrane-water interface. The interfacial membrane binding of kB1 induced a positive membrane curvature, and the lipids were eventually extracted from the membrane through the kB1 ring-like hollow into the space inside the kB1 cluster. These findings provide an alternative view of the mechanism of kB1 bioactivity that corresponds with the concept of an interfacial bioactivity model.
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33
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Zhan H, Lazaridis T. Inclusion of lateral pressure/curvature stress effects in implicit membrane models. Biophys J 2013; 104:643-54. [PMID: 23442915 DOI: 10.1016/j.bpj.2012.12.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 12/06/2012] [Accepted: 12/10/2012] [Indexed: 02/06/2023] Open
Abstract
Implicit membrane models usually treat the membrane as a hydrophobic slab and neglect lateral pressure/curvature stress effects. As a result, they cannot distinguish, for example, PE from PC lipids. Here, the implicit membrane model IMM1 is extended to include these effects using a combination of classical thermodynamics and membrane elasticity theory. The proposed model is tested by molecular dynamics simulation of the peptides alamethicin, melittin, cyclotide kalata B1, 18A, and KKpL15. The lateral pressure term stabilizes interfacial binding due to the negative pressure at the hydrocarbon-water interface. In agreement with experiment, increase in the peptide/lipid molar ratio shifts the equilibrium from the interfacial to the transmembrane orientation. Simulations of mixed DOPC/DOPE bilayers show that increase of the DOPE mole fraction in general stabilizes interfacial orientations and destabilizes transmembrane orientations. The extent of the stabilization or destabilization varies depending on the exact position of the peptides. The computational results are in good agreement with experiments.
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Affiliation(s)
- Huan Zhan
- Department of Chemistry, City College of New York/City University of New York, New York, New York, USA
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34
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Solution NMR studies on the orientation of membrane-bound peptides and proteins by paramagnetic probes. Molecules 2013; 18:7407-35. [PMID: 23799448 PMCID: PMC6269851 DOI: 10.3390/molecules18077407] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/13/2013] [Accepted: 06/20/2013] [Indexed: 12/24/2022] Open
Abstract
Many peptides and proteins are attached to or immersed in a biological membrane. In order to understand their function not only the structure but also their topology in the membrane is important. Solution NMR spectroscopy is one of the most often used approaches to determine the orientation and localization of membrane-bound peptides and proteins. Here we give an application-oriented overview on the use of paramagnetic probes for the investigation of membrane-bound peptides and proteins. The examples discussed range from the large pool of antimicrobial peptides, bacterial toxins, cell penetrating peptides to domains of larger proteins or the calcium regulating protein phospholamban. Topological information is obtained in all these examples by the use of either attached or freely mobile paramagnetic tags. For some examples information obtained from the paramagnetic probes was included in the structure determination.
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35
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Shenkarev ZO, Paramonov AS, Lyukmanova EN, Gizatullina AK, Zhuravleva AV, Tagaev AA, Yakimenko ZA, Telezhinskaya IN, Kirpichnikov MP, Ovchinnikova TV, Arseniev AS. Peptaibol Antiamoebin I: Spatial Structure, Backbone Dynamics, Interaction with Bicelles and Lipid-Protein Nanodiscs, and Pore Formation in Context of Barrel-Stave Model. Chem Biodivers 2013; 10:838-63. [DOI: 10.1002/cbdv.201200421] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Indexed: 11/12/2022]
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36
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Arnison PG, Bibb MJ, Bierbaum G, Bowers AA, Bugni TS, Bulaj G, Camarero JA, Campopiano DJ, Challis GL, Clardy J, Cotter PD, Craik DJ, Dawson M, Dittmann E, Donadio S, Dorrestein PC, Entian KD, Fischbach MA, Garavelli JS, Göransson U, Gruber CW, Haft DH, Hemscheidt TK, Hertweck C, Hill C, Horswill AR, Jaspars M, Kelly WL, Klinman JP, Kuipers OP, Link AJ, Liu W, Marahiel MA, Mitchell DA, Moll GN, Moore BS, Müller R, Nair SK, Nes IF, Norris GE, Olivera BM, Onaka H, Patchett ML, Piel J, Reaney MJT, Rebuffat S, Ross RP, Sahl HG, Schmidt EW, Selsted ME, Severinov K, Shen B, Sivonen K, Smith L, Stein T, Süssmuth RD, Tagg JR, Tang GL, Truman AW, Vederas JC, Walsh CT, Walton JD, Wenzel SC, Willey JM, van der Donk WA. Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep 2013; 30:108-60. [PMID: 23165928 DOI: 10.1039/c2np20085f] [Citation(s) in RCA: 1445] [Impact Index Per Article: 131.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This review presents recommended nomenclature for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), a rapidly growing class of natural products. The current knowledge regarding the biosynthesis of the >20 distinct compound classes is also reviewed, and commonalities are discussed.
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Affiliation(s)
- Paul G Arnison
- Prairie Plant Systems Inc, Botanical Alternatives Inc, Suite 176, 8B-3110 8th Street E, Saskatoon, SK, S7H 0W2, Canada
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37
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Shenkarev ZO, Panteleev PV, Balandin SV, Gizatullina AK, Altukhov DA, Finkina EI, Kokryakov VN, Arseniev AS, Ovchinnikova TV. Recombinant expression and solution structure of antimicrobial peptide aurelin from jellyfish Aurelia aurita. Biochem Biophys Res Commun 2012; 429:63-9. [DOI: 10.1016/j.bbrc.2012.10.092] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 10/25/2012] [Indexed: 12/25/2022]
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38
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Wang CK, Wacklin HP, Craik DJ. Cyclotides insert into lipid bilayers to form membrane pores and destabilize the membrane through hydrophobic and phosphoethanolamine-specific interactions. J Biol Chem 2012; 287:43884-98. [PMID: 23129773 DOI: 10.1074/jbc.m112.421198] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Cyclotides are a family of plant-derived circular proteins with potential therapeutic applications arising from their remarkable stability, broad sequence diversity, and range of bioactivities. Their membrane-binding activity is believed to be a critical component of their mechanism of action. Using isothermal titration calorimetry, we studied the binding of the prototypical cyclotides kalata B1 and kalata B2 (and various mutants) to dodecylphosphocholine micelles and phosphoethanolamine-containing lipid bilayers. Although binding is predominantly an entropy-driven process, suggesting that hydrophobic forces contribute significantly to cyclotide-lipid complex formation, specific binding to the phosphoethanolamine-lipid headgroup is also required, which is evident from the enthalpic changes in the free energy of binding. In addition, using a combination of dissipative quartz crystal microbalance measurements and neutron reflectometry, we elucidated the process by which cyclotides interact with bilayer membranes. Initially, a small number of cyclotides bind to the membrane surface and then insert first into the outer membrane leaflet followed by penetration through the membrane and pore formation. At higher concentrations of cyclotides, destabilization of membranes occurs. Our results provide significant mechanistic insight into how cyclotides exert their bioactivities.
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Affiliation(s)
- Conan K Wang
- University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland 4072, Australia
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39
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Oeemig JS, Lynggaard C, Knudsen DH, Hansen FT, Nørgaard KD, Schneider T, Vad BS, Sandvang DH, Nielsen LA, Neve S, Kristensen HH, Sahl HG, Otzen DE, Wimmer R. Eurocin, a new fungal defensin: structure, lipid binding, and its mode of action. J Biol Chem 2012; 287:42361-72. [PMID: 23093408 DOI: 10.1074/jbc.m112.382028] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Antimicrobial peptides are a new class of antibiotics that are promising for pharmaceutical applications because they have retained efficacy throughout evolution. One class of antimicrobial peptides are the defensins, which have been found in different species. Here we describe a new fungal defensin, eurocin. Eurocin acts against a range of Gram-positive human pathogens but not against Gram-negative bacteria. Eurocin consists of 42 amino acids, forming a cysteine-stabilized α/β-fold. The thermal denaturation data point shows the disulfide bridges being responsible for the stability of the fold. Eurocin does not form pores in cell membranes at physiologically relevant concentrations; it does, however, lead to limited leakage of a fluorophore from small unilamellar vesicles. Eurocin interacts with detergent micelles, and it inhibits the synthesis of cell walls by binding equimolarly to the cell wall precursor lipid II.
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Affiliation(s)
- Jesper S Oeemig
- Department of Biotechnology, Chemistry, and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark
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40
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Yeshak MY, Göransson U, Burman R, Hellman B. Genotoxicity and cellular uptake of cyclotides: Evidence for multiple modes of action. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2012; 747:176-81. [DOI: 10.1016/j.mrgentox.2012.05.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Revised: 03/20/2012] [Accepted: 05/02/2012] [Indexed: 10/28/2022]
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41
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Gly6 of kalata B1 is critical for the selective binding to phosphatidylethanolamine membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2354-61. [DOI: 10.1016/j.bbamem.2012.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 03/29/2012] [Accepted: 04/10/2012] [Indexed: 11/18/2022]
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42
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Henriques ST, Huang YH, Castanho MARB, Bagatolli LA, Sonza S, Tachedjian G, Daly NL, Craik DJ. Phosphatidylethanolamine binding is a conserved feature of cyclotide-membrane interactions. J Biol Chem 2012; 287:33629-43. [PMID: 22854971 DOI: 10.1074/jbc.m112.372011] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Cyclotides are bioactive cyclic peptides isolated from plants that are characterized by a topologically complex structure and exceptional resistance to enzymatic or thermal degradation. With their sequence diversity, ultra-stable core structural motif, and range of bioactivities, cyclotides are regarded as a combinatorial peptide template with potential applications in drug design. The mode of action of cyclotides remains elusive, but all reported biological activities are consistent with a mechanism involving membrane interactions. In this study, a diverse set of cyclotides from the two major subfamilies, Möbius and bracelet, and an all-d mirror image form, were examined to determine their mode of action. Their lipid selectivity and membrane affinity were determined, as were their toxicities against a range of targets (red blood cells, bacteria, and HIV particles). Although they had different membrane-binding affinities, all of the tested cyclotides targeted membranes through binding to phospholipids containing phosphatidylethanolamine headgroups. Furthermore, the biological potency of the tested cyclotides broadly correlated with their ability to target and disrupt cell membranes. The finding that a broad range of cyclotides target a specific lipid suggests their categorization as a new lipid-binding protein family. Knowledge of their membrane specificity has the potential to assist in the design of novel drugs based on the cyclotide framework, perhaps allowing the targeting of peptide drugs to specific cell types.
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Affiliation(s)
- Sónia Troeira Henriques
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072 Queensland, Australia
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43
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Göransson U, Burman R, Gunasekera S, Strömstedt AA, Rosengren KJ. Circular proteins from plants and fungi. J Biol Chem 2012; 287:27001-6. [PMID: 22700984 DOI: 10.1074/jbc.r111.300129] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Circular proteins, defined as head-to-tail cyclized polypeptides originating from ribosomal synthesis, represent a novel class of natural products attracting increasing interest. From a scientific point of view, these compounds raise questions of where and why they occur in nature and how they are formed. From a rational point of view, these proteins and their structural concept may be exploited for crop protection and novel pharmaceuticals. Here, we review the current knowledge of three protein families: cyclotides and circular sunflower trypsin inhibitors from the kingdom of plants and the Amanita toxins from fungi. A particular emphasis is placed on their biological origin, structure, and activity. In addition, the opportunity for discovery of novel circular proteins and recent insights into their mechanism of action are discussed.
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Affiliation(s)
- Ulf Göransson
- Division of Pharmacognosy, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, SE-75123 Uppsala, Sweden.
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44
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Gould A, Ji Y, Aboye TL, Camarero JA. Cyclotides, a novel ultrastable polypeptide scaffold for drug discovery. Curr Pharm Des 2012; 17:4294-307. [PMID: 22204428 DOI: 10.2174/138161211798999438] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Accepted: 09/15/2011] [Indexed: 11/22/2022]
Abstract
Cyclotides are a unique and growing family of backbone cyclized peptides that also contain a cystine knot motif built from six conserved cysteine residues. This unique circular backbone topology and knotted arrangement of three disulfide bonds makes them exceptionally stable to thermal, chemical, and enzymatic degradation compared to other peptides of similar size. Aside from the conserved residues forming the cystine knot, cyclotides have been shown to have high variability in their sequences. Consisting of over 160 known members, cyclotides have many biological activities, ranging from anti-HIV, antimicrobial, hemolytic, and uterotonic capabilities; additionally, some cyclotides have been shown to have cell penetrating properties. Originally discovered and isolated from plants, cyclotides can also be produced synthetically and recombinantly. The high sequence variability, stability, and cell penetrating properties of cyclotides make them potential scaffolds to be used to graft known active peptides or engineer peptide-based drug design. The present review reports recent findings in the biological diversity and therapeutic potential of natural and engineered cyclotides.
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Affiliation(s)
- Andrew Gould
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90033, USA
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Henriques ST, Craik DJ. Importance of the cell membrane on the mechanism of action of cyclotides. ACS Chem Biol 2012; 7:626-36. [PMID: 22260456 DOI: 10.1021/cb200395f] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Their distinctive structures, diverse range of bioactivities, and potential for pharmaceutical or agricultural applications make cyclotides an intriguing family of cyclic peptides. Together with the physiological role in plant host defense, cyclotides possess antimicrobial, anticancer, and anti-HIV activities. In all of the reported activities, cell membranes seem to be the primary target for cyclotide binding. This article examines recent literature on cyclotide-membrane studies and highlights the hypothesis that the activity of cyclotides is dependent on their affinity for lipid bilayers and enhanced by the presence of specific lipids, i.e., phospholipids containing phosphatidylethanolamine headgroups. There is growing evidence that the lipid composition of target cell membranes dictates the amount of cyclotides bound to the cell and the extent of their activity. After membrane targeting and insertion in the bilayer core, cyclotides induce disruption of membranes by a pore formation mechanism. This proposed mechanism of action is supported by biophysical studies with model membranes and by studies on natural biological membranes of known lipid compositions.
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Affiliation(s)
- Sónia Troeira Henriques
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Institute of Molecular Medicine,
Medical School, University of Lisbon, 1649-028
Lisbon, Portugal
| | - David J. Craik
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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Scott JL, Musselman CA, Adu-Gyamfi E, Kutateladze TG, Stahelin RV. Emerging methodologies to investigate lipid-protein interactions. Integr Biol (Camb) 2012; 4:247-58. [PMID: 22327461 DOI: 10.1039/c2ib00143h] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cellular membranes are composed of hundreds of different lipids, ion channels, receptors and scaffolding complexes that act as signalling and trafficking platforms for processes fundamental to life. Cellular signalling and membrane trafficking are often regulated by peripheral proteins, which reversibly interact with lipid molecules in highly regulated spatial and temporal fashions. In most cases, one or more modular lipid-binding domain(s) mediate recruitment of peripheral proteins to specific cellular membranes. These domains, of which more than 10 have been identified since 1989, harbour structurally selective lipid-binding sites. Traditional in vitro and in vivo studies have elucidated how these domains coordinate their cognate lipids and thus how the parent proteins associate with membranes. Cellular activities of peripheral proteins and subsequent physiological processes depend upon lipid binding affinities and selectivity. Thus, the development of novel sensitive and quantitative tools is essential in furthering our understanding of the function and regulation of these proteins. As this field expands into new areas such as computational biology, cellular lipid mapping, single molecule imaging, and lipidomics, there is an urgent need to integrate technologies to detail the molecular architecture and mechanisms of lipid signalling. This review surveys emerging cellular and in vitro approaches for studying protein-lipid interactions and provides perspective on how integration of methodologies directs the future development of the field.
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Affiliation(s)
- Jordan L Scott
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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Craik DJ. Host-defense activities of cyclotides. Toxins (Basel) 2012; 4:139-56. [PMID: 22474571 PMCID: PMC3317112 DOI: 10.3390/toxins4020139] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 01/25/2012] [Accepted: 01/31/2012] [Indexed: 11/27/2022] Open
Abstract
Cyclotides are plant mini-proteins whose natural function is thought to be to protect plants from pest or pathogens, particularly insect pests. They are approximately 30 amino acids in size and are characterized by a cyclic peptide backbone and a cystine knot arrangement of three conserved disulfide bonds. This article provides an overview of the reported pesticidal or toxic activities of cyclotides, discusses a possible common mechanism of action involving disruption of biological membranes in pest species, and describes methods that can be used to produce cyclotides for potential applications as novel pesticidal agents.
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Affiliation(s)
- David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
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Pinto MFS, Fensterseifer ICM, Migliolo L, Sousa DA, de Capdville G, Arboleda-Valencia JW, Colgrave ML, Craik DJ, Magalhães BS, Dias SC, Franco OL. Identification and structural characterization of novel cyclotide with activity against an insect pest of sugar cane. J Biol Chem 2012; 287:134-147. [PMID: 22074926 PMCID: PMC3249065 DOI: 10.1074/jbc.m111.294009] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 10/31/2011] [Indexed: 02/02/2023] Open
Abstract
Cyclotides are a family of plant-derived cyclic peptides comprising six conserved cysteine residues connected by three intermolecular disulfide bonds that form a knotted structure known as a cyclic cystine knot (CCK). This structural motif is responsible for the pronounced stability of cyclotides against chemical, thermal, or proteolytic degradation and has sparked growing interest in this family of peptides. Here, we isolated and characterized a novel cyclotide from Palicourea rigida (Rubiaceae), which was named parigidin-br1. The sequence indicated that this peptide is a member of the bracelet subfamily of cyclotides. Parigidin-br1 showed potent insecticidal activity against neonate larvae of Lepidoptera (Diatraea saccharalis), causing 60% mortality at a concentration of 1 μm but had no detectable antibacterial effects. A decrease in the in vitro viability of the insect cell line from Spodoptera frugiperda (SF-9) was observed in the presence of parigidin-br1, consistent with in vivo insecticidal activity. Transmission electron microscopy and fluorescence microscopy of SF-9 cells after incubation with parigidin-br1 or parigidin-br1-fluorescein isothiocyanate, respectively, revealed extensive cell lysis and swelling of cells, consistent with an insecticidal mechanism involving membrane disruption. This hypothesis was supported by in silico analyses, which suggested that parigidin-br1 is able to complex with cell lipids. Overall, the results suggest promise for the development of parigidin-br1 as a novel biopesticide.
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Affiliation(s)
- Michelle F S Pinto
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
| | - Isabel C M Fensterseifer
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
| | - Ludovico Migliolo
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
| | - Daniel A Sousa
- Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília-DF, Brazil
| | - Guy de Capdville
- CENARGEN (Centro Nacional de Pesquisa de Recursos Genéticos e Biotecnologia), Embrapa Recursos Genéticos e Biotecnologia, Brasília-DF, Brazil
| | - Jorge W Arboleda-Valencia
- CENARGEN (Centro Nacional de Pesquisa de Recursos Genéticos e Biotecnologia), Embrapa Recursos Genéticos e Biotecnologia, Brasília-DF, Brazil; Departamento de Biologia Celular, Universidade de Brasília, Brasília-DF, Brazil
| | - Michelle L Colgrave
- Commonwealth Scientific and Industrial Research Organization Livestock Industries, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
| | - David J Craik
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Beatriz S Magalhães
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
| | - Simoni C Dias
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
| | - Octávio L Franco
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil.
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Pinto MFS, Almeida RG, Porto WF, Fensterseifer ICM, Lima LA, Dias SC, Franco OL. Cyclotides. J Evid Based Complementary Altern Med 2011. [DOI: 10.1177/2156587211428077] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In recent years, a number of peptides containing a cyclic structural fold have been described. Among them, the cyclotides family was widely reported in different plant tissues, being composed of small cyclic peptides containing 6 conserved cysteine residues connected by disulfide bonds and forming a cysteine-binding cyclic structure known as a cyclic cysteine knot. This structural scaffold is responsible for an enhanced structural stability against chemical, thermal, and proteolytic degradation. Because of the observed stability and multifunctionality, including insecticidal, antimicrobial, and anti-HIV (human immunodeficiency virus) action, much effort has gone into trying to elucidate the structural-function relations of cyclotide compounds. This review focuses on the novelties involving gene structure, precursor formation and processing, and protein folding of the cyclotide family, shedding some light on molecular mechanisms of cyclotide production. Because cyclotides are clear targets for drug development and also biotechnology applications, their chemical synthesis, heterologous systems production, and protein grafting are also addressed.
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