1
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Ragonis-Bachar P, Axel G, Blau S, Ben-Tal N, Kolodny R, Landau M. What can AlphaFold do for antimicrobial amyloids? Proteins 2024; 92:265-281. [PMID: 37855235 DOI: 10.1002/prot.26618] [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: 07/13/2023] [Revised: 09/05/2023] [Accepted: 10/05/2023] [Indexed: 10/20/2023]
Abstract
Amyloids, protein, and peptide assemblies in various organisms are crucial in physiological and pathological processes. Their intricate structures, however, present significant challenges, limiting our understanding of their functions, regulatory mechanisms, and potential applications in biomedicine and technology. This study evaluated the AlphaFold2 ColabFold method's structure predictions for antimicrobial amyloids, using eight antimicrobial peptides (AMPs), including those with experimentally determined structures and AMPs known for their distinct amyloidogenic morphological features. Additionally, two well-known human amyloids, amyloid-β and islet amyloid polypeptide, were included in the analysis due to their disease relevance, short sequences, and antimicrobial properties. Amyloids typically exhibit tightly mated β-strand sheets forming a cross-β configuration. However, certain amphipathic α-helical subunits can also form amyloid fibrils adopting a cross-α structure. Some AMPs in the study exhibited a combination of cross-α and cross-β amyloid fibrils, adding complexity to structure prediction. The results showed that the AlphaFold2 ColabFold models favored α-helical structures in the tested amyloids, successfully predicting the presence of α-helical mated sheets and a hydrophobic core resembling the cross-α configuration. This implies that the AI-based algorithms prefer assemblies of the monomeric state, which was frequently predicted as helical, or capture an α-helical membrane-active form of toxic peptides, which is triggered upon interaction with lipid membranes.
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Affiliation(s)
| | - Gabriel Axel
- George S. Wise Faculty of Life Sciences, Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel
| | - Shahar Blau
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Nir Ben-Tal
- George S. Wise Faculty of Life Sciences, Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel
| | - Rachel Kolodny
- Department of Computer Science, University of Haifa, Haifa, Israel
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- The Center for Experimental Medicine, Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany
- European Molecular Biology Laboratory (EMBL), Hamburg, Germany
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2
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Tang Y, Zhang D, Zheng J. Repurposing Antimicrobial Protegrin-1 as a Dual-Function Amyloid Inhibitor via Cross-seeding. ACS Chem Neurosci 2023; 14:3143-3155. [PMID: 37589476 DOI: 10.1021/acschemneuro.3c00293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023] Open
Abstract
Amyloids and antimicrobial peptides have traditionally been recognized as distinct families with separate biological functions and targets. However, certain amyloids and antimicrobial peptides share structural and functional characteristics that contribute to the development of neurodegenerative diseases. Specifically, the aggregation of amyloid-β (Aβ) and microbial infections are interconnected pathological factors in Alzheimer's disease (AD). In this study, we propose and demonstrate a novel repurposing strategy for an antimicrobial peptide of protegrin-1 (PG-1), which exhibits the ability to simultaneously prevent Aβ aggregation and microbial infection both in vitro and in vivo. Through a comprehensive analysis using protein, cell, and worm assays, we uncover multiple functions of PG-1 against Aβ, including the following: (i) complete inhibition of Aβ aggregation at a low molar ratio of PG-1/Aβ = 0.25:1, (ii) disassembly of the preformed Aβ fibrils into amorphous aggregates, (iii) reduction of Aβ-induced cytotoxicity in SH-SY5Y cells and transgenic GMC101 nematodes, and (iv) preservation of original antimicrobial activity against P.A., E.coli., S.A., and S.E. strains in the presence of Aβ. Mechanistically, the dual anti-amyloid and anti-bacterial functions of PG-1 primarily arise from its strong binding to distinct Aβ seeds (KD = 1.24-1.90 μM) through conformationally similar β-sheet associations. This work introduces a promising strategy to repurpose antimicrobial peptides as amyloid inhibitors, effectively targeting multiple pathological pathways in AD.
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Affiliation(s)
- Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Dong Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, Ohio 44325, United States
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3
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Buchanan JA, Varghese NR, Johnston CL, Sunde M. Functional Amyloids: Where Supramolecular Amyloid Assembly Controls Biological Activity or Generates New Functionality. J Mol Biol 2023; 435:167919. [PMID: 37330295 DOI: 10.1016/j.jmb.2022.167919] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 06/19/2023]
Abstract
Functional amyloids are a rapidly expanding class of fibrillar protein structures, with a core cross-β scaffold, where novel and advantageous biological function is generated by the assembly of the amyloid. The growing number of amyloid structures determined at high resolution reveal how this supramolecular template both accommodates a wide variety of amino acid sequences and also imposes selectivity on the assembly process. The amyloid fibril can no longer be considered a generic aggregate, even when associated with disease and loss of function. In functional amyloids the polymeric β-sheet rich structure provides multiple different examples of unique control mechanisms and structures that are finely tuned to deliver assembly or disassembly in response to physiological or environmental cues. Here we review the range of mechanisms at play in natural, functional amyloids, where tight control of amyloidogenicity is achieved by environmental triggers of conformational change, proteolytic generation of amyloidogenic fragments, or heteromeric seeding and amyloid fibril stability. In the amyloid fibril form, activity can be regulated by pH, ligand binding and higher order protofilament or fibril architectures that impact the arrangement of associated domains and amyloid stability. The growing understanding of the molecular basis for the control of structure and functionality delivered by natural amyloids in nearly all life forms should inform the development of therapies for amyloid-associated diseases and guide the design of innovative biomaterials.
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Affiliation(s)
- Jessica A Buchanan
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Nikhil R Varghese
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Caitlin L Johnston
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Margaret Sunde
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
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4
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Ermakova E, Makshakova O, Kurbanov R, Ibraev I, Zuev Y, Sedov I. Aggregation of Amyloidogenic Peptide Uperin-Molecular Dynamics Simulations. Molecules 2023; 28:molecules28104070. [PMID: 37241811 DOI: 10.3390/molecules28104070] [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: 04/18/2023] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Uperin 3.5 is a remarkable natural peptide obtained from the skin of toadlets comprised of 17 amino acids which exhibits both antimicrobial and amyloidogenic properties. Molecular dynamics simulations were performed to study the β-aggregation process of uperin 3.5 as well as two of its mutants, in which the positively charged residues Arg7 and Lys8 have been replaced by alanine. All three peptides rapidly underwent spontaneous aggregation and conformational transition from random coils to beta-rich structures. The simulations reveal that the initial and essential step of the aggregation process involves peptide dimerization and the formation of small beta-sheets. A decrease in positive charge and an increase in the number of hydrophobic residues in the mutant peptides lead to an increase in the rate of their aggregation.
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Affiliation(s)
- Elena Ermakova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, Russia
| | - Olga Makshakova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, Russia
| | - Rauf Kurbanov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, Russia
| | - Ilya Ibraev
- Chemical Institute, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Yuriy Zuev
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, Russia
| | - Igor Sedov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, Russia
- Chemical Institute, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
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5
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John T, Piantavigna S, Dealey TJA, Abel B, Risselada HJ, Martin LL. Lipid oxidation controls peptide self-assembly near membranes through a surface attraction mechanism. Chem Sci 2023; 14:3730-3741. [PMID: 37035708 PMCID: PMC10074436 DOI: 10.1039/d3sc00159h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/17/2023] [Indexed: 03/06/2023] Open
Abstract
The self-assembly of peptides into supramolecular structures has been linked to neurodegenerative diseases but has also been observed in functional roles. Peptides are physiologically exposed to crowded environments of biomacromolecules, and particularly cellular membrane lipids. Previous research has shown that membranes can both accelerate and inhibit peptide self-assembly. Here, we studied the impact of membrane models that mimic cellular oxidative stress and compared this to mammalian and bacterial membranes. Using molecular dynamics simulations and experiments, we propose a model that explains how changes in peptide-membrane binding, electrostatics, and peptide secondary structure stabilization determine the nature of peptide self-assembly. We explored the influence of zwitterionic (POPC), anionic (POPG) and oxidized (PazePC) phospholipids, as well as cholesterol, and mixtures thereof, on the self-assembly kinetics of the amyloid β (1-40) peptide (Aβ40), linked to Alzheimer's disease, and the amyloid-forming antimicrobial peptide uperin 3.5 (U3.5). We show that the presence of an oxidized lipid had similar effects on peptide self-assembly as the bacterial mimetic membrane. While Aβ40 fibril formation was accelerated, U3.5 aggregation was inhibited by the same lipids at the same peptide-to-lipid ratio. We attribute these findings and peptide-specific effects to differences in peptide-membrane adsorption with U3.5 being more strongly bound to the membrane surface and stabilized in an α-helical conformation compared to Aβ40. Different peptide-to-lipid ratios resulted in different effects. We found that electrostatic interactions are a primary driving force for peptide-membrane interaction, enabling us to propose a model for predicting how cellular changes might impact peptide self-assembly in vivo.
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Affiliation(s)
- Torsten John
- School of Chemistry, Monash University Clayton VIC 3800 Australia
- Leibniz Institute of Surface Engineering (IOM) Permoserstraße 15 04318 Leipzig Germany
- Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Institute of Chemical Technology, Leipzig University Linnéstraße 3 04103 Leipzig Germany
| | | | - Tiara J A Dealey
- School of Chemistry, Monash University Clayton VIC 3800 Australia
| | - Bernd Abel
- Leibniz Institute of Surface Engineering (IOM) Permoserstraße 15 04318 Leipzig Germany
- Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Institute of Chemical Technology, Leipzig University Linnéstraße 3 04103 Leipzig Germany
| | - Herre Jelger Risselada
- Leibniz Institute of Surface Engineering (IOM) Permoserstraße 15 04318 Leipzig Germany
- Institute for Theoretical Physics, Georg-August-Universität Göttingen Friedrich-Hund-Platz 1 37077 Göttingen Germany
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6
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Ermakova EA, Kurbanov RK. Interaction of Uperin Peptides with Model Membranes: Molecular Dynamics Study. MEMBRANES 2023; 13:370. [PMID: 37103797 PMCID: PMC10146956 DOI: 10.3390/membranes13040370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/13/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
The interaction of antimicrobial and amyloid peptides with cell membranes is a critical step in their activities. Peptides of the uperin family obtained from the skin secretion of Australian amphibians demonstrate antimicrobial and amyloidogenic properties. All-atomic molecular dynamics and an umbrella sampling approach were used to study the interaction of uperins with model bacterial membrane. Two stable configurations of peptides were found. In the bound state, the peptides in helical form were located right under the head group region in parallel orientation with respect to the bilayer surface. Stable transmembrane configuration was observed for wild-type uperin and its alanine mutant in both alpha-helical and extended unstructured forms. The potential of mean force characterized the process of peptide binding from water to the lipid bilayer and its insertion into the membrane, and revealed that the transition of uperins from the bound state to the transmembrane position was accompanied by the rotation of peptides and passes through the energy barrier of 4-5 kcal/mol. Uperins have a weak effect on membrane properties.
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7
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Baltutis V, O'Leary PD, Martin LL. Self-Assembly of Linear, Natural Antimicrobial Peptides: An Evolutionary Perspective. Chempluschem 2022; 87:e202200240. [PMID: 36198638 DOI: 10.1002/cplu.202200240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/29/2022] [Indexed: 01/31/2023]
Abstract
Antimicrobial peptides are an ancient and innate system of host defence against a wide range of microbial assailants. Mechanistically, unstructured peptides undergo a secondary structure transition into amphipathic α-helices, upon contact with membrane surfaces. This leads to peptide binding and removal of the membrane components in a detergent-like manner or via self-organisation into trans-membrane pores (either barrel-stave or toroidal pore) thereby destroying the microbe. Self-assembly of antimicrobial peptides into oligomers and ultimately amyloid has been mostly examined in parallel, however recent findings link diseases, such as Alzheimer's disease as an aberrant activity of a protective neuropeptide with antimicrobial activity. These self-assembled oligomers can also interact with membranes. Here, we review those antimicrobial peptides reported to self-assemble into amyloid, where supported by structural evidence. We consider their membrane activities as antimicrobial peptides and present evidence of consistent self-assembly patterns across major evolutionary groups. Trends are apparent across these groups, supporting the mounting data that self-assembly of antimicrobial peptides into amyloid should be considered as synergistic to the antimicrobial peptide response.
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Affiliation(s)
- Verity Baltutis
- School of Chemistry, Monash University, 3800, Clayton, Vic, Australia
| | - Paul D O'Leary
- School of Chemistry, Monash University, 3800, Clayton, Vic, Australia
| | - Lisandra L Martin
- School of Chemistry, Monash University, 3800, Clayton, Vic, Australia
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8
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Dudek D, Dzień E, Wątły J, Matera-Witkiewicz A, Mikołajczyk A, Hajda A, Olesiak-Bańska J, Rowińska-Żyrek M. Zn(II) binding to pramlintide results in a structural kink, fibril formation and antifungal activity. Sci Rep 2022; 12:20543. [PMID: 36446825 PMCID: PMC9708664 DOI: 10.1038/s41598-022-24968-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022] Open
Abstract
The antimicrobial properties of amylin, a 37-amino acid peptide hormone, co-secreted with insulin from the pancreas, are far less known than its antidiabetic function. We provide insight into the bioinorganic chemistry of amylin analogues, showing that the coordination of zinc(II) enhances the antifungal properties of pramlintide, a non-fibrillating therapeutic analogue of amylin. Zinc binds to the N-terminal amino group and His18 imidazole, inducing a kink in the peptide structure, which, in turn, triggers a fibrillization process of the complex, resulting in an amyloid structure most likely responsible for the disruption of the fungal cell.
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Affiliation(s)
- Dorota Dudek
- grid.8505.80000 0001 1010 5103Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Emilia Dzień
- grid.8505.80000 0001 1010 5103Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Joanna Wątły
- grid.8505.80000 0001 1010 5103Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Agnieszka Matera-Witkiewicz
- grid.4495.c0000 0001 1090 049XScreening of Biological Activity Assays and Collection of Biological Material Laboratory, Faculty of Pharmacy, Wrocław Medical University Biobank, Wrocław Medical University, Wrocław, Poland
| | - Aleksandra Mikołajczyk
- grid.4495.c0000 0001 1090 049XScreening of Biological Activity Assays and Collection of Biological Material Laboratory, Faculty of Pharmacy, Wrocław Medical University Biobank, Wrocław Medical University, Wrocław, Poland
| | - Agata Hajda
- grid.7005.20000 0000 9805 3178Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Joanna Olesiak-Bańska
- grid.7005.20000 0000 9805 3178Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Magdalena Rowińska-Żyrek
- grid.8505.80000 0001 1010 5103Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
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9
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Sedov I, Khaibrakhmanova D. Molecular Mechanisms of Inhibition of Protein Amyloid Fibril Formation: Evidence and Perspectives Based on Kinetic Models. Int J Mol Sci 2022; 23:ijms232113428. [PMID: 36362217 PMCID: PMC9657184 DOI: 10.3390/ijms232113428] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/29/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
Inhibition of fibril formation is considered a possible treatment strategy for amyloid-related diseases. Understanding the molecular nature of inhibitor action is crucial for the design of drug candidates. In the present review, we describe the common kinetic models of fibril formation and classify known inhibitors by the mechanism of their interactions with the aggregating protein and its oligomers. This mechanism determines the step or steps of the aggregation process that become inhibited and the observed changes in kinetics and equilibrium of fibril formation. The results of numerous studies indicate that possible approaches to antiamyloid inhibitor discovery include the search for the strong binders of protein monomers, cappers blocking the ends of the growing fibril, or the species absorbing on the surface of oligomers preventing nucleation. Strongly binding inhibitors stabilizing the native state can be promising for the structured proteins while designing the drug candidates targeting disordered proteins is challenging.
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Affiliation(s)
- Igor Sedov
- Chemical Institute, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111 Kazan, Russia
- Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russia
- Correspondence: ; Tel.: +7-9600503916
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10
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The Extracellular Molecular Chaperone Clusterin Inhibits Amyloid Fibril Formation and Suppresses Cytotoxicity Associated with Semen-Derived Enhancer of Virus Infection (SEVI). Cells 2022; 11:cells11203259. [PMID: 36291126 PMCID: PMC9600718 DOI: 10.3390/cells11203259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/07/2022] [Accepted: 10/13/2022] [Indexed: 11/17/2022] Open
Abstract
Clusterin is a glycoprotein present at high concentrations in many extracellular fluids, including semen. Its increased expression accompanies disorders associated with extracellular amyloid fibril accumulation such as Alzheimer’s disease. Clusterin is an extracellular molecular chaperone which prevents the misfolding and amorphous and amyloid fibrillar aggregation of a wide variety of unfolding proteins. In semen, amyloid fibrils formed from a 39-amino acid fragment of prostatic acid phosphatase, termed Semen-derived Enhancer of Virus Infection (SEVI), potentiate HIV infectivity. In this study, clusterin potently inhibited the in vitro formation of SEVI fibrils, along with dissociating them. Furthermore, clusterin reduced the toxicity of SEVI to pheochromocytoma-12 cells. In semen, clusterin may play an important role in preventing SEVI amyloid fibril formation, in dissociating SEVI fibrils and in mitigating their enhancement of HIV infection.
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11
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Ragonis-Bachar P, Rayan B, Barnea E, Engelberg Y, Upcher A, Landau M. Natural Antimicrobial Peptides Self-assemble as α/β Chameleon Amyloids. Biomacromolecules 2022; 23:3713-3727. [PMID: 35947777 DOI: 10.1021/acs.biomac.2c00582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amyloid protein fibrils and some antimicrobial peptides (AMPs) share biophysical and structural properties. This observation suggests that ordered self-assembly can act as an AMP-regulating mechanism, and, vice versa, that human amyloids play a role in host defense against pathogens, as opposed to their common association with neurodegenerative and systemic diseases. Based on previous structural information on toxic amyloid peptides, we developed a sequence-based bioinformatics platform and, led by its predictions, experimentally identified 14 fibril-forming AMPs (ffAMPs) from living organisms, which demonstrated cross-β and cross-α amyloid properties. The results support the amyloid-antimicrobial link. The high prevalence of ffAMPs produced by amphibians and marine creatures among other species suggests that they confer unique advantageous properties in distinctive environments, potentially providing stability and adherence properties. Most of the newly identified 14 ffAMPs showed lipid-induced and/or time-dependent secondary structure transitions in the fibril form, indicating structural and functional cross-α/β chameleons. Specifically, ffAMP cytotoxicity against human cells correlated with the inherent or lipid-induced α-helical fibril structure. The findings raise hypotheses about the role of fibril secondary structure switching in regulation of processes, such as the transition between a stable storage conformation and an active state with toxicity against specific cell types.
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Affiliation(s)
- Peleg Ragonis-Bachar
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Bader Rayan
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Eilon Barnea
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Yizhaq Engelberg
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Alexander Upcher
- Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel.,European Molecular Biology Laboratory (EMBL) and Centre for Structural Systems Biology, Hamburg 22607, Germany
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12
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Bücker R, Seuring C, Cazey C, Veith K, García-Alai M, Grünewald K, Landau M. The Cryo-EM structures of two amphibian antimicrobial cross-β amyloid fibrils. Nat Commun 2022; 13:4356. [PMID: 35896552 PMCID: PMC9329304 DOI: 10.1038/s41467-022-32039-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/13/2022] [Indexed: 12/14/2022] Open
Abstract
The amyloid-antimicrobial link hypothesis is based on antimicrobial properties found in human amyloids involved in neurodegenerative and systemic diseases, along with amyloidal structural properties found in antimicrobial peptides (AMPs). Supporting this hypothesis, we here determined the fibril structure of two AMPs from amphibians, uperin 3.5 and aurein 3.3, by cryogenic electron microscopy (cryo-EM), revealing amyloid cross-β fibrils of mated β-sheets at atomic resolution. Uperin 3.5 formed a 3-blade symmetrical propeller of nine peptides per fibril layer including tight β-sheet interfaces. This cross-β cryo-EM structure complements the cross-α fibril conformation previously determined by crystallography, substantiating a secondary structure switch mechanism of uperin 3.5. The aurein 3.3 arrangement consisted of six peptides per fibril layer, all showing kinked β-sheets allowing a rounded compactness of the fibril. The kinked β-sheets are similar to LARKS (Low-complexity, Amyloid-like, Reversible, Kinked Segments) found in human functional amyloids. In this work the authors provide high-resolution structural support for the amyloid-antimicrobial link via functional amyloids displaying propeller-like and kinked cross-β fibrils.
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Affiliation(s)
- Robert Bücker
- Centre for Structural Systems Biology, Hamburg, Germany.,Department of Chemistry, University of Hamburg, Hamburg, Germany.,Rigaku Europe SE, Neu-Isenburg, Germany.,Leibniz Institute of Virology, Hamburg, Germany
| | - Carolin Seuring
- Centre for Structural Systems Biology, Hamburg, Germany.,Department of Chemistry, University of Hamburg, Hamburg, Germany.,Leibniz Institute of Virology, Hamburg, Germany
| | - Cornelia Cazey
- Centre for Structural Systems Biology, Hamburg, Germany.,Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Katharina Veith
- European Molecular Biology Laboratory, EMBL Hamburg, Hamburg, Germany
| | - Maria García-Alai
- Centre for Structural Systems Biology, Hamburg, Germany.,European Molecular Biology Laboratory, EMBL Hamburg, Hamburg, Germany
| | - Kay Grünewald
- Centre for Structural Systems Biology, Hamburg, Germany. .,Department of Chemistry, University of Hamburg, Hamburg, Germany. .,Leibniz Institute of Virology, Hamburg, Germany. .,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Meytal Landau
- Centre for Structural Systems Biology, Hamburg, Germany. .,European Molecular Biology Laboratory, EMBL Hamburg, Hamburg, Germany. .,Department of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel.
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13
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Pohl C, Effantin G, Kandiah E, Meier S, Zeng G, Streicher W, Segura DR, Mygind PH, Sandvang D, Nielsen LA, Peters GHJ, Schoehn G, Mueller-Dieckmann C, Noergaard A, Harris P. pH- and concentration-dependent supramolecular assembly of a fungal defensin plectasin variant into helical non-amyloid fibrils. Nat Commun 2022; 13:3162. [PMID: 35672293 PMCID: PMC9174238 DOI: 10.1038/s41467-022-30462-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Self-assembly and fibril formation play important roles in protein behaviour. Amyloid fibril formation is well-studied due to its role in neurodegenerative diseases and characterized by refolding of the protein into predominantly β-sheet form. However, much less is known about the assembly of proteins into other types of supramolecular structures. Using cryo-electron microscopy at a resolution of 1.97 Å, we show that a triple-mutant of the anti-microbial peptide plectasin, PPI42, assembles into helical non-amyloid fibrils. The in vitro anti-microbial activity was determined and shown to be enhanced compared to the wildtype. Plectasin contains a cysteine-stabilised α-helix-β-sheet structure, which remains intact upon fibril formation. Two protofilaments form a right-handed protein fibril. The fibril formation is reversible and follows sigmoidal kinetics with a pH- and concentration dependent equilibrium between soluble monomer and protein fibril. This high-resolution structure reveals that α/β proteins can natively assemble into fibrils. Here the authors report the cryo-EM structure of a triple-mutant of the anti-microbial peptide plectasin, PPI42, assembling in a pH- and concentration dependent manner into helical non-amyloid fibrils. The fibrils formation is reversible, and follows a sigmoidal kinetics. The fibrils adopt a right-handed helical superstructure composed by two protofilaments, stabilized by an outer hydrophobic ring and an inner hydrophobic centre. These findings reveal that α/β proteins can natively assemble into fibrils.
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14
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Prasad AK, Tiwari C, Ray S, Holden S, Armstrong DA, Rosengren KJ, Rodger A, Panwar AS, Martin LL. Secondary Structure Transitions for a Family of Amyloidogenic, Antimicrobial Uperin 3 Peptides in Contact with Sodium Dodecyl Sulfate. Chempluschem 2022; 87:e202100408. [DOI: 10.1002/cplu.202100408] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/10/2021] [Indexed: 11/10/2022]
Affiliation(s)
- Anup K. Prasad
- IITB-Monash Research Academy Indian Institute of Technology Bombay Powai Mumbai 400076 India
- Department of Metallurgical Engineering and Materials Science Indian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Chandni Tiwari
- IITB-Monash Research Academy Indian Institute of Technology Bombay Powai Mumbai 400076 India
- School of Chemistry Monash University Clayton VIC 3800 Australia
| | - Sourav Ray
- IITB-Monash Research Academy Indian Institute of Technology Bombay Powai Mumbai 400076 India
- Department of Metallurgical Engineering and Materials Science Indian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Stephanie Holden
- School of Chemistry Monash University Clayton VIC 3800 Australia
| | - David A. Armstrong
- School of Biomedical Sciences The University of Queensland Brisbane QLD, 4072 Australia
| | - K. Johan Rosengren
- School of Biomedical Sciences The University of Queensland Brisbane QLD, 4072 Australia
| | - Alison Rodger
- Department of Molecular Sciences Macquarie University Macquarie Park NSW, 2109 Australia
| | - Ajay S. Panwar
- Department of Metallurgical Engineering and Materials Science Indian Institute of Technology Bombay Powai Mumbai 400076 India
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15
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Tang Y, Zhang D, Gong X, Zheng J. Repurposing of intestinal defensins as multi-target, dual-function amyloid inhibitors via cross-seeding. Chem Sci 2022; 13:7143-7156. [PMID: 35799805 PMCID: PMC9214849 DOI: 10.1039/d2sc01447e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/19/2022] [Indexed: 12/13/2022] Open
Abstract
Amyloid formation and microbial infection are the two common pathological causes of neurogenerative diseases, including Alzheimer's disease (AD), type II diabetes (T2D), and medullary thyroid carcinoma (MTC). While significant efforts have been made to develop different prevention strategies and preclinical hits for these diseases, conventional design strategies of amyloid inhibitors are mostly limited to either a single prevention mechanism (amyloid cascade vs. microbial infection) or a single amyloid protein (Aβ, hIAPP, or hCT), which has prevented the launch of any successful drug on the market. Here, we propose and demonstrate a new “anti-amyloid and anti-bacteria” strategy to repurpose two intestinal defensins, human α-defensin 6 (HD-6) and human β-defensin 1 (HBD-1), as multiple-target, dual-function, amyloid inhibitors. Both HD-6 and HBD-1 can cross-seed with three amyloid peptides, Aβ (associated with AD), hIAPP (associated with T2D), and hCT (associated with MTC), to prevent their aggregation towards amyloid fibrils from monomers and oligomers, rescue SH-SY5Y and RIN-m5F cells from amyloid-induced cytotoxicity, and retain their original antimicrobial activity against four common bacterial strains at sub-stoichiometric concentrations. Such sequence-independent anti-amyloid and anti-bacterial functions of intestinal defensins mainly stem from their cross-interactions with amyloid proteins through amyloid-like mimicry of β-sheet associations. In a broader view, this work provides a new out-of-the-box thinking to search and repurpose a huge source of antimicrobial peptides as amyloid inhibitors, allowing the blocking of the two interlinked pathological pathways and bidirectional communication between the central nervous system and intestines via the gut–brain axis associated with neurodegenerative diseases. Amyloid formation and microbial infection are the two common pathological causes of neurogenerative diseases. Here, we proposed a new “anti-amyloid and anti-bacteria” strategy to repurpose two intestinal defensins as multiple-target, dual-function amyloid inhibitors.![]()
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Affiliation(s)
- Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Ohio, USA
| | - Dong Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Ohio, USA
| | - Xiong Gong
- School of Polymer Science and Polymer Engineering, The University of Akron, Ohio, USA
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Ohio, USA
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16
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Tang Y, Zhang D, Gong X, Zheng J. A mechanistic survey of Alzheimer's disease. Biophys Chem 2021; 281:106735. [PMID: 34894476 DOI: 10.1016/j.bpc.2021.106735] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/26/2021] [Accepted: 11/26/2021] [Indexed: 02/06/2023]
Abstract
Alzheimer's disease (AD) is the most common, age-dependent neurodegenerative disorder. While AD has been intensively studied from different aspects, there is no effective cure for AD, largely due to a lack of a clear mechanistic understanding of AD. In this mini-review, we mainly focus on the discussion and summary of mechanistic causes of Alzheimer's disease (AD). While different AD mechanisms illustrate different molecular and cellular pathways in AD pathogenesis, they do not necessarily exclude each other. Instead, some of them could work together to initiate, trigger, and promote the onset and development of AD. In a broader viewpoint, some AD mechanisms (e.g., amyloid aggregation mechanism, microbial infection/neuroinflammation mechanism, and amyloid cross-seeding mechanism) could also be applicable to other amyloid diseases including type II diabetes, Parkinson's disease, and prion disease. Such common mechanisms for AD and other amyloid diseases explain not only the pathogenesis of individual amyloid diseases, but also the spreading of pathologies between these diseases, which will inspire new strategies for therapeutic intervention and prevention for AD.
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Affiliation(s)
- Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, OH, United States of America
| | - Dong Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, OH, United States of America
| | - Xiong Gong
- Department of Polymer Engineering, The University of Akron, OH, United States of America
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, OH, United States of America.
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17
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Zhang Y, Liu Y, Tang Y, Zhang D, He H, Wu J, Zheng J. Antimicrobial α-defensins as multi-target inhibitors against amyloid formation and microbial infection. Chem Sci 2021; 12:9124-9139. [PMID: 34276942 PMCID: PMC8261786 DOI: 10.1039/d1sc01133b] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/27/2021] [Indexed: 12/22/2022] Open
Abstract
Amyloid aggregation and microbial infection are considered as pathological risk factors for developing amyloid diseases, including Alzheimer's disease (AD), type II diabetes (T2D), Parkinson's disease (PD), and medullary thyroid carcinoma (MTC). Due to the multifactorial nature of amyloid diseases, single-target drugs and treatments have mostly failed to inhibit amyloid aggregation and microbial infection simultaneously, thus leading to marginal benefits for amyloid inhibition and medical treatments. Herein, we proposed and demonstrated a new "anti-amyloid and antimicrobial hypothesis" to discover two host-defense antimicrobial peptides of α-defensins containing β-rich structures (human neutrophil peptide of HNP-1 and rabbit neutrophil peptide of NP-3A), which have demonstrated multi-target, sequence-independent functions to (i) prevent the aggregation and misfolding of different amyloid proteins of amyloid-β (Aβ, associated with AD), human islet amyloid polypeptide (hIAPP, associated with T2D), and human calcitonin (hCT, associated with MTC) at sub-stoichiometric concentrations, (ii) reduce amyloid-induced cell toxicity, and (iii) retain their original antimicrobial activity upon the formation of complexes with amyloid peptides. Further structural analysis showed that the sequence-independent amyloid inhibition function of α-defensins mainly stems from their cross-interactions with amyloid proteins via β-structure interactions. The discovery of antimicrobial peptides containing β-structures to inhibit both microbial infection and amyloid aggregation greatly expands the new therapeutic potential of antimicrobial peptides as multi-target amyloid inhibitors for better understanding pathological causes and treatments of amyloid diseases.
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Affiliation(s)
- Yanxian Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron Ohio USA
| | - Yonglan Liu
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron Ohio USA
| | - Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron Ohio USA
| | - Dong Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron Ohio USA
| | - Huacheng He
- College of Chemistry and Materials Engineering, Wenzhou University Zhejiang China
| | - Jiang Wu
- School of Pharmaceutical Sciences, Wenzhou Medical University Zhejiang China
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron Ohio USA
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18
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The amphibian antimicrobial peptide uperin 3.5 is a cross-α/cross-β chameleon functional amyloid. Proc Natl Acad Sci U S A 2021; 118:2014442118. [PMID: 33431675 DOI: 10.1073/pnas.2014442118] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial activity is being increasingly linked to amyloid fibril formation, suggesting physiological roles for some human amyloids, which have historically been viewed as strictly pathological agents. This work reports on formation of functional cross-α amyloid fibrils of the amphibian antimicrobial peptide uperin 3.5 at atomic resolution, an architecture initially discovered in the bacterial PSMα3 cytotoxin. The fibrils of uperin 3.5 and PSMα3 comprised antiparallel and parallel helical sheets, respectively, recapitulating properties of β-sheets. Uperin 3.5 demonstrated chameleon properties of a secondary structure switch, forming mostly cross-β fibrils in the absence of lipids. Uperin 3.5 helical fibril formation was largely induced by, and formed on, bacterial cells or membrane mimetics, and led to membrane damage and cell death. These findings suggest a regulation mechanism, which includes storage of inactive peptides as well as environmentally induced activation of uperin 3.5, via chameleon cross-α/β amyloid fibrils.
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19
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Ray S, Holden S, Prasad AK, Martin LL, Panwar AS. Exploring the Role of Peptide Helical Stability in the Propensity of Uperin 3. x Peptides toward Beta-Aggregation. J Phys Chem B 2020; 124:11659-11670. [PMID: 33322900 DOI: 10.1021/acs.jpcb.0c10000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Antimicrobial peptides of the uperin 3.x family, obtained from the skin secretions of Uperoleia mjobergii, have an inherent ability to form amyloid with possible functional roles and can serve as model peptides to understand mechanistic aspects of amyloidogenesis. The substitution of a positively charged amino acid with a nonpolar alanine residue increased aggregation, fibril content, and propensity for β-sheet formation for the uperin 3.5 R7A variant when compared with the uperin 3.5 wild-type peptides. We use molecular dynamics (MD) simulations and circular dichroism (CD) measurements on three uperin 3.x peptides and their corresponding seventh position alanine variants to understand the effect of substitution of a positively charged amino acid with a nonpolar alanine residue on the process of β-aggregation. Both CD experiments and simulations show that the uperin 3.x wild-type peptides demonstrated lower β-sheet content and propensity than with the corresponding alanine variants. Significantly, simulations of helix-to-coil transitions in individual peptides show an inverse relationship between the helical stability of peptides and their propensity to form structures rich in β-sheets as observed in CD experiments. A simulation scheme based on a conformational search of helix-to-coil transition trajectories to select peptide conformers was used to assemble propagating peptide oligomers. Whereas octamers consisting of lower helical stability peptide conformers evolve into compact aggregates with a large β-sheet component, octamers composed of high helical stability conformers disintegrate and show the least amounts of β-sheet components. The highlight of the current work is that MD simulations are able to predict the correct order of β-sheet propensity among the six peptides derived from the CD experiments and indicate the importance of helical intermediates in the amyloidogenesis pathway for uperin 3.x peptides.
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Affiliation(s)
- Sourav Ray
- IITB-Monash Research Academy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.,School of Chemistry, Monash University, Clayton 3800, Victoria, Australia.,Department of Metallurgical Engineering and Materials Science, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Stephanie Holden
- School of Chemistry, Monash University, Clayton 3800, Victoria, Australia
| | - Anup Kumar Prasad
- IITB-Monash Research Academy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.,School of Chemistry, Monash University, Clayton 3800, Victoria, Australia.,Department of Metallurgical Engineering and Materials Science, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Lisandra L Martin
- School of Chemistry, Monash University, Clayton 3800, Victoria, Australia
| | - Ajay Singh Panwar
- Department of Metallurgical Engineering and Materials Science, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
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20
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Functional Amyloids Are the Rule Rather Than the Exception in Cellular Biology. Microorganisms 2020; 8:microorganisms8121951. [PMID: 33316961 PMCID: PMC7764130 DOI: 10.3390/microorganisms8121951] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 11/28/2020] [Accepted: 12/04/2020] [Indexed: 12/15/2022] Open
Abstract
Amyloids are a class of protein aggregates that have been historically characterized by their relationship with human disease. Indeed, amyloids can be the result of misfolded proteins that self-associate to form insoluble, extracellular plaques in diseased tissue. For the first 150 years of their study, the pathogen-first definition of amyloids was sufficient. However, new observations of amyloids foster an appreciation for non-pathological roles for amyloids in cellular systems. There is now evidence from all domains of life that amyloids can be non-pathogenic and functional, and that their formation can be the result of purposeful and controlled cellular processes. So-called functional amyloids fulfill an assortment of biological functions including acting as structural scaffolds, regulatory mechanisms, and storage mechanisms. The conceptual convergence of amyloids serving a functional role has been repeatedly confirmed by discoveries of additional functional amyloids. With dozens already known, and with the vigorous rate of discovery, the biology of amyloids is robustly represented by non-pathogenic amyloids.
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21
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Juhl DW, Glattard E, Lointier M, Bampilis P, Bechinger B. The Reversible Non-covalent Aggregation Into Fibers of PGLa and Magainin 2 Preserves Their Antimicrobial Activity and Synergism. Front Cell Infect Microbiol 2020; 10:526459. [PMID: 33102247 PMCID: PMC7554302 DOI: 10.3389/fcimb.2020.526459] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 08/18/2020] [Indexed: 01/29/2023] Open
Abstract
Magainin 2 and PGLa are antimicrobial peptides found together in frog skin secretions. When added as a mixture they show an order of magnitude increase in antibacterial activity and in model membrane permeation assays. Here we demonstrate that both peptides can form fibers with beta-sheet/turn signature in ATR-FTIR- and CD-spectroscopic analyses, but with different morphologies in EM images. Whereas, fiber formation results in acute reduction of the antimicrobial activity of the individual peptides, the synergistic enhancement of activity remains for the equimolar mixture of PGLa and magainin 2 also after fibril formation. The biological significance and potential applications of such supramolecular aggregates are discussed.
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Affiliation(s)
- Dennis Wilkens Juhl
- University of Strasbourg/CNRS, UMR7177, Institut de Chimie de Strasbourg, Strasbourg, France
| | - Elise Glattard
- University of Strasbourg/CNRS, UMR7177, Institut de Chimie de Strasbourg, Strasbourg, France
| | - Morane Lointier
- University of Strasbourg/CNRS, UMR7177, Institut de Chimie de Strasbourg, Strasbourg, France
| | - Panos Bampilis
- University of Strasbourg/CNRS, UMR7177, Institut de Chimie de Strasbourg, Strasbourg, France
| | - Burkhard Bechinger
- University of Strasbourg/CNRS, UMR7177, Institut de Chimie de Strasbourg, Strasbourg, France
- Institut Universitaire de France (IUF), Paris, France
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22
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Bioinformatic Analysis of 1000 Amphibian Antimicrobial Peptides Uncovers Multiple Length-Dependent Correlations for Peptide Design and Prediction. Antibiotics (Basel) 2020; 9:antibiotics9080491. [PMID: 32784626 PMCID: PMC7459754 DOI: 10.3390/antibiotics9080491] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/29/2020] [Accepted: 08/03/2020] [Indexed: 12/18/2022] Open
Abstract
Amphibians are widely distributed on different continents, except for the polar regions. They are important sources for the isolation, purification and characterization of natural compounds, including peptides with various functions. Innate immune antimicrobial peptides (AMPs) play a critical role in warding off invading pathogens, such as bacteria, fungi, parasites, and viruses. They may also have other biological functions such as endotoxin neutralization, chemotaxis, anti-inflammation, and wound healing. This article documents a bioinformatic analysis of over 1000 amphibian antimicrobial peptides registered in the Antimicrobial Peptide Database (APD) in the past 18 years. These anuran peptides were discovered in Africa, Asia, Australia, Europe, and America from 1985 to 2019. Genomic and peptidomic studies accelerated the discovery pace and underscored the necessity in establishing criteria for peptide entry into the APD. A total of 99.9% of the anuran antimicrobial peptides are less than 50 amino acids with an average length of 24 and a net charge of +2.5. Interestingly, the various amphibian peptide families (e.g., temporins, brevinins, esculentins) can be connected through multiple length-dependent relationships. With an increase in length, peptide net charge increases, while the hydrophobic content decreases. In addition, glycine, leucine, lysine, and proline all show linear correlations with peptide length. These correlations improve our understanding of amphibian peptides and may be useful for prediction and design of new linear peptides with potential applications in treating infectious diseases, cancer and diabetes.
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23
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Lee EY, Srinivasan Y, de Anda J, Nicastro LK, Tükel Ç, Wong GCL. Functional Reciprocity of Amyloids and Antimicrobial Peptides: Rethinking the Role of Supramolecular Assembly in Host Defense, Immune Activation, and Inflammation. Front Immunol 2020; 11:1629. [PMID: 32849553 PMCID: PMC7412598 DOI: 10.3389/fimmu.2020.01629] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
Pathological self-assembly is a concept that is classically associated with amyloids, such as amyloid-β (Aβ) in Alzheimer's disease and α-synuclein in Parkinson's disease. In prokaryotic organisms, amyloids are assembled extracellularly in a similar fashion to human amyloids. Pathogenicity of amyloids is attributed to their ability to transform into several distinct structural states that reflect their downstream biological consequences. While the oligomeric forms of amyloids are thought to be responsible for their cytotoxicity via membrane permeation, their fibrillar conformations are known to interact with the innate immune system to induce inflammation. Furthermore, both eukaryotic and prokaryotic amyloids can self-assemble into molecular chaperones to bind nucleic acids, enabling amplification of Toll-like receptor (TLR) signaling. Recent work has shown that antimicrobial peptides (AMPs) follow a strikingly similar paradigm. Previously, AMPs were thought of as peptides with the primary function of permeating microbial membranes. Consistent with this, many AMPs are facially amphiphilic and can facilitate membrane remodeling processes such as pore formation and fusion. We show that various AMPs and chemokines can also chaperone and organize immune ligands into amyloid-like ordered supramolecular structures that are geometrically optimized for binding to TLRs, thereby amplifying immune signaling. The ability of amphiphilic AMPs to self-assemble cooperatively into superhelical protofibrils that form structural scaffolds for the ordered presentation of immune ligands like DNA and dsRNA is central to inflammation. It is interesting to explore the notion that the assembly of AMP protofibrils may be analogous to that of amyloid aggregates. Coming full circle, recent work has suggested that Aβ and other amyloids also have AMP-like antimicrobial functions. The emerging perspective is one in which assembly affords a more finely calibrated system of recognition and response: the detection of single immune ligands, immune ligands bound to AMPs, and immune ligands spatially organized to varying degrees by AMPs, result in different immunologic outcomes. In this framework, not all ordered structures generated during multi-stepped AMP (or amyloid) assembly are pathological in origin. Supramolecular structures formed during this process serve as signatures to the innate immune system to orchestrate immune amplification in a proportional, situation-dependent manner.
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Affiliation(s)
- Ernest Y Lee
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, United States.,UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Yashes Srinivasan
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jaime de Anda
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, United States
| | - Lauren K Nicastro
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Çagla Tükel
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States.,California Nano Systems Institute, University of California, Los Angeles, Los Angeles, CA, United States
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24
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John T, Greene GW, Patil NA, Dealey TJA, Hossain MA, Abel B, Martin LL. Adsorption of Amyloidogenic Peptides to Functionalized Surfaces Is Biased by Charge and Hydrophilicity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:14522-14531. [PMID: 31537064 DOI: 10.1021/acs.langmuir.9b02063] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Surfaces are abundant in living systems, such as in the form of cellular membranes, and govern many biological processes. In this study, the adsorption of the amyloidogenic model peptides GNNQQNY, NNFGAIL, and VQIVYK as well as the amyloid-forming antimicrobial peptide uperin 3.5 (U3.5) were studied at low concentrations (100 μM) to different surfaces. The technique of a quartz crystal microbalance with dissipation monitoring (QCM-D) was applied as it enables the monitoring of mass binding to sensors at nanogram sensitivity. Gold-coated quartz sensors were used as unmodified gold surfaces or functionalized with self-assembled monolayers (SAMs) of alkanethiols (terminated as methyl, amino, carboxyl, and hydroxyl) resulting in different adsorption affinities of the peptides. Our objective was to evaluate the underlying role of the nature and feature of interfaces in biological systems which could concentrate peptides and impact or trigger peptide aggregation processes. In overall, the largely hydrophobic peptides adsorbed with preference to hydrophobic or countercharged surfaces. Further, the glycoprotein lubricin (LUB) was tested as an antiadhesive coating. Despite its hydrophilicity, the adsorption of peptides to LUB coated sensors was similar to the adsorption to unmodified gold surfaces, which indicates that some peptides diffused through the LUB layer to reach the underlying gold sensor surface. The LUB protein-antiadhesive is thus more effective as a biomaterial coating against larger biomolecules than small peptides under the conditions used here. This study provides directions toward a better understanding of amyloid peptide adsorption to biologically relevant interfaces, such as cellular membranes.
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Affiliation(s)
- Torsten John
- School of Chemistry , Monash University , Clayton , Victoria 3800 , Australia
- Leibniz Institute of Surface Engineering (IOM) , Permoserstraße 15 , 04318 Leipzig , Germany
- Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry , Leipzig University , Linnéstraße 3 , 04103 Leipzig , Germany
| | - George W Greene
- Institute for Frontier Materials , Deakin University , 75 Pigdons Road , Waurn Ponds , Victoria 3216 , Australia
| | - Nitin A Patil
- Florey Institute of Neuroscience and Mental Health , The University of Melbourne , Parkville , Victoria 3010 , Australia
| | - Tiara J A Dealey
- School of Chemistry , Monash University , Clayton , Victoria 3800 , Australia
| | - Mohammed A Hossain
- Florey Institute of Neuroscience and Mental Health , The University of Melbourne , Parkville , Victoria 3010 , Australia
| | - Bernd Abel
- Leibniz Institute of Surface Engineering (IOM) , Permoserstraße 15 , 04318 Leipzig , Germany
- Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry , Leipzig University , Linnéstraße 3 , 04103 Leipzig , Germany
| | - Lisandra L Martin
- School of Chemistry , Monash University , Clayton , Victoria 3800 , Australia
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25
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John T, Dealey TJA, Gray NP, Patil NA, Hossain MA, Abel B, Carver JA, Hong Y, Martin LL. The Kinetics of Amyloid Fibrillar Aggregation of Uperin 3.5 Is Directed by the Peptide’s Secondary Structure. Biochemistry 2019; 58:3656-3668. [DOI: 10.1021/acs.biochem.9b00536] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Torsten John
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany
- Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
| | - Tiara J. A. Dealey
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| | - Nicholas P. Gray
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| | - Nitin A. Patil
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mohammed A. Hossain
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Bernd Abel
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany
- Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
| | - John A. Carver
- Research School of Chemistry, The Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Yuning Hong
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Lisandra L. Martin
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
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Ray S, Holden S, Martin LL, Panwar AS. Mechanistic insight into the early stages of amyloid formation using an anuran peptide. Pept Sci (Hoboken) 2019. [DOI: 10.1002/pep2.24120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sourav Ray
- IITB‐Monash Research AcademyIndian Institute of Technology Bombay Powai Mumbai India
- School of ChemistryMonash University Clayton Victoria Australia
- Department of Metallurgical Engineering and Materials ScienceIndian Institute of Technology Bombay Powai Mumbai India
| | | | | | - Ajay Singh Panwar
- Department of Metallurgical Engineering and Materials ScienceIndian Institute of Technology Bombay Powai Mumbai India
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Gour S, Kumar V, Singh A, Gadhave K, Goyal P, Pandey J, Giri R, Yadav JK. Mammalian antimicrobial peptide protegrin‐4 self assembles and forms amyloid‐like aggregates: Assessment of its functional relevance. J Pept Sci 2019; 25:e3151. [DOI: 10.1002/psc.3151] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 12/18/2018] [Accepted: 01/13/2019] [Indexed: 01/06/2023]
Affiliation(s)
- Shalini Gour
- Department of BiotechnologyCentral University of Rajasthan Ajmer India
| | - Vijay Kumar
- Department of BiotechnologyCentral University of Rajasthan Ajmer India
| | - Ashutosh Singh
- School of Basic SciencesIndian Institute of Technology Mandi Kamand India
| | - Kundlik Gadhave
- School of Basic SciencesIndian Institute of Technology Mandi Kamand India
| | - Pankaj Goyal
- Department of BiotechnologyCentral University of Rajasthan Ajmer India
| | - Janmejay Pandey
- Department of BiotechnologyCentral University of Rajasthan Ajmer India
| | - Rajanish Giri
- School of Basic SciencesIndian Institute of Technology Mandi Kamand India
| | - Jay Kant Yadav
- Department of BiotechnologyCentral University of Rajasthan Ajmer India
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Ye Z, Zhu X, Acosta S, Kumar D, Sang T, Aparicio C. Self-assembly dynamics and antimicrobial activity of all l- and d-amino acid enantiomers of a designer peptide. NANOSCALE 2018; 11:266-275. [PMID: 30534763 PMCID: PMC6319268 DOI: 10.1039/c8nr07334a] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Recent studies have shown that antimicrobial peptides (AMPs) can self-assemble into supramolecular structures, but this has been overlooked as causative of their antimicrobial activity. Also, the higher antimicrobial potency of d-enantiomers compared to l-enantiomers of AMPs cannot always be attributed to their different resistance to protease degradation. Here, we tested all l- and d-amino acid versions of GL13K, an AMP derived from a human protein, to study structural links between the AMP secondary structure, supramolecular self-assembly dynamics, and antimicrobial activity. pH dependence and the evolution of secondary structures were related to a self-assembly process with differences among these AMPs. The two GL13K enantiomers formed analogous self-assembled twisted nanoribbon structures, but d-GL13K initiated self-assembly faster and had notably higher antimicrobial potency than l-GL13K. A non-antimicrobial scrambled amino acid version of l-GL13K assembled at a much higher pH to form distinctively different self-assembled structures than l-GL13K. Our results support a functional relationship between the AMP self-assembly and their antimicrobial activity.
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Affiliation(s)
- Zhou Ye
- MDRCBB, Minnesota Dental Research Center for Biomaterials and Biomechanics, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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Brevinin-2 Drug Family—New Applied Peptide Candidates Against Methicillin-Resistant Staphylococcus aureus and Their Effects on Lys-7 Expression of Innate Immune Pathway DAF-2/DAF-16 in Caenorhabditis elegans. APPLIED SCIENCES-BASEL 2018. [DOI: 10.3390/app8122627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The issue of Staphylococcus aureus (MRSA) developing a resistance to drugs such as methicillin has long been the focus for new drug development. In recent years, antimicrobial peptides, such as small molecular peptides with broad-spectrum antibacterial activity and special antibacterial mechanism, have shown a strong medicinal potential. In particular, the Brevinin-2 family has been shown to have a significant inhibitory effect against gram-positive bacteria (G+). In this study, we researched the influence of MRSA on the behavior and survival rate of nematodes. We established an assay of Caenorhabditis elegans–MRSA antimicrobial peptides to screen for new potent anti-infective peptides against MRSA. From the Brevinin-2 family, 13 peptides that had shown strong effects on G+ were screened for their ability to prolong the lifespan of infected worms. Real-time Polymerase Chain Reaction (PCR) tests were used to evaluate the effect on the innate immune pathway dauer formation defective (DAF)-2/DAF-16 of C. elegans. The assay successfully screened and filtered out four of the 13 peptides that significantly improved the survival rate of MRSA-infected worms. The result of real-time PCR indicated that the mRNA and protein expression levels of lys-7 were consistently upregulated by being treated with four of the Brevinin-2 family. The Brevinin-2 family peptides, including Brevinin-2, Brevinin-2-OA3, Brevinin-2ISb, and Brevinin-2TSa, also played an active role in the DAF-2/DAF-16 pathway in C. elegans. We successfully demonstrated the utility of anti-infective peptides that prolong the survival rate of the MRSA-infected host and discovered the relationship between antibacterial peptides and the innate immune system of C. elegans. We demonstrated the antimicrobial effects of Brevinin-2 family peptides, indicating their potential for use as new drug candidates against MRSA infections.
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Novel Antimicrobial Peptides from the Arctic Polychaeta Nicomache minor Provide New Molecular Insight into Biological Role of the BRICHOS Domain. Mar Drugs 2018; 16:md16110401. [PMID: 30360541 PMCID: PMC6265681 DOI: 10.3390/md16110401] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 10/16/2018] [Accepted: 10/20/2018] [Indexed: 12/12/2022] Open
Abstract
Endogenous antimicrobial peptides (AMPs) are among the earliest molecular factors in the evolution of animal innate immunity. In this study, novel AMPs named nicomicins were identified in the small marine polychaeta Nicomache minor in the Maldanidae family. Full-length mRNA sequences encoded 239-residue prepropeptides consisting of a putative signal sequence region, the BRICHOS domain within an acidic proregion, and 33-residue mature cationic peptides. Nicomicin-1 was expressed in the bacterial system, and its spatial structure was analyzed by circular dichroism and nuclear magnetic resonance spectroscopy. Nicomicins are unique among polychaeta AMPs scaffolds, combining an amphipathic N-terminal α-helix and C-terminal extended part with a six-residue loop stabilized by a disulfide bridge. This structural arrangement resembles the Rana-box motif observed in the α-helical host-defense peptides isolated from frog skin. Nicomicin-1 exhibited strong in vitro antimicrobial activity against Gram-positive bacteria at submicromolar concentrations. The main mechanism of nicomicin-1 action is based on membrane damage but not on the inhibition of bacterial translation. The peptide possessed cytotoxicity against cancer and normal adherent cells as well as toward human erythrocytes.
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Martin LL, Kubeil C, Piantavigna S, Tikkoo T, Gray NP, John T, Calabrese AN, Liu Y, Hong Y, Hossain MA, Patil N, Abel B, Hoffmann R, Bowie JH, Carver JA. Amyloid aggregation and membrane activity of the antimicrobial peptide uperin 3.5. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24052] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | - Clemens Kubeil
- School of Chemistry; Monash University; Clayton Victoria 3800 Australia
| | | | - Tarun Tikkoo
- School of Chemistry; Monash University; Clayton Victoria 3800 Australia
| | - Nicholas P. Gray
- School of Chemistry; Monash University; Clayton Victoria 3800 Australia
| | - Torsten John
- School of Chemistry; Monash University; Clayton Victoria 3800 Australia
- Leibniz Institute of Surface Engineering (IOM) and Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry; Leipzig University; Leipzig 04318 Germany
| | - Antonio N. Calabrese
- Department of Chemistry and School of Physical Sciences; The University of Adelaide; Adelaide South Australia 5005 Australia
| | - Yanqin Liu
- Department of Chemistry and School of Physical Sciences; The University of Adelaide; Adelaide South Australia 5005 Australia
| | - Yuning Hong
- Department of Chemistry and Physics; La Trobe Institute for Molecular Science, La Trobe University; Melbourne Victoria 3086 Australia
| | - Mohammed A. Hossain
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne; Parkville Victoria 3010 Australia
| | - Nitin Patil
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne; Parkville Victoria 3010 Australia
| | - Bernd Abel
- Leibniz Institute of Surface Engineering (IOM) and Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry; Leipzig University; Leipzig 04318 Germany
| | - Ralf Hoffmann
- Institute of Bioanalytical Chemistry, and Center for Biotechnology and Biomedicine (BBZ), Universität Leipzig; Leipzig 04103 Germany
| | - John H. Bowie
- Department of Chemistry and School of Physical Sciences; The University of Adelaide; Adelaide South Australia 5005 Australia
| | - John A. Carver
- Research School of Chemistry; The Australian National University; Acton Australian Capital Territory 2601 Australia
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John T, Abel B, Martin LL. The Quartz Crystal Microbalance with Dissipation Monitoring (QCM-D) Technique Applied to the Study of Membrane-Active Peptides. Aust J Chem 2018. [DOI: 10.1071/ch18129] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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