1
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Melcrová A, Klein C, Roos WH. Membrane-Active Antibiotics Affect Domains in Bacterial Membranes as the First Step of Their Activity. NANO LETTERS 2024. [PMID: 39145544 DOI: 10.1021/acs.nanolett.4c01873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
The need to combat antimicrobial resistance is becoming more and more pressing. Here we investigate the working mechanism of a small cationic agent, N-alkylamide 3d, by conventional and high-speed atomic force microscopy. We show that N-alkylamide 3d interacts with the membrane of Staphylococcus aureus, where it changes the organization and dynamics of lipid domains. After this initial step, supramolecular structures of the antimicrobial agent attach on top of the affected membrane gradually, covering it entirely. These results demonstrate that lateral domains in the bacterial membranes might be affected by small antimicrobial agents more often than anticipated. At the same time, we show a new dual-step activity of N-alkylamide 3d that not only destroys the lateral membrane organization but also effectively covers the whole membrane with aggregates. This final step could render the membrane inaccessible from the outside and possibly prevent signaling and waste disposal of living bacteria.
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Affiliation(s)
- Adéla Melcrová
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, 9712 AG Groningen, The Netherlands
| | - Christiaan Klein
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, 9712 AG Groningen, The Netherlands
| | - Wouter H Roos
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, 9712 AG Groningen, The Netherlands
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2
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Javed A, Oedairadjsingh T, Ludwig IS, Wood TM, Martin NI, Broere F, Weingarth MH, Veldhuizen EJA. Antimicrobial and immunomodulatory activities of porcine cathelicidin Protegrin-1. Mol Immunol 2024; 173:100-109. [PMID: 39094445 DOI: 10.1016/j.molimm.2024.07.011] [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: 05/23/2024] [Revised: 07/11/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
Antimicrobial peptides (AMPs) are a promising alternative to antibiotics in the fight against multi-drug resistant and immune system-evading bacterial infections. Protegrins are porcine cathelicidins which have been identified in porcine leukocytes. Protegrin-1 is the best characterized family member and has broad antibacterial activity by interacting and permeabilizing bacterial membranes. Many host defense peptides (HDPs) like LL-37 or chicken cathelicidin 2 (CATH-2) have also been shown to have protective biological functions during infections. In this regard, it is interesting to study if Protegrin-1 has the immune modulating potential to suppress unnecessary immune activation by neutralizing endotoxins or by influencing the macrophage functionality in addition to its direct antimicrobial properties. This study showed that Protegrin-1 neutralized lipopolysaccharide- (LPS) and bacteria-induced activation of RAW macrophages by binding and preventing LPS from cell surface attachment. Furthermore, the peptide treatment not only inhibited bacterial phagocytosis by murine and porcine macrophages but also interfered with cell surface and intracellular bacterial survival. Lastly, Protegrin-1 pre-treatment was shown to inhibit the amastigote survival in Leishmania infected macrophages. These experiments describe an extended potential of Protegrin-1's protective role during microbial infections and add to the research towards clinical application of cationic AMPs.
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Affiliation(s)
- Ali Javed
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases & Immunology, Section Immunology, Utrecht University, the Netherlands; NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, the Netherlands
| | - Trishana Oedairadjsingh
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases & Immunology, Section Immunology, Utrecht University, the Netherlands
| | - Irene S Ludwig
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases & Immunology, Section Immunology, Utrecht University, the Netherlands
| | - Thomas M Wood
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, the Netherlands
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, the Netherlands
| | - Femke Broere
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases & Immunology, Section Immunology, Utrecht University, the Netherlands
| | - Markus H Weingarth
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, the Netherlands
| | - Edwin J A Veldhuizen
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases & Immunology, Section Immunology, Utrecht University, the Netherlands.
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3
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Tang Y, Zhang Y, Zhang D, Liu Y, Nussinov R, Zheng J. Exploring pathological link between antimicrobial and amyloid peptides. Chem Soc Rev 2024. [PMID: 39041297 DOI: 10.1039/d3cs00878a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Amyloid peptides (AMYs) and antimicrobial peptides (AMPs) are considered as the two distinct families of peptides, characterized by their unique sequences, structures, biological functions, and specific pathological targets. However, accumulating evidence has revealed intriguing pathological connections between these peptide families in the context of microbial infection and neurodegenerative diseases. Some AMYs and AMPs share certain structural and functional characteristics, including the ability to self-assemble, the presence of β-sheet-rich structures, and membrane-disrupting mechanisms. These shared features enable AMYs to possess antimicrobial activity and AMPs to acquire amyloidogenic properties. Despite limited studies on AMYs-AMPs systems, the cross-seeding phenomenon between AMYs and AMPs has emerged as a crucial factor in the bidirectional communication between the pathogenesis of neurodegenerative diseases and host defense against microbial infections. In this review, we examine recent developments in the potential interplay between AMYs and AMPs, as well as their pathological implications for both infectious and neurodegenerative diseases. By discussing the current progress and challenges in this emerging field, this account aims to inspire further research and investments to enhance our understanding of the intricate molecular crosstalk between AMYs and AMPs. This knowledge holds great promise for the development of innovative therapies to combat both microbial infections and neurodegenerative disorders.
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Affiliation(s)
- Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Ohio 44325, USA.
| | - Yanxian Zhang
- Division of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Dong Zhang
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
| | - Yonglan Liu
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
- Department of Human Molecular Genetics and Biochemistry Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Ohio 44325, USA.
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4
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Ostroumova OS, Efimova SS. Lipid-Centric Approaches in Combating Infectious Diseases: Antibacterials, Antifungals and Antivirals with Lipid-Associated Mechanisms of Action. Antibiotics (Basel) 2023; 12:1716. [PMID: 38136750 PMCID: PMC10741038 DOI: 10.3390/antibiotics12121716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
One of the global challenges of the 21st century is the increase in mortality from infectious diseases against the backdrop of the spread of antibiotic-resistant pathogenic microorganisms. In this regard, it is worth targeting antibacterials towards the membranes of pathogens that are quite conservative and not amenable to elimination. This review is an attempt to critically analyze the possibilities of targeting antimicrobial agents towards enzymes involved in pathogen lipid biosynthesis or towards bacterial, fungal, and viral lipid membranes, to increase the permeability via pore formation and to modulate the membranes' properties in a manner that makes them incompatible with the pathogen's life cycle. This review discusses the advantages and disadvantages of each approach in the search for highly effective but nontoxic antimicrobial agents. Examples of compounds with a proven molecular mechanism of action are presented, and the types of the most promising pharmacophores for further research and the improvement of the characteristics of antibiotics are discussed. The strategies that pathogens use for survival in terms of modulating the lipid composition and physical properties of the membrane, achieving a balance between resistance to antibiotics and the ability to facilitate all necessary transport and signaling processes, are also considered.
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Affiliation(s)
- Olga S. Ostroumova
- Laboratory of Membrane and Ion Channel Modeling, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg 194064, Russia;
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5
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Bolosov IA, Panteleev PV, Sychev SV, Khokhlova VA, Safronova VN, Toropygin IY, Kombarova TI, Korobova OV, Pereskokova ES, Borzilov AI, Ovchinnikova TV, Balandin SV. Design of Protegrin-1 Analogs with Improved Antibacterial Selectivity. Pharmaceutics 2023; 15:2047. [PMID: 37631261 PMCID: PMC10458893 DOI: 10.3390/pharmaceutics15082047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/27/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Protegrin-1 (PG-1) is a cationic β-hairpin pore-forming antimicrobial peptide having a membranolytic mechanism of action. It possesses in vitro a potent antimicrobial activity against a panel of clinically relevant MDR ESKAPE pathogens. However, its extremely high hemolytic activity and cytotoxicity toward mammalian cells prevent the further development of the protegrin-based antibiotic for systemic administration. In this study, we rationally modulated the PG-1 charge and hydrophobicity by substituting selected residues in the central β-sheet region of PG-1 to design its analogs, which retain a high antimicrobial activity but have a reduced toxicity toward mammalian cells. In this work, eight PG-1 analogs with single amino acid substitutions and five analogs with double substitutions were obtained. These analogs were produced as thioredoxin fusions in Escherichia coli. It was shown that a significant reduction in hemolytic activity without any loss of antimicrobial activity could be achieved by a single amino acid substitution, V16R in the C-terminal β-strand, which is responsible for the PG-1 oligomerization. As the result, a selective analog with a ≥30-fold improved therapeutic index was obtained. FTIR spectroscopy analysis of analog, [V16R], revealed that the peptide is unable to form oligomeric structures in a membrane-mimicking environment, in contrast to wild-type PG-1. Analog [V16R] showed a reasonable efficacy in septicemia infection mice model as a systemic antibiotic and could be considered as a promising lead for further drug design.
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Affiliation(s)
- Ilia A. Bolosov
- M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, 117997 Moscow, Russia; (I.A.B.); (P.V.P.); (T.V.O.)
| | - Pavel V. Panteleev
- M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, 117997 Moscow, Russia; (I.A.B.); (P.V.P.); (T.V.O.)
| | - Sergei V. Sychev
- M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, 117997 Moscow, Russia; (I.A.B.); (P.V.P.); (T.V.O.)
| | - Veronika A. Khokhlova
- M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, 117997 Moscow, Russia; (I.A.B.); (P.V.P.); (T.V.O.)
| | - Victoria N. Safronova
- M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, 117997 Moscow, Russia; (I.A.B.); (P.V.P.); (T.V.O.)
| | - Ilia Yu. Toropygin
- V. N. Orekhovich Research Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Tatiana I. Kombarova
- State Research Center for Applied Microbiology & Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Olga V. Korobova
- State Research Center for Applied Microbiology & Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Eugenia S. Pereskokova
- State Research Center for Applied Microbiology & Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Alexander I. Borzilov
- State Research Center for Applied Microbiology & Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Tatiana V. Ovchinnikova
- M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, 117997 Moscow, Russia; (I.A.B.); (P.V.P.); (T.V.O.)
- Department of Biotechnology, I. M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Sergey V. Balandin
- M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, 117997 Moscow, Russia; (I.A.B.); (P.V.P.); (T.V.O.)
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6
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Blair JMA, Zeth K, Bavro VN, Sancho-Vaello E. The role of bacterial transport systems in the removal of host antimicrobial peptides in Gram-negative bacteria. FEMS Microbiol Rev 2022; 46:6617596. [PMID: 35749576 PMCID: PMC9629497 DOI: 10.1093/femsre/fuac032] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/23/2022] [Accepted: 06/22/2022] [Indexed: 01/09/2023] Open
Abstract
Antibiotic resistance is a global issue that threatens our progress in healthcare and life expectancy. In recent years, antimicrobial peptides (AMPs) have been considered as promising alternatives to the classic antibiotics. AMPs are potentially superior due to their lower rate of resistance development, since they primarily target the bacterial membrane ('Achilles' heel' of the bacteria). However, bacteria have developed mechanisms of AMP resistance, including the removal of AMPs to the extracellular space by efflux pumps such as the MtrCDE or AcrAB-TolC systems, and the internalization of AMPs to the cytoplasm by the Sap transporter, followed by proteolytic digestion. In this review, we focus on AMP transport as a resistance mechanism compiling all the experimental evidence for the involvement of efflux in AMP resistance in Gram-negative bacteria and combine this information with the analysis of the structures of the efflux systems involved. Finally, we expose some open questions with the aim of arousing the interest of the scientific community towards the AMPs-efflux pumps interactions. All the collected information broadens our understanding of AMP removal by efflux pumps and gives some clues to assist the rational design of AMP-derivatives as inhibitors of the efflux pumps.
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Affiliation(s)
- Jessica M A Blair
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Kornelius Zeth
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
| | - Vassiliy N Bavro
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
| | - Enea Sancho-Vaello
- Corresponding author. College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom. E-mail:
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7
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Tyagi A, Mishra A. Methacrylamide based antibiotic polymers with no detectable bacterial resistance. SOFT MATTER 2021; 17:3404-3416. [PMID: 33645619 DOI: 10.1039/d0sm02176h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The growing number of multidrug-resistant pathogens is a major healthcare concern. In search of alternatives to antibiotics, synthetic mimics of antimicrobial peptides (SMAMPs) in the form of antimicrobial polymers have gained tremendous attention. Here, we report the synthesis of a set of 7 amphiphilic water-soluble cationic copolymers using aminopropyl methacrylamide and benzyl methacrylamide repeat units that show significant antibacterial activity. The antibacterial activity was evaluated using a broth microdilution assay against S. aureus and E. coli, while toxicity to mammalian cells was quantified by hemolysis assay with human red blood cells (RBCs). We find that the antibacterial activity and selectivity of the polymers depends on the mole fraction of aromatic benzyl units (fbenzyl) and the average molecular weight (Mn). Polymers with fbenzyl of 0.10 and 0.19, named AB-10 and AB-19 respectively, exhibited the highest antibacterial efficacy without inducing hemolysis and were chosen for further study. Liposome dye leakage study and observations from confocal and scanning electron microscopy indicate that the AB polymers killed bacterial cells primarily by disrupting the cytoplasmic membrane. No resistant mutants of E. coli and S. aureus were obtained with AB-19 in a 30 day serial passage study.
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Affiliation(s)
- Anju Tyagi
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
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8
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Žerovnik E. Viroporins vs. Other Pore-Forming Proteins: What Lessons Can We Take? Front Chem 2021; 9:626059. [PMID: 33681145 PMCID: PMC7930612 DOI: 10.3389/fchem.2021.626059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/07/2021] [Indexed: 11/13/2022] Open
Abstract
Pore-forming proteins (PFPs) exist in virtually all domains of life, and by disrupting cellular membranes, depending on the pore size, they cause ion dis-balance, small substances, or even protein efflux/influx, influencing cell’s signaling routes and fate. Such pore-forming proteins exist from bacteria to viruses and also shape host defense systems, including innate immunity. There is strong evidence that amyloid toxicity is also caused by prefibrillar oligomers making “amyloid pores” into cellular membranes. For most of the PFPs, a 2-step mechanism of protein-membrane interaction takes place on the “lipid rafts,” membrane microdomains rich in gangliosides and cholesterol. In this mini-review paper, common traits of different PFPs are looked at. Possible ways for therapy of channelopathies and/or modulating immunity relevant to the new threat of SARS-CoV-2 infections could be learnt from such comparisons.
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Affiliation(s)
- Eva Žerovnik
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Ljubljana, Slovenia
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9
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Zuttion F, Colom A, Matile S, Farago D, Pompeo F, Kokavecz J, Galinier A, Sturgis J, Casuso I. High-speed atomic force microscopy highlights new molecular mechanism of daptomycin action. Nat Commun 2020; 11:6312. [PMID: 33298927 PMCID: PMC7725780 DOI: 10.1038/s41467-020-19710-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 10/15/2020] [Indexed: 02/08/2023] Open
Abstract
The increase in speed of the high-speed atomic force microscopy (HS-AFM) compared to that of the conventional AFM made possible the first-ever visualisation at the molecular-level of the activity of an antimicrobial peptide on a membrane. We investigated the medically prescribed but poorly understood lipopeptide Daptomycin under infection-like conditions (37 °C, bacterial lipid composition and antibiotic concentrations). We confirmed so far hypothetical models: Dap oligomerization and the existence of half pores. Moreover, we detected unknown molecular mechanisms: new mechanisms to form toroidal pores or to resist Dap action, and to unprecedently quantify the energy profile of interacting oligomers. Finally, the biological and medical relevance of the findings was ensured by a multi-scale multi-nativeness-from the molecule to the cell-correlation of molecular-level information from living bacteria (Bacillus subtilis strains) to liquid-suspended vesicles and supported-membranes using electron and optical microscopies and the lipid tension probe FliptR, where we found that the cells with a healthier state of their cell wall show smaller membrane deformations.
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Affiliation(s)
| | - Adai Colom
- Biochemistry Department, University of Geneva, Geneva, Switzerland
| | - Stefan Matile
- Organic Chemistry Department, University of Geneva, Geneva, Switzerland
| | - Denes Farago
- Department of Technical Informatics University of Szeged, Szeged, Hungary
| | - Frédérique Pompeo
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie de la Méditerranée (IMM), CNRS, UMR 7283, Aix Marseille Université, Marseille, France
| | - Janos Kokavecz
- Institute of Environmental Science and Engineering, University of Szeged, Szeged, Hungary
| | - Anne Galinier
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie de la Méditerranée (IMM), CNRS, UMR 7283, Aix Marseille Université, Marseille, France
| | - James Sturgis
- LISM, UMR 7255, CNRS, Aix Marseille Université, Marseille, France
| | - Ignacio Casuso
- U1067 INSERM, Aix-Marseille Université, Marseille, France.
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10
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Varnava KG, Edwards PJB, Cameron AJ, Harjes E, Sarojini V. Cyclic peptides bearing the d-Phe-2-Abz turn motif: Structural characterization and antimicrobial potential. J Pept Sci 2020; 27:e3291. [PMID: 33283398 DOI: 10.1002/psc.3291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/07/2020] [Accepted: 10/14/2020] [Indexed: 11/10/2022]
Abstract
The effect on secondary structure and antimicrobial activity of introducing different cyclic constraints in linear β-hairpin antimicrobial peptides has been investigated with the intention of generating cyclic β sheets as promising antimicrobials with improved therapeutic potential. The linear peptides were cyclized head to tail either directly or after the addition of either a second turn motif or a disulfide bridge. The propensity of these peptides to adopt a cyclic β-sheet structure has been correlated to their antibacterial activity. All cyclic peptides showed enhanced activity, compared with their linear counterparts against methicillin-resistant Staphylococcus aureus. Scanning electron microscopy and transmission electron microscopy studies showed that this family kills bacteria through membrane lysis. The peptide that showed the best efficacy against all strains (exhibiting nanomolar activity), while retaining low haemolysis, bears two symmetrical, homochiral d-phe-2-Abz-d-ala turns and adopted a flexible structure. Its twin peptide that bears heterochiral turns (one with d-ala and one with L-Ala) showed reduced antibacterial activity and higher percentage of haemolysis. Circular dichroism and nuclear magnetic resonance spectroscopy indicate that heterochirality in the two turns leads to oligomerization of the peptide at higher concentrations, stabilizing the β-sheet secondary structure. More rigid secondary structure is associated with lower activity against bacteria and loss of selectivity.
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Affiliation(s)
- Kyriakos G Varnava
- School of Chemical Sciences, The University of Auckland, Auckland, 1142, New Zealand
| | - Patrick J B Edwards
- School of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand.,Maurice Wilkins Centre for Molecular BioDiscovery, Auckland, 1142, New Zealand
| | - Alan J Cameron
- School of Chemical Sciences, The University of Auckland, Auckland, 1142, New Zealand.,Maurice Wilkins Centre for Molecular BioDiscovery, Auckland, 1142, New Zealand
| | - Elena Harjes
- School of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand.,Maurice Wilkins Centre for Molecular BioDiscovery, Auckland, 1142, New Zealand
| | - Vijayalekshmi Sarojini
- School of Chemical Sciences, The University of Auckland, Auckland, 1142, New Zealand.,The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, 6140, New Zealand
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11
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Magana M, Pushpanathan M, Santos AL, Leanse L, Fernandez M, Ioannidis A, Giulianotti MA, Apidianakis Y, Bradfute S, Ferguson AL, Cherkasov A, Seleem MN, Pinilla C, de la Fuente-Nunez C, Lazaridis T, Dai T, Houghten RA, Hancock REW, Tegos GP. The value of antimicrobial peptides in the age of resistance. THE LANCET. INFECTIOUS DISEASES 2020; 20:e216-e230. [PMID: 32653070 DOI: 10.1016/s1473-3099(20)30327-3] [Citation(s) in RCA: 514] [Impact Index Per Article: 128.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/29/2020] [Accepted: 04/16/2020] [Indexed: 12/20/2022]
Abstract
Accelerating growth and global expansion of antimicrobial resistance has deepened the need for discovery of novel antimicrobial agents. Antimicrobial peptides have clear advantages over conventional antibiotics which include slower emergence of resistance, broad-spectrum antibiofilm activity, and the ability to favourably modulate the host immune response. Broad bacterial susceptibility to antimicrobial peptides offers an additional tool to expand knowledge about the evolution of antimicrobial resistance. Structural and functional limitations, combined with a stricter regulatory environment, have hampered the clinical translation of antimicrobial peptides as potential therapeutic agents. Existing computational and experimental tools attempt to ease the preclinical and clinical development of antimicrobial peptides as novel therapeutics. This Review identifies the benefits, challenges, and opportunities of using antimicrobial peptides against multidrug-resistant pathogens, highlights advances in the deployment of novel promising antimicrobial peptides, and underlines the needs and priorities in designing focused development strategies taking into account the most advanced tools available.
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Affiliation(s)
- Maria Magana
- Department of Biopathology and Clinical Microbiology, Aeginition Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Ana L Santos
- Department of Chemistry, Rice University, Houston, TX, USA; Investigación Sanitaria de las Islas Baleares, Palma, Spain
| | - Leon Leanse
- Department of Dermatology, Harvard Medical School, Boston, MA, USA; Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
| | - Michael Fernandez
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | | | | | | | - Steven Bradfute
- Department of Internal Medicine, Center for Global Health, University of New Mexico, Albuquerque, NM, USA
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Artem Cherkasov
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Mohamed N Seleem
- Department of Comparative Pathobiology, Purdue University College of Veterinary Medicine, West Lafayette, IN, USA
| | - Clemencia Pinilla
- Torrey Pines Institute for Molecular Studies, Port St Lucie, FL, USA
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Themis Lazaridis
- Department of Chemistry, The City College of New York, New York, NY, USA; Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, NY, USA
| | - Tianhong Dai
- Department of Dermatology, Harvard Medical School, Boston, MA, USA; Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Robert E W Hancock
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - George P Tegos
- Reading Hospital, Tower Health, West Reading, PA, USA; Micromoria, Venture X Marlborough, Marlborough, MA, USA.
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12
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Deplazes E, Chin YKY, King GF, Mancera RL. The unusual conformation of cross-strand disulfide bonds is critical to the stability of β-hairpin peptides. Proteins 2019; 88:485-502. [PMID: 31589791 DOI: 10.1002/prot.25828] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/27/2019] [Accepted: 09/17/2019] [Indexed: 01/04/2023]
Abstract
The cross-strand disulfides (CSDs) found in β-hairpin antimicrobial peptides (β-AMPs) show a unique disulfide geometry that is characterized by unusual torsion angles and a short Cα-Cα distance. While the sequence and disulfide bond connectivity of disulfide-rich peptides is well studied, much less is known about the disulfide geometry found in CSDs and their role in the stability of β-AMPs. To address this, we solved the nuclear magnetic resonance (NMR) structure of the β-AMP gomesin (Gm) at 278, 298, and 310 K, examined the disulfide bond geometry of over 800 disulfide-rich peptides, and carried out extensive molecular dynamics (MD) simulation of the peptides Gm and protegrin. The NMR data suggests Cα-Cα distances characteristic for CSDs are independent of temperature. Analysis of disulfide-rich peptides from the Protein Data Bank revealed that right-handed and left-handed rotamers are equally likely in CSDs. The previously reported preference for right-handed rotamers was likely biased by restricting the analysis to peptides and proteins solved using X-ray crystallography. Furthermore, data from MD simulations showed that the short Cα-Cα distance is critical for the stability of these peptides. The unique disulfide geometry of CSDs poses a challenge to biomolecular force fields and to retain the stability of β-hairpin fold over long simulation times, restraints on the torsion angles might be required.
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Affiliation(s)
- Evelyne Deplazes
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth, Western Australia, Australia
| | - Yanni K-Y Chin
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Ricardo L Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth, Western Australia, Australia
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13
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Penney J, Li J. Protegrin 1 Enhances Innate Cellular Defense via the Insulin-Like Growth Factor 1 Receptor Pathway. Front Cell Infect Microbiol 2018; 8:331. [PMID: 30324092 PMCID: PMC6173103 DOI: 10.3389/fcimb.2018.00331] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 08/28/2018] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial peptides (AMPs) represent a promising area of research to help combat the ever-growing problem of antibiotic resistance. Protegrin-1 is an AMP from the cathelicidin family. It is produced naturally in pigs and its mature form (mPG-1) has potent bactericidal properties and a unique β-hairpin structure that separates it from most AMPs found in mice and humans. While the antibacterial properties of protegrin-1 are well established, the role it plays in immune modulation has yet to be investigated, and our current study sought to explore this alternate role and potential mechanism behind. We found that mPG-1 stimulated intestinal cell migration, this is accompanied with altered expression of genes associated with cell migration, in addition to increased expression of pro-inflammatory cytokines and immune-related factors. Further study suggested that mPG-1 activates insulin-like growth factor 1 receptor (IGF1R) and through this receptor it modulates immune activity as well as cell migration. Our study revealed a novel function of mPG-1, and its associated pathway, suggesting therapeutic potential of the antimicrobial peptide for infection and/or immune disorders, particularly ones affecting the gastrointestinal tract such as inflammatory bowel syndrome.
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Affiliation(s)
- Jenna Penney
- Department of Life Science and Engineering, Foshan University, Foshan Shi, China.,Department of Animal Bioscience, University of Guelph, Guelph, ON, Canada
| | - Julang Li
- Department of Life Science and Engineering, Foshan University, Foshan Shi, China.,Department of Animal Bioscience, University of Guelph, Guelph, ON, Canada
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14
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Lipkin R, Lazaridis T. Computational studies of peptide-induced membrane pore formation. Philos Trans R Soc Lond B Biol Sci 2018. [PMID: 28630158 DOI: 10.1098/rstb.2016.0219] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A variety of peptides induce pores in biological membranes; the most common ones are naturally produced antimicrobial peptides (AMPs), which are small, usually cationic, and defend diverse organisms against biological threats. Because it is not possible to observe these pores directly on a molecular scale, the structure of AMP-induced pores and the exact sequence of steps leading to their formation remain uncertain. Hence, these questions have been investigated via molecular modelling. In this article, we review computational studies of AMP pore formation using all-atom, coarse-grained, and implicit solvent models; evaluate the results obtained and suggest future research directions to further elucidate the pore formation mechanism of AMPs.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.
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Affiliation(s)
- Richard Lipkin
- Department of Chemistry, City College of New York, 160 Convent Avenue, New York, NY 10031, USA.,Graduate Program in Chemistry, The Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, 160 Convent Avenue, New York, NY 10031, USA
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15
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Cardoso MH, Oshiro KG, Rezende SB, Cândido ES, Franco OL. The Structure/Function Relationship in Antimicrobial Peptides: What Can we Obtain From Structural Data? THERAPEUTIC PROTEINS AND PEPTIDES 2018; 112:359-384. [DOI: 10.1016/bs.apcsb.2018.01.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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16
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Lipkin R, Pino-Angeles A, Lazaridis T. Transmembrane Pore Structures of β-Hairpin Antimicrobial Peptides by All-Atom Simulations. J Phys Chem B 2017; 121:9126-9140. [PMID: 28879767 DOI: 10.1021/acs.jpcb.7b06591] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Protegrin-1 is an 18-residue β-hairpin antimicrobial peptide (AMP) that has been suggested to form transmembrane β-barrels in biological membranes. However, alternative structures have also been proposed. Here, we performed multimicrosecond, all-atom molecular dynamics simulations of various protegrin-1 oligomers on the membrane surface and in transmembrane topologies. The membrane surface simulations indicated that protegrin dimers are stable, whereas trimers and tetramers break down. Tetrameric arcs remained stably inserted in lipid membranes, but the pore water was displaced by lipid molecules. Unsheared protegrin β-barrels opened into β-sheets that surrounded stable aqueous pores, whereas tilted barrels with sheared hydrogen bonding patterns were stable in most topologies. A third type of observed pore consisted of multiple small oligomers surrounding a small, partially lipidic pore. We also considered the β-hairpin AMP tachyplesin, which showed less tendency to oligomerize than protegrin: the octameric bundle resulted in small pores surrounded by six peptides as monomers and dimers, with some peptides returning to the membrane surface. The results imply that multiple configurations of protegrin oligomers may produce aqueous pores and illustrate the relationship between topology and putative steps in protegrin-1's pore formation. However, the long-term stability of these structures needs to be assessed further.
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Affiliation(s)
- Richard Lipkin
- Department of Chemistry, City College of New York , 160 Convent Avenue, New York, New York 10031, United States.,Graduate Program in Chemistry, The Graduate Center, City University of New York , 365 Fifth Avenue, New York, New York 10016, United States
| | - Almudena Pino-Angeles
- Department of Chemistry, City College of New York , 160 Convent Avenue, New York, New York 10031, United States
| | - Themis Lazaridis
- Department of Chemistry, City College of New York , 160 Convent Avenue, New York, New York 10031, United States
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17
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Lipkin R, Lazaridis T. Computational prediction of the optimal oligomeric state for membrane-inserted β-barrels of protegrin-1 and related mutants. J Pept Sci 2017; 23:334-345. [PMID: 28382709 DOI: 10.1002/psc.2992] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 02/17/2017] [Accepted: 02/18/2017] [Indexed: 11/07/2022]
Abstract
Protegrin-1 is a widely studied 18-residue β-hairpin antimicrobial peptide. Evidence suggests that it acts via a β-barrel pore formation mechanism, but the exact number of peptides comprising the pore state is unknown. In this study, we performed molecular dynamics simulations of β-barrels of protegrin and three related mutants (v14v16l, v14v16a, and r4n) in NCNC parallel topology in implicit membrane pores of varying radius and curvature for oligomeric numbers 6-14. We then identified the optimal pore radius and curvature values for all constructs and determined the total effective energy and the translational and rotational entropic losses. These, along with an estimate of membrane deformation free energy from experimental line tension values, provided an estimate of the overall energetics of formation of each pore state. The results indicated that oligomeric numbers 7-13 are generally stable, allowing the possibility of a heterogeneous pore state. The optimal oligomeric state for protegrin is the nonamer, shifting to higher numbers for the mutants. Protegrin, v14v16l, and r4n are stable as membrane-inserted β-barrels, but v14v16a seems much less so because of its decreased hydrophobicity. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Richard Lipkin
- Department of Chemistry, City College of New York, 160 Convent Ave., New York, NY, 10031, USA.,Graduate Program in Chemistry, Graduate Center, City University of New York, 365 Fifth Ave, New York, NY, 10016, USA
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, 160 Convent Ave., New York, NY, 10031, USA
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18
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Oligomerization of the antimicrobial peptide Protegrin-5 in a membrane-mimicking environment. Structural studies by high-resolution NMR spectroscopy. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 46:293-300. [PMID: 27589857 DOI: 10.1007/s00249-016-1167-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/23/2016] [Accepted: 08/26/2016] [Indexed: 10/21/2022]
Abstract
Protegrin pore formation is believed to occur in a stepwise fashion that begins with a nonspecific peptide interaction with the negatively charged bacterial cell walls via hydrophobic and positively charged amphipathic surfaces. There are five known nature protegrins (PG1-PG5), and early studies of PG-1 (PDB ID:1PG1) shown that it could form antiparallel dimer in membrane mimicking environment which could be a first step for further oligomeric membrane pore formation. Later, we solved PG-2 (PDB ID:2MUH) and PG-3 (PDB ID:2MZ6) structures in the same environment and for PG-3 observed a strong dαα NOE effects between residues R18 and F12, V14, and V16. These "inconsistent" with monomer structure NOEs appears due to formation of an additional antiparallel β-sheet between two monomers. It was also suggested that there is a possible association of protegrins dimers to form octameric or decameric β-barrels in an oligomer state. In order to investigate a more detailed oligomerization process of protegrins, in the present article we report the monomer (PDB ID: 2NC7) and octamer pore structures of the protegrin-5 (PG-5) in the presence of DPC micelles studied by solution NMR spectroscopy. In contrast to PG-1, PG-2, and PG-3 studies, for PG-5 we observed not only dimer NOEs but also several additional NOEs between side chains, which allows us to calculate an octamer pore structure of PG-5 that was in good agreement with previous AFM and PMF data.
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19
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Souza ALA, Faria RX, Calabrese KS, Hardoim DJ, Taniwaki N, Alves LA, De Simone SG. Temporizin and Temporizin-1 Peptides as Novel Candidates for Eliminating Trypanosoma cruzi. PLoS One 2016; 11:e0157673. [PMID: 27384541 PMCID: PMC4934777 DOI: 10.1371/journal.pone.0157673] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 06/02/2016] [Indexed: 12/21/2022] Open
Abstract
Tropical diseases caused by parasitic infections continue to cause socioeconomic distress worldwide. Among these, Chagas disease has become a great concern because of globalization. Caused by Trypanosoma cruzi, there is an increasing need to discover new, more effective methods to manage infections that minimize disease onset. Antimicrobial peptides represent a possible solution to this challenge. As effector molecules of the innate immune response against pathogens, they are the first line of defense found in all multi-cellular organisms. In amphibians, temporins are a large family of antimicrobial peptides found in skin secretions. Their functional roles and modes of action present unique properties that indicate possible candidates for therapeutic applications. Here, we investigated the trypanocide activity of temporizin and temporizin-1. Temporizin is an artificial, hybrid peptide containing the N-terminal region of temporin A, the pore-forming region of gramicidin and a C-terminus consisting of alternating leucine and lysine. Temporizin-1 is a modification of temporizin with a reduction in the region responsible for insertion into membranes. Their activities were evaluated in a cell permeabilization assay by flow cytometry, an LDH release assay, electron microscopy, an MTT assay and patch clamp experiments. Both temporizin and temporizin-1 demonstrated toxicity against T. cruzi with temporizin displaying slightly more potency. At concentrations up to 100 μg/ ml, both peptides exhibited low toxicity in J774 cells, a macrophage lineage cell line, and no toxicity was observed in mouse primary peritoneal macrophages. In contrast, the peptides showed some toxicity in rat adenoma GH3 cells and Jurkat human lymphoma cells with temporizin-1 displaying lower toxicity. In summary, a shortened form of the hybrid temporizin peptide, temporizin-1, was efficient at killing T. cruzi and it has low toxicity in wild-type mammalian cells. These data suggest that temporizin-1 might be a candidate for Chagas disease therapy.
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Affiliation(s)
- André L. A. Souza
- FIOCRUZ, Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation on Neglected Diseases (INCT-IDN), Rio de Janeiro, RJ, Brazil
- FIOCRUZ, Oswaldo Cruz Institute, Laboratory of Experimental and Computational Biochemistry of Pharmaceuticals, Rio de Janeiro, RJ, Brazil
| | - Robson X. Faria
- FIOCRUZ, Oswaldo Cruz Institute, Laboratory of Toxoplasmosis and other Protozoosis, Rio de Janeiro, RJ, Brazil
| | - Kátia S. Calabrese
- FIOCRUZ, Oswaldo Cruz Institute, Laboratory of Imunomodulation and Protozoology, Rio de Janeiro, RJ, Brazil
| | - Daiane J. Hardoim
- FIOCRUZ, Oswaldo Cruz Institute, Laboratory of Imunomodulation and Protozoology, Rio de Janeiro, RJ, Brazil
| | - Noemi Taniwaki
- FIOCRUZ, Adolfo Lutz Institute, Electronic Microscopy section, Araçatuba, São Paulo, SP, Brazil
| | - Luiz A. Alves
- FIOCRUZ, Oswaldo Cruz Institute, Laboratory of Cellular Communication, Rio de Janeiro, RJ, Brazil
| | - Salvatore G. De Simone
- FIOCRUZ, Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation on Neglected Diseases (INCT-IDN), Rio de Janeiro, RJ, Brazil
- Federal Fluminense University, Biology Institute, Department of Cellular and Molecular Biology, Niterói, RJ, Brazil
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20
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Wang CK, King GJ, Conibear AC, Ramos MC, Chaousis S, Henriques ST, Craik DJ. Mirror Images of Antimicrobial Peptides Provide Reflections on Their Functions and Amyloidogenic Properties. J Am Chem Soc 2016; 138:5706-13. [PMID: 27064294 DOI: 10.1021/jacs.6b02575] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Enantiomeric forms of BTD-2, PG-1, and PM-1 were synthesized to delineate the structure and function of these β-sheet antimicrobial peptides. Activity and lipid-binding assays confirm that these peptides act via a receptor-independent mechanism involving membrane interaction. The racemic crystal structure of BTD-2 solved at 1.45 Å revealed a novel oligomeric form of β-sheet antimicrobial peptides within the unit cell: an antiparallel trimer, which we suggest might be related to its membrane-active form. The BTD-2 oligomer extends into a larger supramolecular state that spans the crystal lattice, featuring a steric-zipper motif that is common in structures of amyloid-forming peptides. The supramolecular structure of BTD-2 thus represents a new mode of fibril-like assembly not previously observed for antimicrobial peptides, providing structural evidence linking antimicrobial and amyloid peptides.
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Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland 4072, Australia
| | - Gordon J King
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland 4072, Australia
| | - Anne C Conibear
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland 4072, Australia
| | - Mariana C Ramos
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland 4072, Australia
| | - Stephanie Chaousis
- 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
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland 4072, Australia
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21
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Jang H, Banerjee A, Chavan TS, Lu S, Zhang J, Gaponenko V, Nussinov R. The higher level of complexity of K-Ras4B activation at the membrane. FASEB J 2016; 30:1643-55. [PMID: 26718888 PMCID: PMC4799498 DOI: 10.1096/fj.15-279091] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/14/2015] [Indexed: 12/19/2022]
Abstract
Is nucleotide exchange sufficient to activate K-Ras4B? To signal, oncogenic rat sarcoma (Ras) anchors in the membrane and recruits effectors by exposing its effector lobe. With the use of NMR and molecular dynamics (MD) simulations, we observed that in solution, farnesylated guanosine 5'-diphosphate (GDP)-bound K-Ras4B is predominantly autoinhibited by its hypervariable region (HVR), whereas the GTP-bound state favors an activated, HVR-released state. On the anionic membrane, the catalytic domain adopts multiple orientations, including parallel (∼180°) and perpendicular (∼90°) alignments of the allosteric helices, with respect to the membrane surface direction. In the autoinhibited state, the HVR is sandwiched between the effector lobe and the membrane; in the active state, with membrane-anchored farnesyl and unrestrained HVR, the catalytic domain fluctuates reinlessly, exposing its effector-binding site. Dimerization and clustering can reduce the fluctuations. This achieves preorganized, productive conformations. Notably, we also observe HVR-autoinhibited K-Ras4B-GTP states, with GDP-bound-like orientations of the helices. Thus, we propose that the GDP/GTP exchange may not be sufficient for activation; instead, our results suggest that the GDP/GTP exchange, HVR sequestration, farnesyl insertion, and orientation/localization of the catalytic domain at the membrane conjointly determine the active or inactive state of K-Ras4B. Importantly, K-Ras4B-GTP can exist in active and inactive states; on its own, GTP binding may not compel K-Ras4B activation.-Jang, H., Banerjee, A., Chavan, T. S, Lu, S., Zhang, J., Gaponenko, V., Nussinov, R. The higher level of complexity of K-Ras4B activation at the membrane.
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Affiliation(s)
- Hyunbum Jang
- *Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, Maryland, USA; Department of Chemistry, Department of Medicinal Chemistry, and Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, USA; Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis, Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine, Shanghai, China; and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Avik Banerjee
- *Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, Maryland, USA; Department of Chemistry, Department of Medicinal Chemistry, and Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, USA; Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis, Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine, Shanghai, China; and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tanmay S Chavan
- *Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, Maryland, USA; Department of Chemistry, Department of Medicinal Chemistry, and Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, USA; Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis, Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine, Shanghai, China; and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shaoyong Lu
- *Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, Maryland, USA; Department of Chemistry, Department of Medicinal Chemistry, and Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, USA; Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis, Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine, Shanghai, China; and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jian Zhang
- *Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, Maryland, USA; Department of Chemistry, Department of Medicinal Chemistry, and Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, USA; Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis, Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine, Shanghai, China; and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Vadim Gaponenko
- *Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, Maryland, USA; Department of Chemistry, Department of Medicinal Chemistry, and Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, USA; Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis, Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine, Shanghai, China; and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ruth Nussinov
- *Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, Maryland, USA; Department of Chemistry, Department of Medicinal Chemistry, and Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, USA; Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis, Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine, Shanghai, China; and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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22
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Jang H, Arce FT, Lee J, Gillman AL, Ramachandran S, Kagan BL, Lal R, Nussinov R. Computational Methods for Structural and Functional Studies of Alzheimer's Amyloid Ion Channels. Methods Mol Biol 2016; 1345:251-68. [PMID: 26453217 PMCID: PMC7511997 DOI: 10.1007/978-1-4939-2978-8_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Aggregation can be studied by a range of methods, experimental and computational. Aggregates form in solution, across solid surfaces, and on and in the membrane, where they may assemble into unregulated leaking ion channels. Experimental probes of ion channel conformations and dynamics are challenging. Atomistic molecular dynamics (MD) simulations are capable of providing insight into structural details of amyloid ion channels in the membrane at a resolution not achievable experimentally. Since data suggest that late stage Alzheimer's disease involves formation of toxic ion channels, MD simulations have been used aiming to gain insight into the channel shapes, morphologies, pore dimensions, conformational heterogeneity, and activity. These can be exploited for drug discovery. Here we describe computational methods to model amyloid ion channels containing the β-sheet motif at atomic scale and to calculate toxic pore activity in the membrane.
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Affiliation(s)
- Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, 1050 Boyles Street, Frederick, MD, 21702, USA.
| | - Fernando Teran Arce
- Department of Bioengineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Mechanical and Aerospace Engineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Joon Lee
- Department of Mechanical and Aerospace Engineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Alan L Gillman
- Department of Bioengineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Srinivasan Ramachandran
- Department of Bioengineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Mechanical and Aerospace Engineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Bruce L Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, 90024, USA
| | - Ratnesh Lal
- Department of Bioengineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Mechanical and Aerospace Engineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, 1050 Boyles Street, Frederick, MD, 21702, USA.
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
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23
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Gilbert RJC. Protein-lipid interactions and non-lamellar lipidic structures in membrane pore formation and membrane fusion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:487-99. [PMID: 26654785 DOI: 10.1016/j.bbamem.2015.11.026] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 10/23/2015] [Accepted: 11/30/2015] [Indexed: 12/27/2022]
Abstract
Pore-forming proteins and peptides act on their targeted lipid bilayer membranes to increase permeability. This approach to the modulation of biological function is relevant to a great number of living processes, including; infection, parasitism, immunity, apoptosis, development and neurodegeneration. While some pore-forming proteins/peptides assemble into rings of subunits to generate discrete, well-defined pore-forming structures, an increasing number is recognised to form pores via mechanisms which co-opt membrane lipids themselves. Among these, membrane attack complex-perforin/cholesterol-dependent cytolysin (MACPF/CDC) family proteins, Bax/colicin family proteins and actinoporins are especially prominent and among the mechanisms believed to apply are the formation of non-lamellar (semi-toroidal or toroidal) lipidic structures. In this review I focus on the ways in which lipids contribute to pore formation and contrast this with the ways in which lipids are co-opted also in membrane fusion and fission events. A variety of mechanisms for pore formation that involve lipids exists, but they consistently result in stable hybrid proteolipidic structures. These structures are stabilised by mechanisms in which pore-forming proteins modify the innate capacity of lipid membranes to respond to their environment, changing shape and/or phase and binding individual lipid molecules directly. In contrast, and despite the diversity in fusion protein types, mechanisms for membrane fusion are rather similar to each other, mapping out a pathway from pairs of separated compartments to fully confluent fused membranes. Fusion proteins generate metastable structures along the way which, like long-lived proteolipidic pore-forming complexes, rely on the basic physical properties of lipid bilayers. Membrane fission involves similar intermediates, in the reverse order. I conclude by considering the possibility that at least some pore-forming and fusion proteins are evolutionarily related homologues. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Mauro Dalla Serra and Franco Gambale.
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Affiliation(s)
- Robert J C Gilbert
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
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24
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Jang H, Abraham SJ, Chavan TS, Hitchinson B, Khavrutskii L, Tarasova NI, Nussinov R, Gaponenko V. Mechanisms of membrane binding of small GTPase K-Ras4B farnesylated hypervariable region. J Biol Chem 2015; 290:9465-77. [PMID: 25713064 PMCID: PMC4392252 DOI: 10.1074/jbc.m114.620724] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 02/19/2015] [Indexed: 01/08/2023] Open
Abstract
K-Ras4B belongs to a family of small GTPases that regulates cell growth, differentiation and survival. K-ras is frequently mutated in cancer. K-Ras4B association with the plasma membrane through its farnesylated and positively charged C-terminal hypervariable region (HVR) is critical to its oncogenic function. However, the structural mechanisms of membrane association are not fully understood. Here, using confocal microscopy, surface plasmon resonance, and molecular dynamics simulations, we observed that K-Ras4B can be distributed in rigid and loosely packed membrane domains. Its membrane binding domain interaction with phospholipids is driven by membrane fluidity. The farnesyl group spontaneously inserts into the disordered lipid microdomains, whereas the rigid microdomains restrict the farnesyl group penetration. We speculate that the resulting farnesyl protrusion toward the cell interior allows oligomerization of the K-Ras4B membrane binding domain in rigid microdomains. Unlike other Ras isoforms, K-Ras4B HVR contains a single farnesyl modification and positively charged polylysine sequence. The high positive charge not only modulates specific HVR binding to anionic phospholipids but farnesyl membrane orientation. Phosphorylation of Ser-181 prohibits spontaneous farnesyl membrane insertion. The mechanism illuminates the roles of HVR modifications in K-Ras4B targeting microdomains of the plasma membrane and suggests an additional function for HVR in regulation of Ras signaling.
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Affiliation(s)
- Hyunbum Jang
- From the Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research and Cancer and Inflammation Program, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702
| | - Sherwin J Abraham
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, Departments of Biochemistry and Molecular Genetics and
| | - Tanmay S Chavan
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, Medicinal Chemistry, University of Illinois, Chicago, Illinois 60607, and
| | | | - Lyuba Khavrutskii
- From the Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research and Cancer and Inflammation Program, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702
| | - Nadya I Tarasova
- Cancer and Inflammation Program, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702,
| | - Ruth Nussinov
- From the Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research and Cancer and Inflammation Program, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Vadim Gaponenko
- Departments of Biochemistry and Molecular Genetics and Medicinal Chemistry, University of Illinois, Chicago, Illinois 60607, and
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25
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NIU MINGFU, CHAI SHUMAO, YOU XIAOYAN, WANG WENHUI, QIN CUILI, GONG QIANG, ZHANG TINGTING, WAN PENG. Expression of porcine protegrin-1 in Pichia pastoris and its anticancer activity in vitro.. Exp Ther Med 2015; 9:1075-1079. [PMID: 25667681 PMCID: PMC4316971 DOI: 10.3892/etm.2015.2202] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 01/15/2015] [Indexed: 12/27/2022] Open
Abstract
Protegrin-1 (PG-1), a β-hairpin antimicrobial peptide (AMP), is amongst the shortest AMPs in sequence length while remaining active against a variety of microorganisms. The aim of this study was produce recombinant PG-1 and investigate its anticancer activity. A DNA sequence encoding the mature PG-1, fused with a 6His-tag, was cloned into the pPICZα-A vector and transformed into Pichia pastoris. Expression was induced following culture for ~96 h with 1% methanol at 28°C, and ~15.6 mg PG-1 was expressed in 100 ml culture medium. Following purification using a Ni-chelating Sepharose column, ~20 mg pure active PG-1 was obtained from 500 ml culture broth supernatant. The expressed PG-1/6His exhibited strong dose- and time-dependent anticancer activity against HepG2 cells in vitro.
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Affiliation(s)
- MINGFU NIU
- Correspondence to: Professor Mingfu Niu, Food and Bioengineering College, Henan University of Science and Technology, 263 Kaiyuan Avenue, Luoyang, Henan 471003, P.R. China, E-mail:
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26
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Borkar MR, Pissurlenkar RRS, Coutinho EC. Mapping activity elements of protegrin antimicrobial peptides by HomoSAR. RSC Adv 2015. [DOI: 10.1039/c5ra14402g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
HomoSAR has been able to shed light on the relationship between sequences of protegrin peptides and their activity on six specific micro-organisms.
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Affiliation(s)
| | | | - Evans C. Coutinho
- Department of Pharmaceutical Chemistry
- Bombay College of Pharmacy
- Mumbai 400098
- India
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27
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Lipkin RB, Lazaridis T. Implicit Membrane Investigation of the Stability of Antimicrobial Peptide β-Barrels and Arcs. J Membr Biol 2014; 248:469-86. [PMID: 25430621 DOI: 10.1007/s00232-014-9759-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 11/18/2014] [Indexed: 12/31/2022]
Abstract
Previous simulations showed that the β-hairpin antimicrobial peptide (AMP) protegrin-1 can form stable octameric β-barrels and tetrameric arcs (half barrels) in both implicit and explicit membranes. Here, we extend this investigation to several AMPs of similar structure: tachyplesin, androctonin, polyphemusin, gomesin, and the retrocyclin θ-defensin. These peptides form short β-hairpins stabilized by 2-3 disulfide bonds. We also examine synthetic β-sheet peptides selected from a combinatorial library for their ability or inability to form pores in lipid membranes. When heptameric, octameric, and decameric β-barrels and tetrameric arcs of these peptides were embedded in pre-formed neutral or anionic lipid pores (i.e., pores in neutral or anionic membranes, respectively), a variety of behaviors and membrane binding energies were observed. Due to the cationic charge of the peptides, more favorable transfer energies and more stable binding were observed in anionic than neutral pores. The synthetic peptides bound very strongly and formed stable barrels and arcs in both neutral and anionic pores. The natural AMPs exhibited unfavorable or marginally favorable binding energy and kinetic stability in neutral pores, consistent with the lower hemolytic activity of some of them compared with protegrin-1. Binding to anionic pores was more favorable, but significant distortions of the barrel or arc structures were sometimes noted. These results are discussed in light of the available experimental data. The diversity of behaviors obtained makes it unlikely that the barrel and arc mechanisms are valid for the entire family of β-hairpin AMPs.
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Affiliation(s)
- Richard B Lipkin
- Department of Chemistry, City College of the City University of New York, 160 Convent Ave., New York, NY, 10031, USA
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28
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Zhang M, Zhao J, Zheng J. Molecular understanding of a potential functional link between antimicrobial and amyloid peptides. SOFT MATTER 2014; 10:7425-7451. [PMID: 25105988 DOI: 10.1039/c4sm00907j] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Antimicrobial and amyloid peptides do not share common sequences, typical secondary structures, or normal biological activity but both the classes of peptides exhibit membrane-disruption ability to induce cell toxicity. Different membrane-disruption mechanisms have been proposed for antimicrobial and amyloid peptides, individually, some of which are not exclusive to either peptide type, implying that certain common principles may govern the folding and functions of different cytolytic peptides and associated membrane disruption mechanisms. Particularly, some antimicrobial and amyloid peptides have been identified to have dual complementary amyloid and antimicrobial properties, suggesting a potential functional link between amyloid and antimicrobial peptides. Given that some similar structural and membrane-disruption characteristics exist between the two classes of peptides, this review summarizes major findings, recent advances, and future challenges related to antimicrobial and amyloid peptides and strives to illustrate the similarities, differences, and relationships in the sequences, structures, and membrane interaction modes between amyloid and antimicrobial peptides, with a special focus on direct interactions of the peptides with the membranes. We hope that this review will stimulate further research at the interface of antimicrobial and amyloid peptides - which has been studied less intensively than either type of peptides - to decipher a possible link between both amyloid pathology and antimicrobial activity, which can guide drug design and peptide engineering to influence peptide-membrane interactions important in human health and diseases.
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Affiliation(s)
- Mingzhen Zhang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA.
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29
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Jang H, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R. Disordered amyloidogenic peptides may insert into the membrane and assemble into common cyclic structural motifs. Chem Soc Rev 2014; 43:6750-64. [PMID: 24566672 PMCID: PMC4143503 DOI: 10.1039/c3cs60459d] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Aggregation of disordered amyloidogenic peptides into oligomers is the causative agent of amyloid-related diseases. In solution, disordered protein states are characterized by heterogeneous ensembles. Among these, β-rich conformers self-assemble via a conformational selection mechanism to form energetically-favored cross-β structures, regardless of their precise sequences. These disordered peptides can also penetrate the membrane, and electrophysiological data indicate that they form ion-conducting channels. Based on these and additional data, including imaging and molecular dynamics simulations of a range of amyloid peptides, Alzheimer's amyloid-β (Aβ) peptide, its disease-related variants with point mutations and N-terminal truncated species, other amyloidogenic peptides, as well as a cytolytic peptide and a synthetic gel-forming peptide, we suggest that disordered amyloidogenic peptides can also present a common motif in the membrane. The motif consists of curved, moon-like β-rich oligomers associated into annular organizations. The motif is favored in the lipid bilayer since it permits hydrophobic side chains to face and interact with the membrane and the charged/polar residues to face the solvated channel pores. Such channels are toxic since their pores allow uncontrolled leakage of ions into/out of the cell, destabilizing cellular ionic homeostasis. Here we detail Aβ, whose aggregation is associated with Alzheimer's disease (AD) and for which there are the most abundant data. AD is a protein misfolding disease characterized by a build-up of Aβ peptide as senile plaques, neurodegeneration, and memory loss. Excessively produced Aβ peptides may directly induce cellular toxicity, even without the involvement of membrane receptors through Aβ peptide-plasma membrane interactions.
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Affiliation(s)
- Hyunbum Jang
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, U.S.A
| | - Fernando Teran Arce
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Srinivasan Ramachandran
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Bruce L. Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, California 90024, U.S.A
| | - Ratnesh Lal
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Ruth Nussinov
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, U.S.A
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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30
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Gillman AL, Jang H, Lee J, Ramachandran S, Kagan B, Nussinov R, Teran Arce F. Activity and architecture of pyroglutamate-modified amyloid-β (AβpE3-42) pores. J Phys Chem B 2014; 118:7335-44. [PMID: 24922585 PMCID: PMC4096221 DOI: 10.1021/jp5040954] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Revised: 06/10/2014] [Indexed: 12/17/2022]
Abstract
Among the family of Aβ peptides, pyroglutamate-modified Aβ (AβpE) peptides are particularly associated with cytotoxicity in Alzheimer's disease (AD). They represent the dominant fraction of Aβ oligomers in the brains of AD patients, but their accumulation in the brains of elderly individuals with normal cognition is significantly lower. Accumulation of AβpE plaques precedes the formation of plaques of full-length Aβ (Aβ1-40/42). Most of these properties appear to be associated with the higher hydrophobicity of AβpE as well as an increased resistance to enzymatic degradation. However, the important question of whether AβpE peptides induce pore activity in lipid membranes and their potential toxicity compared with other Aβ pores is still open. Here we examine the activity of AβpE pores in anionic membranes using planar bilayer electrical recording and provide their structures using molecular dynamics simulations. We find that AβpE pores spontaneously induce ionic current across the membrane and have some similar properties to the other previously studied pores of the Aβ family. However, there are also some significant differences. The onset of AβpE3-42 pore activity is generally delayed compared with Aβ1-42 pores. However, once formed, AβpE3-42 pores produce increased ion permeability of the membrane, as indicated by a greater occurrence of higher conductance electrical events. Structurally, the lactam ring of AβpE peptides induces a change in the conformation of the N-terminal strands of the AβpE3-42 pores. While the N-termini of wild-type Aβ1-42 peptides normally reside in the bulk water region, the N-termini of AβpE3-42 peptides tend to reside in the hydrophobic lipid core. These studies provide a first step to an understanding of the enhanced toxicity attributed to AβpE peptides.
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Affiliation(s)
- Alan L. Gillman
- Department
of Bioengineering, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
| | - Hyunbum Jang
- Cancer
and Inflammation Program, National Cancer Institute at Frederick,
Leidos Biomedical Research, Inc., Frederick
National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Joon Lee
- Department
of Mechanical and Aerospace Engineering and Material Science Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Srinivasan Ramachandran
- Department
of Bioengineering, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
- Department
of Mechanical and Aerospace Engineering and Material Science Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Bruce
L. Kagan
- Department
of Psychiatry, David Geffen School of Medicine, Semel Institute for
Neuroscience and Human Behavior, University
of California, 760 Westwood
Plaza, Los Angeles, California 90024, United States
| | - Ruth Nussinov
- Cancer
and Inflammation Program, National Cancer Institute at Frederick,
Leidos Biomedical Research, Inc., Frederick
National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
- Department
of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Fernando Teran Arce
- Department
of Bioengineering, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
- Department
of Mechanical and Aerospace Engineering and Material Science Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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31
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Poojari C, Strodel B. Stability of transmembrane amyloid β-peptide and membrane integrity tested by molecular modeling of site-specific Aβ42 mutations. PLoS One 2013; 8:e78399. [PMID: 24244308 PMCID: PMC3820573 DOI: 10.1371/journal.pone.0078399] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 09/11/2013] [Indexed: 11/20/2022] Open
Abstract
Interactions of the amyloid β-protein (Aβ) with neuronal cell membranes, leading to the disruption of membrane integrity, are considered to play a key role in the development of Alzheimer’s disease. Natural mutations in Aβ42, such as the Arctic mutation (E22G) have been shown to increase Aβ42 aggregation and neurotoxicity, leading to the early-onset of Alzheimer’s disease. A correlation between the propensity of Aβ42 to form protofibrils and its effect on neuronal dysfunction and degeneration has been established. Using rational mutagenesis of the Aβ42 peptide it was further revealed that the aggregation of different Aβ42 mutants in lipid membranes results in a variety of polymorphic aggregates in a mutation dependent manner. The mutant peptides also have a variable ability to disrupt bilayer integrity. To further test the connection between Aβ42 mutation and peptide–membrane interactions, we perform molecular dynamics simulations of membrane-inserted Aβ42 variants (wild-type and E22G, D23G, E22G/D23G, K16M/K28M and K16M/E22G/D23G/K28M mutants) as β-sheet monomers and tetramers. The effects of charged residues on transmembrane Aβ42 stability and membrane integrity are analyzed at atomistic level. We observe an increased stability for the E22G Aβ42 peptide and a decreased stability for D23G compared to wild-type Aβ42, while D23G has the largest membrane-disruptive effect. These results support the experimental observation that the altered toxicity arising from mutations in Aβ is not only a result of the altered aggregation propensity, but also originates from modified Aβ interactions with neuronal membranes.
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Affiliation(s)
- Chetan Poojari
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- * E-mail:
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32
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Gupta K, Jang H, Harlen K, Puri A, Nussinov R, Schneider JP, Blumenthal R. Mechanism of membrane permeation induced by synthetic β-hairpin peptides. Biophys J 2013; 105:2093-103. [PMID: 24209854 PMCID: PMC3824417 DOI: 10.1016/j.bpj.2013.09.040] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/23/2013] [Accepted: 09/26/2013] [Indexed: 11/16/2022] Open
Abstract
We have investigated the membrane destabilizing properties of synthetic amphiphilic cationic peptides, MAX1 and MAX35, which have the propensity to form β-hairpin structures under certain conditions, and a control non-β-hairpin-forming peptide MAX8V16E. All three peptides bind to liposomes containing a mixture of zwitterionic POPC and negatively charged POPS lipids as determined by Zeta potential measurements. Circular dichroism measurements indicated folding of MAX1 and MAX35 in the presence of the POPC/POPS liposomes, whereas no such folding was observed with MAX8V16E. There was no binding or folding of these peptides to liposomes containing only POPC. MAX1 and MAX35 induced release of contents from negatively charged liposomes, whereas MAX8V16E failed to promote solute release under identical conditions. Thus, MAX1 and MAX35 bind to, and fold at the surface of negatively charged liposomes adopting a lytic conformation. We ruled out leaky fusion as a mechanism of release by including 2 mol % PEG-PE in the liposomes, which inhibits aggregation/fusion but not folding of MAX or MAX-induced leakage. Using a concentration-dependent quenching probe (calcein), we determined that MAX-induced leakage of liposome contents was an all-or-none process. At MAX1 concentrations, which cause release of ~50% of the liposomes that contain small (R(h) <1.5 nm) markers, only ~15% of those liposomes release a fluorescent dextran of 40 kDa. A multimeric model of the pore is presented based on these results. Atomistic molecular dynamics simulations show that barrels consisting of 10 β-hairpin MAX1 and MAX35 peptides are relatively more stable than MAX8V16E barrels in the bilayer, suggesting that barrels of this size are responsible for the peptides lytic action.
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Affiliation(s)
- Kshitij Gupta
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland
| | - Hyunbum Jang
- Basic Science Program, SAIC-Frederick, National Cancer Institute, National Institutes of Health, Frederick, Maryland
| | - Kevin Harlen
- Peptide Design and Materials Section, Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland
| | - Anu Puri
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, National Cancer Institute, National Institutes of Health, Frederick, Maryland
| | - Joel P. Schneider
- Peptide Design and Materials Section, Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland
| | - Robert Blumenthal
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland
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33
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Jang H, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R. Familial Alzheimer's disease Osaka mutant (ΔE22) β-barrels suggest an explanation for the different Aβ1-40/42 preferred conformational states observed by experiment. J Phys Chem B 2013; 117:11518-29. [PMID: 24000923 PMCID: PMC3946471 DOI: 10.1021/jp405389n] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An unusual ΔE693 mutation in the amyloid precursor protein (APP) producing a β-amyloid (Aβ) peptide lacking glutamic acid at position 22 (Glu22) was recently discovered, and dabbed the Osaka mutant (ΔE22). Previously, several point mutations in the Aβ peptide involving Glu22 substitutions were identified and implicated in the early onset of familial Alzheimer's disease (FAD). Despite the absence of Glu22, the Osaka mutant is also associated with FAD, showing a recessive inheritance in families affected by the disease. To see whether this aggregation-prone Aβ mutant could directly relate to the Aβ ion channel-mediated mechanism as observed for the wild type (WT) Aβ peptide in AD pathology, we modeled Osaka mutant β-barrels in a lipid bilayer. Using molecular dynamics (MD) simulations, two conformer ΔE22 barrels with the U-shaped monomer conformation derived from NMR-based WT Aβ fibrils were simulated in explicit lipid environment. Here, we show that the ΔE22 barrels obtain the lipid-relaxed β-sheet channel topology, indistinguishable from the WT Aβ1-42 barrels, as do the outer and pore dimensions of octadecameric (18-mer) ΔE22 barrels. Although the ΔE22 barrels lose the cationic binding site in the pore which is normally provided by the negatively charged Glu22 side chains, the mutant pores gain a new cationic binding site by Glu11 at the lower bilayer leaflet, and exhibit ion fluctuations similar to the WT barrels. Of particular interest, this deletion mutant suggests that toxic WT Aβ1-42 would preferentially adopt a less C-terminal turn similar to that observed for Aβ17-42, and explains why the solid state NMR data for Aβ1-40 point to a more C-terminal turn conformation. The observed ΔE22 barrels conformational preferences also suggest an explanation for the lower neurotoxicity in rat primary neurons as compared to WT Aβ1-42.
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Affiliation(s)
- Hyunbum Jang
- Basic Science Program, SAIC-Frederick, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Fernando Teran Arce
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, USA
| | - Srinivasan Ramachandran
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, USA
| | - Bruce L. Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, California 90024, USA
| | - Ratnesh Lal
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, USA
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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34
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Lazaridis T, He Y, Prieto L. Membrane interactions and pore formation by the antimicrobial peptide protegrin. Biophys J 2013; 104:633-42. [PMID: 23442914 DOI: 10.1016/j.bpj.2012.12.038] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Revised: 12/06/2012] [Accepted: 12/21/2012] [Indexed: 11/18/2022] Open
Abstract
Protegrin is an antimicrobial peptide with a β-hairpin structure stabilized by a pair of disulfide bonds. It has been extensively studied by solid-state NMR and computational methods. Here we use implicit membrane models to examine the binding of monomers on the surface and in the interior of the membrane, the energetics of dimerization, the binding to membrane pores, and the stability of different membrane barrel structures in pores. Our results challenge a number of conclusions based on previous experimental and theoretical work. The burial of monomers into the membrane interior is found to be unfavorable for any membrane thickness. Because of its imperfect amphipathicity, protegrin binds weakly, at most, on the surface of zwitterionic membranes. However, it binds more favorably onto toroidal pores. Anionic charge on the membrane facilitates the binding due to electrostatic interactions. Solid-state NMR results have suggested a parallel NCCN association of monomers in dimers and association of dimers to form octameric or decameric β-barrels. We find that this structure is not energetically plausible for binding to bilayers, because in this configuration the hydrophobic sides of two monomers point in opposite directions. In contrast, the antiparallel NCCN and especially the parallel NCNC octamers are stable and exhibit a favorable binding energy to the pore. The results of 100-ns simulations in explicit bilayers corroborate the higher stability of the parallel NCNC barrel compared with the parallel NCCN barrel. The ability to form pores in zwitterionic membranes provides a rationalization for the peptide's cytotoxicity. The discrepancies between our results and experiment are discussed, and new experiments are proposed to resolve them and to test the validity of the models.
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Affiliation(s)
- Themis Lazaridis
- Department of Chemistry, City College of New York/CUNY, New York, New York, USA.
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35
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Last NB, Schlamadinger DE, Miranker AD. A common landscape for membrane-active peptides. Protein Sci 2013; 22:870-82. [PMID: 23649542 DOI: 10.1002/pro.2274] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 04/23/2013] [Accepted: 04/24/2013] [Indexed: 10/26/2022]
Abstract
Three families of membrane-active peptides are commonly found in nature and are classified according to their initial apparent activity. Antimicrobial peptides are ancient components of the innate immune system and typically act by disruption of microbial membranes leading to cell death. Amyloid peptides contribute to the pathology of diverse diseases from Alzheimer's to type II diabetes. Preamyloid states of these peptides can act as toxins by binding to and permeabilizing cellular membranes. Cell-penetrating peptides are natural or engineered short sequences that can spontaneously translocate across a membrane. Despite these differences in classification, many similarities in sequence, structure, and activity suggest that peptides from all three classes act through a small, common set of physical principles. Namely, these peptides alter the Brownian properties of phospholipid bilayers, enhancing the sampling of intrinsic fluctuations that include membrane defects. A complete energy landscape for such systems can be described by the innate membrane properties, differential partition, and the associated kinetics of peptides dividing between surface and defect regions of the bilayer. The goal of this review is to argue that the activities of these membrane-active families of peptides simply represent different facets of what is a shared energy landscape.
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Affiliation(s)
- Nicholas B Last
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA
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36
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Semen-derived enhancer of viral infection (SEVI) binds bacteria, enhances bacterial phagocytosis by macrophages, and can protect against vaginal infection by a sexually transmitted bacterial pathogen. Antimicrob Agents Chemother 2013; 57:2443-50. [PMID: 23507280 DOI: 10.1128/aac.02464-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The semen-derived enhancer of viral infection (SEVI) is a positively charged amyloid fibril that is derived from a self-assembling proteolytic cleavage fragment of prostatic acid phosphatase (PAP(248-286)). SEVI efficiently facilitates HIV-1 infection in vitro, but its normal physiologic function remains unknown. In light of the fact that other amyloidogenic peptides have been shown to possess direct antibacterial activity, we investigated whether SEVI could inhibit bacterial growth. Neither SEVI fibrils nor the unassembled PAP(248-286) peptide had significant direct antibacterial activity in vitro. However, SEVI fibrils bound to both Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli and Neisseria gonorrhoeae) bacteria, in a charge-dependent fashion. Furthermore, SEVI fibrils but not the monomeric PAP(248-286) peptide promoted bacterial aggregation and enhanced the phagocytosis of bacteria by primary human macrophages. SEVI also enhanced binding of bacteria to macrophages and the subsequent release of bacterially induced proinflammatory cytokines (tumor necrosis factor alpha [TNF-α], interleukin-6 [IL-6], and IL-1β). Finally, SEVI fibrils inhibited murine vaginal colonization with Neisseria gonorrhoeae. These findings demonstrate that SEVI has indirect antimicrobial activity and that this activity is dependent on both the cationic charge and the fibrillar nature of SEVI.
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Bhattacharya M, Jain N, Dogra P, Samai S, Mukhopadhyay S. Nanoscopic Amyloid Pores Formed via Stepwise Protein Assembly. J Phys Chem Lett 2013; 4:480-485. [PMID: 26281744 DOI: 10.1021/jz3019786] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protein aggregation leading to various nanoscale assemblies is under scrutiny due to its implications in a broad range of human diseases. In the present study, we have used ovalbumin, a model non-inhibitory serpin, to elucidate the molecular events involved in amyloid assembly using a diverse array of spectroscopic and imaging tools such as fluorescence, laser Raman, circular dichroism spectroscopy, and atomic force microscopy (AFM). The AFM images revealed a progressive morphological transition from spherical oligomers to nanoscopic annular pores that further served as templates for higher-order supramolecular assembly into larger amyloid pores. Raman spectroscopic investigations illuminated in-depth molecular details into the secondary structural changes of the protein during amyloid assembly and pore formation. Additionally, Raman measurements indicated the presence of antiparallel β-sheets in the amyloid core. Overall, our studies revealed that the protein conformational switch in the context of the oligomers triggers the hierarchical assembly into nanoscopic amyloid pores. Our results will have broad implications in the structural characterization of amyloid pores derived from a variety of disease-related proteins.
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Affiliation(s)
- Mily Bhattacharya
- †Department of Chemical Sciences and ‡Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector 81, S.A.S. Nagar, Mohali-140306, India
| | - Neha Jain
- †Department of Chemical Sciences and ‡Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector 81, S.A.S. Nagar, Mohali-140306, India
| | - Priyanka Dogra
- †Department of Chemical Sciences and ‡Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector 81, S.A.S. Nagar, Mohali-140306, India
| | - Soumyadyuti Samai
- †Department of Chemical Sciences and ‡Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector 81, S.A.S. Nagar, Mohali-140306, India
| | - Samrat Mukhopadhyay
- †Department of Chemical Sciences and ‡Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector 81, S.A.S. Nagar, Mohali-140306, India
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38
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Poojari C, Kukol A, Strodel B. How the amyloid-β peptide and membranes affect each other: An extensive simulation study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:327-39. [DOI: 10.1016/j.bbamem.2012.09.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 09/03/2012] [Accepted: 09/04/2012] [Indexed: 11/24/2022]
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39
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Jang H, Connelly L, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R. Mechanisms for the Insertion of Toxic, Fibril-like β-Amyloid Oligomers into the Membrane. J Chem Theory Comput 2013; 9:822-833. [PMID: 23316126 PMCID: PMC3539805 DOI: 10.1021/ct300916f] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amyloid-β (Aβ) oligomers destabilize cellular ionic homeostasis, mediating Alzheimer's disease (AD). It is still unclear whether the mechanism (i) is mediated by cell surface receptors; (ii) is direct, with Aβ oligomers interacting with membrane lipids; or (iii) both mechanisms take place. Recent studies indicate that Aβ oligomers may act by either of the last two. Little is known about the oligomers' structures and how they spontaneously insert into the membrane. Using explicit solvent molecular dynamics (MD) simulations, we show that fibril-like Aβ(17-42) (p3) oligomer is capable of penetrating the membrane. Insertion is similar to that observed for protegrin-1 (PG-1), a cytolytic β-sheet-rich antimicrobial peptide (AMP). Both Aβ and PG-1 favor the amphipathic interface of the lipid bilayer in the early stage of interaction with the membrane. U-shaped Aβ oligomers are observed in solution and in the membrane, suggesting that the preformed seeds can be shared by amyloid fibrils in the growth phase and membrane toxicity. Here we provide sequential events in possible Aβ oligomer membrane-insertion pathways. We speculate that for the U-shaped motif, a trimer is the minimal oligomer size to insert effectively. We propose that monomers and dimers may insert in (apparently on-pathway) aggregation-intermediate β-hairpin state, and may (or may not) convert to a U-shape in the bilayer. Together with earlier observations, our results point to a non-specific, broadly heterogeneous landscape of membrane-inserting oligomer conformations, pathways, and membrane-mediated toxicity of β-rich oligomers.
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Affiliation(s)
- Hyunbum Jang
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Laura Connelly
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, USA
| | - Fernando Teran Arce
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, USA
| | - Srinivasan Ramachandran
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, USA
| | - Bruce L. Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, California 90024, USA
| | - Ratnesh Lal
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, USA
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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Bobone S, Roversi D, Giordano L, De Zotti M, Formaggio F, Toniolo C, Park Y, Stella L. The Lipid Dependence of Antimicrobial Peptide Activity Is an Unreliable Experimental Test for Different Pore Models. Biochemistry 2012; 51:10124-6. [DOI: 10.1021/bi3015086] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sara Bobone
- Department of Chemical Sciences
and Technologies, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Daniela Roversi
- Department of Chemical Sciences
and Technologies, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Lorenzo Giordano
- Department of Chemical Sciences
and Technologies, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Marta De Zotti
- ICB,
Padova Unit, CNR, Department
of Chemistry, University of Padova, 35131
Padova, Italy
| | - Fernando Formaggio
- ICB,
Padova Unit, CNR, Department
of Chemistry, University of Padova, 35131
Padova, Italy
| | - Claudio Toniolo
- ICB,
Padova Unit, CNR, Department
of Chemistry, University of Padova, 35131
Padova, Italy
| | - Yoonkyung Park
- Department
of Biotechnology and
Research Center for Proteineous Materials, Chosun University, Gwangju 501-759, Korea
| | - Lorenzo Stella
- Department of Chemical Sciences
and Technologies, University of Rome “Tor Vergata”, 00133 Rome, Italy
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41
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Anderluh G, Zerovnik E. Pore formation by human stefin B in its native and oligomeric states and the consequent amyloid induced toxicity. Front Mol Neurosci 2012; 5:85. [PMID: 22876218 PMCID: PMC3410518 DOI: 10.3389/fnmol.2012.00085] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 07/17/2012] [Indexed: 11/13/2022] Open
Abstract
It is well documented that amyloid forming peptides and proteins interact with membranes and that this correlates with cytotoxicity. To introduce the theme we give a brief description of some amyloidogenic proteins and note their similarities with pore forming toxins (PFTs) and cell penetrating peptides. Human stefin B, a member of the family of cystatins, is an amyloidogenic protein in vitro. This review describes our studies of the interaction of stefin B oligomers and prefibrillar aggregates with model membranes leading to pore formation. We have studied the interaction between human stefin B and artificial membranes of various compositions. We also have prepared distinct sizes and morphologies of stefin B prefibrillar states and assessed their toxicity. Furthermore, we have measured electrical currents through pores formed by stefin B prefibrillar oligomers in a planar lipid bilayer setup. We finally discuss the possible functional and pathological significance of such pores formed by human stefin B.
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42
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Kagan BL, Jang H, Capone R, Arce FT, Ramachandran S, Lal R, Nussinov R. Antimicrobial properties of amyloid peptides. Mol Pharm 2012; 9:708-17. [PMID: 22081976 PMCID: PMC3297685 DOI: 10.1021/mp200419b] [Citation(s) in RCA: 166] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
More than two dozen clinical syndromes known as amyloid diseases are characterized by the buildup of extended insoluble fibrillar deposits in tissues. These amorphous Congo red staining deposits known as amyloids exhibit a characteristic green birefringence and cross-β structure. Substantial evidence implicates oligomeric intermediates of amyloids as toxic species in the pathogenesis of these chronic disease states. A growing body of data has suggested that these toxic species form ion channels in cellular membranes causing disruption of calcium homeostasis, membrane depolarization, energy drainage, and in some cases apoptosis. Amyloid peptide channels exhibit a number of common biological properties including the universal U-shape β-strand-turn-β-strand structure, irreversible and spontaneous insertion into membranes, production of large heterogeneous single-channel conductances, relatively poor ion selectivity, inhibition by Congo red, and channel blockade by zinc. Recent evidence has suggested that increased amounts of amyloids not only are toxic to its host target cells but also possess antimicrobial activity. Furthermore, at least one human antimicrobial peptide, protegrin-1, which kills microbes by a channel-forming mechanism, has been shown to possess the ability to form extended amyloid fibrils very similar to those of classic disease-forming amyloids. In this paper, we will review the reported antimicrobial properties of amyloids and the implications of these discoveries for our understanding of amyloid structure and function.
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Affiliation(s)
- Bruce L. Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, California 90024, U.S.A
| | - Hyunbum Jang
- Center for Cancer Research Nanobiology Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, U.S.A
| | - Ricardo Capone
- Departments of Bioengineering and of Mechanical and Aerospace Engineering and Material Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Fernando Teran Arce
- Departments of Bioengineering and of Mechanical and Aerospace Engineering and Material Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Srinivasan Ramachandran
- Departments of Bioengineering and of Mechanical and Aerospace Engineering and Material Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Ratnesh Lal
- Departments of Bioengineering and of Mechanical and Aerospace Engineering and Material Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Ruth Nussinov
- Center for Cancer Research Nanobiology Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, U.S.A
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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43
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Capone R, Jang H, Kotler SA, Connelly L, Teran Arce F, Ramachandran S, Kagan BL, Nussinov R, Lal R. All-d-Enantiomer of β-Amyloid Peptide Forms Ion Channels in Lipid Bilayers. J Chem Theory Comput 2012; 8:1143-1152. [PMID: 22423218 PMCID: PMC3302213 DOI: 10.1021/ct200885r] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Indexed: 12/11/2022]
Abstract
Alzheimer's disease (AD) is the most common type of senile dementia in aging populations. Amyloid β (Aβ)-mediated dysregulation of ionic homeostasis is the prevailing underlying mechanism leading to synaptic degeneration and neuronal death. Aβ-dependent ionic dysregulation most likely occurs either directly via unregulated ionic transport through the membrane or indirectly via Aβ binding to cell membrane receptors and subsequent opening of existing ion channels or transporters. Receptor binding is expected to involve a high degree of stereospecificity. Here, we investigated whether an Aβ peptide enantiomer, whose entire sequence consists of d-amino acids, can form ion-conducting channels; these channels can directly mediate Aβ effects even in the absence of receptor-peptide interactions. Using complementary approaches of planar lipid bilayer (PLB) electrophysiological recordings and molecular dynamics (MD) simulations, we show that the d-Aβ isomer exhibits ion conductance behavior in the bilayer indistinguishable from that described earlier for the l-Aβ isomer. The d isomer forms channel-like pores with heterogeneous ionic conductance similar to the l-Aβ isomer channels, and the d-isomer channel conductance is blocked by Zn(2+), a known blocker of l-Aβ isomer channels. MD simulations further verify formation of β-barrel-like Aβ channels with d- and l-isomers, illustrating that both d- and l-Aβ barrels can conduct cations. The calculated values of the single-channel conductance are approximately in the range of the experimental values. These findings are in agreement with amyloids forming Ca(2+) leaking, unregulated channels in AD, and suggest that Aβ toxicity is mediated through a receptor-independent, nonstereoselective mechanism.
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Affiliation(s)
- Ricardo Capone
- Departments of Bioengineering
and Mechanical and Aerospace Engineering and Material Science Program, University of California—San Diego, La Jolla,
California 92093, United States
| | - Hyunbum Jang
- Center for Cancer Research Nanobiology
Program, SAIC-Frederick, Incorporated,
NCI-Frederick, Frederick, Maryland 21702, United States
| | - Samuel A. Kotler
- Departments of Bioengineering
and Mechanical and Aerospace Engineering and Material Science Program, University of California—San Diego, La Jolla,
California 92093, United States
| | - Laura Connelly
- Departments of Bioengineering
and Mechanical and Aerospace Engineering and Material Science Program, University of California—San Diego, La Jolla,
California 92093, United States
| | - Fernando Teran Arce
- Departments of Bioengineering
and Mechanical and Aerospace Engineering and Material Science Program, University of California—San Diego, La Jolla,
California 92093, United States
| | - Srinivasan Ramachandran
- Departments of Bioengineering
and Mechanical and Aerospace Engineering and Material Science Program, University of California—San Diego, La Jolla,
California 92093, United States
| | - Bruce L. Kagan
- Department of Psychiatry, David
Geffen School of Medicine, Semel Institute for Neuroscience and Human
Behavior, University of California—Los Angeles, Los Angeles, California 90024, United States
| | - Ruth Nussinov
- Center for Cancer Research Nanobiology
Program, SAIC-Frederick, Incorporated,
NCI-Frederick, Frederick, Maryland 21702, United States
- Department of Human Molecular
Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ratnesh Lal
- Departments of Bioengineering
and Mechanical and Aerospace Engineering and Material Science Program, University of California—San Diego, La Jolla,
California 92093, United States
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44
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Lam KLH, Wang H, Siaw TA, Chapman MR, Waring AJ, Kindt JT, Lee KYC. Mechanism of structural transformations induced by antimicrobial peptides in lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:194-204. [PMID: 22100601 DOI: 10.1016/j.bbamem.2011.11.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 11/01/2011] [Accepted: 11/02/2011] [Indexed: 01/14/2023]
Abstract
It has long been suggested that pore formation is responsible for the increase in membrane permeability by antimicrobial peptides (AMPs). To better understand the mechanism of AMP activity, the disruption of model membrane by protegrin-1 (PG-1), a cationic antimicrobial peptide, was studied using atomic force microscopy. We present here the direct visualization of the full range of structural transformations in supported lipid bilayer patches induced by PG-1 on zwitterionic 1,2-dimyristoyl-snglycero-phospho-choline (DMPC) membranes. When PG-1 is added to DMPC, the peptide first induces edge instability at low concentrations, then pore-like surface defects at intermediate concentrations, and finally wormlike structures with a specific length scale at high concentrations. The formation of these structures can be understood using a mesophase framework of a binary mixture of lipids and peptides, where PG-1 acts as a line-active agent. Atomistic molecular dynamics simulations on lipid bilayer ribbons with PG-1 molecules placed at the edge or interior positions are carried out to calculate the effect of PG-1 in reducing line tension. Further investigation of the placement of PG-1 and its association with defects in the bilayer is carried out using unbiased assembly of a PG-1 containing bilayer from a random mixture of PG-1, DMPC, and water. A generalized model of AMP induced structural transformations is also presented in this work. This article is part of a Special Issue entitled: Membrane protein structure and function.
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Affiliation(s)
- Kin Lok H Lam
- Department of Physics, The University of Chicago, Chicago, IL, USA
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45
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Allen MJ, Lacroix JJ, Ramachandran S, Capone R, Whitlock JL, Ghadge GD, Arnsdorf MF, Roos RP, Lal R. Mutant SOD1 forms ion channel: implications for ALS pathophysiology. Neurobiol Dis 2011; 45:831-8. [PMID: 21930207 DOI: 10.1016/j.nbd.2011.08.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 08/18/2011] [Accepted: 08/31/2011] [Indexed: 10/17/2022] Open
Abstract
Point mutations in the gene encoding copper-zinc superoxide dismutase (SOD1) impart a gain-of-function to this protein that underlies 20-25% of all familial amyotrophic lateral sclerosis (FALS) cases. However, the specific mechanism of mutant SOD1 toxicity has remained elusive. Using the complementary techniques of atomic force microscopy (AFM), electrophysiology, and cell and molecular biology, here we examine the structure and activity of A4VSOD1, a mutant SOD1. AFM of A4VSOD1 reconstituted in lipid membrane shows discrete tetrameric pore-like structure with outer and inner diameters 12.2 and 3.0nm respectively. Electrophysiological recordings show distinct ionic conductances across bilayer for A4VSOD1 and none for wildtype SOD1. Mouse neuroblastoma cells exposed to A4VSOD1 undergo membrane depolarization and increases in intracellular calcium. These results provide compelling new evidence that a mutant SOD1 is capable of disrupting cellular homeostasis via an unregulated ion channel mechanism. Such a "toxic channel" mechanism presents a new therapeutic direction for ALS research.
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Affiliation(s)
- Michael J Allen
- Center for Nanomedicine and Section of Pulmonary/Critical Care, Department of Medicine, The University of Chicago, Chicago, IL, USA
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46
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Jang H, Arce F, Mustata M, Ramachandran S, Capone R, Nussinov R, Lal R. Antimicrobial protegrin-1 forms amyloid-like fibrils with rapid kinetics suggesting a functional link. Biophys J 2011; 100:1775-83. [PMID: 21463591 PMCID: PMC3072611 DOI: 10.1016/j.bpj.2011.01.072] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 01/19/2011] [Accepted: 01/21/2011] [Indexed: 11/17/2022] Open
Abstract
Protegrin-1 (PG-1) is an 18 residues long, cysteine-rich β-sheet antimicrobial peptide (AMP). PG-1 induces strong cytotoxic activities on cell membrane and acts as a potent antibiotic agent. Earlier we reported that its cytotoxicity is mediated by its channel-forming ability. In this study, we have examined the amyloidogenic fibril formation properties of PG-1 in comparison with a well-defined amyloid, the amyloid-β (Aβ(1-42)) peptide. We have used atomic force microscopy (AFM) and thioflavin-T staining to investigate the kinetics of PG-1 fibrils growth and molecular dynamics simulations to elucidate the underlying mechanism. AFM images of PG-1 on a highly hydrophilic surface (mica) show fibrils with morphological similarities to Aβ(1-42) fibrils. Real-time AFM imaging of fibril growth suggests that PG-1 fibril growth follows a relatively fast kinetics compared to the Aβ(1-42) fibrils. The AFM results are in close agreement with results from thioflavin-T staining data. Furthermore, the results indicate that PG-1 forms fibrils in solution. Significantly, in contrast, we do not detect fibrillar structures of PG-1 on an anionic lipid bilayer 2-dioleoyl-sn-glycero-3-phospho-L-serine/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine; only small PG-1 oligomers can be observed. Molecular dynamics simulations are able to identify the presence of these small oligomers on the membrane bilayer. Thus, our current results show that cytotoxic AMP PG-1 is amyloidogenic and capable of forming fibrils. Overall, comparing β-rich AMPs and amyloids such as Aβ, in addition to cytotoxicity and amyloidogenicity, they share a common structural motif, and are channel forming. These combined properties support a functional relationship between amyloidogenic peptides and β-sheet-rich cytolytic AMPs, suggesting that amyloids channels may have an antimicrobial function.
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Affiliation(s)
- Hyunbum Jang
- Center for Cancer Research Nanobiology Program, National Cancer Institute-Frederick, SAIC-Frederick, Frederick, Maryland
| | - Fernando Teran Arce
- Department of Bioengineering and Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California
| | - Mirela Mustata
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois
| | - Srinivasan Ramachandran
- Department of Bioengineering and Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California
| | - Ricardo Capone
- Department of Bioengineering and Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California
| | - Ruth Nussinov
- Center for Cancer Research Nanobiology Program, National Cancer Institute-Frederick, SAIC-Frederick, Frederick, Maryland
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ratnesh Lal
- Department of Bioengineering and Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California
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47
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Bolintineanu DS, Kaznessis YN. Computational studies of protegrin antimicrobial peptides: a review. Peptides 2011; 32:188-201. [PMID: 20946928 PMCID: PMC3013618 DOI: 10.1016/j.peptides.2010.10.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 10/05/2010] [Accepted: 10/05/2010] [Indexed: 10/19/2022]
Abstract
Antimicrobial peptides (AMPs) are small, naturally occurring peptides that exhibit strong antibacterial properties generally believed to be a result of selective bacterial membrane disruption. As a result, there has been significant interest in the development of therapeutic antibiotics based on AMPs; however, the poor understanding of the fundamental mechanism of action of these peptides has largely hampered such efforts. We present a summary of computational and theoretical investigations of protegrin, a particularly potent peptide that is both an excellent model for the mechanism of action of AMPs and a promising therapeutic candidate. Experimental investigations have shed light on many of the key steps in the action of protegrin: protegrin monomers are known to dimerize in various lipid environments; protegrin peptides interact strongly with lipid bilayer membranes, particularly anionic lipids; protegrins have been shown to form pores in lipid bilayers, which results in uncontrolled ion transport and may be a key factor in bacterial death. In this work, we present a comprehensive review of the computational and theoretical studies that have complemented and extended the information obtained from experimental work with protegrins, as well as a brief survey of the experimental biophysical studies that are most pertinent to such computational work. We show that a consistent, mechanistic description of the bactericidal mechanism of action of protegrins is emerging, and briefly outline areas where the current understanding is deficient. We hope that the research reviewed herein offers compelling evidence of the benefits of computational investigations of protegrins and other AMPs, as well as providing a useful guide to future work in this area.
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Affiliation(s)
- Dan S. Bolintineanu
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave SE, Minneapolis MN 55455
| | - Yiannis N. Kaznessis
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave SE, Minneapolis MN 55455
- Corresponding author: , Tel: 612 624 4945, Fax: 612-626-7246
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48
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Jang H, Arce FT, Ramachandran S, Capone R, Lal R, Nussinov R. β-Barrel topology of Alzheimer's β-amyloid ion channels. J Mol Biol 2010; 404:917-34. [PMID: 20970427 PMCID: PMC7291702 DOI: 10.1016/j.jmb.2010.10.025] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 10/06/2010] [Accepted: 10/15/2010] [Indexed: 11/19/2022]
Abstract
Emerging evidence supports the ion channel mechanism for Alzheimer's disease pathophysiology wherein small β-amyloid (Aβ) oligomers insert into the cell membrane, forming toxic ion channels and destabilizing the cellular ionic homeostasis. Solid-state NMR-based data of amyloid oligomers in solution indicate that they consist of a double-layered β-sheets where each monomer folds into β-strand-turn-β-strand and the monomers are stacked atop each other. In the membrane, Aβ peptides are proposed to be β-type structures. Experimental structural data available from atomic force microscopy (AFM) imaging of Aβ oligomers in membranes reveal heterogeneous channel morphologies. Previously, we modeled the channels in a non-tilted organization, parallel with the cross-membrane normal. Here, we modeled a β-barrel-like organization. β-Barrels are common in transmembrane toxin pores, typically consisting of a monomeric chain forming a pore, organized in a single-layered β-sheet with antiparallel β-strands and a right-handed twist. Our explicit solvent molecular dynamics simulations of a range of channel sizes and polymorphic turns and comparisons of these with AFM image dimensions support a β-barrel channel organization. Different from the transmembrane β-barrels where the monomers are folded into a circular β-sheet with antiparallel β-strands stabilized by the connecting loops, these Aβ barrels consist of multimeric chains forming double β-sheets with parallel β-strands, where the strands of each monomer are connected by a turn. Although the Aβ barrels adopt the right-handed β-sheet twist, the barrels still break into heterogeneous, loosely attached subunits, in good agreement with AFM images and previous modeling. The subunits appear mobile, allowing unregulated, hence toxic, ion flux.
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Affiliation(s)
- Hyunbum Jang
- Center for Cancer Research Nanobiology Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - Fernando Teran Arce
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Srinivasan Ramachandran
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ricardo Capone
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ratnesh Lal
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ruth Nussinov
- Center for Cancer Research Nanobiology Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, MD 21702, USA
- Department of Human Molecular Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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Jang H, Teran Arce F, Ramachandran S, Capone R, Lal R, Nussinov R. Structural convergence among diverse, toxic beta-sheet ion channels. J Phys Chem B 2010; 114:9445-51. [PMID: 20608696 PMCID: PMC2908347 DOI: 10.1021/jp104073k] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 06/22/2010] [Indexed: 12/11/2022]
Abstract
Recent studies show that an array of beta-sheet peptides, including N-terminally truncated Abeta peptides (Abeta(11-42/17-42)), K3 (a beta(2)-microglobulin fragment), and protegrin-1 (PG-1) peptides form ion channel-like structures and elicit single channel ion conductance when reconstituted in lipid bilayers and induce cell damage through cell calcium overload. Striking similarities are observed in the dimensions of these toxic channels irrespective of their amino acid sequences. However, the intriguing question of preferred channel sizes is still unresolved. Here, exploiting ssNMR-based, U-shaped, beta-strand-turn-beta-strand coordinates, we modeled truncated Abeta peptide (p3) channels with different sizes (12- to 36-mer). Molecular dynamics (MD) simulations show that optimal channel sizes of the ion channels presenting toxic ionic flux range between 16- and 24-mer. This observation is in good agreement with channel dimensions imaged by AFM for Abeta(9-42), K3 fragment, and PG-1 channels and highlights the bilayer-supported preferred toxic beta-channel sizes and organization, regardless of the peptide sequence.
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Affiliation(s)
| | | | | | | | - Ratnesh Lal
- Corresponding authors. (R.N.) Phone: 301-846-5579. Fax: 301-846-5598. E-mail: . (R.L.) E-mail:
| | - Ruth Nussinov
- Corresponding authors. (R.N.) Phone: 301-846-5579. Fax: 301-846-5598. E-mail: . (R.L.) E-mail:
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