1
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Richardson JD, Van Lehn RC. Free Energy Analysis of Peptide-Induced Pore Formation in Lipid Membranes by Bridging Atomistic and Coarse-Grained Simulations. J Phys Chem B 2024; 128:8737-8752. [PMID: 39207202 DOI: 10.1021/acs.jpcb.4c03276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Antimicrobial peptides (AMPs) are attractive materials for combating the antimicrobial resistance crisis because they can kill target microbes by directly disrupting cell membranes. Although thousands of AMPs have been discovered, their molecular mechanisms of action are still poorly understood. One broad mechanism for membrane disruption is the formation of membrane-spanning hydrophilic pores which can be stabilized by AMPs. In this study, we use molecular dynamics simulations to investigate the thermodynamics of pore formation in model single-component lipid membranes in the presence of one of three AMPs: aurein 1.2, melittin and magainin 2. To overcome the general challenge of modeling long time scale membrane-related behaviors, including AMP binding, clustering, and pore formation, we develop a generalizable methodology for sampling AMP-induced pore formation. This approach involves the long equilibration of peptides around a pore created with a nucleation collective variable by performing coarse-grained simulations, then backmapping equilibrated AMP-membrane configurations to all-atom resolution. We then perform all-atom simulations to resolve free energy profiles for pore formation while accurately modeling the interplay of lipid-peptide-solvent interactions that dictate pore formation free energies. Using this approach, we quantify free energy barriers for pore formation without direct biases on peptides or whole lipids, allowing us to investigate mechanisms of pore formation for these 3 AMPs that are a consequence of unbiased peptide diffusion and clustering. Further analysis of simulation trajectories then relates variations in pore lining by AMPs, AMP-induced lipid disruptions, and salt bridges between AMPs to the observed pore formation free energies and corresponding mechanisms. This methodology and mechanistic analysis have the potential to generalize beyond the AMPs in this study to improve our understanding of pore formation by AMPs and related antimicrobial materials.
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Affiliation(s)
- Joshua D Richardson
- Department of Chemical and Biological Engineering, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
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2
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Stephani J, Gerhards L, Khairalla B, Solov’yov IA, Brand I. How do Antimicrobial Peptides Interact with the Outer Membrane of Gram-Negative Bacteria? Role of Lipopolysaccharides in Peptide Binding, Anchoring, and Penetration. ACS Infect Dis 2024; 10:763-778. [PMID: 38259029 PMCID: PMC10862549 DOI: 10.1021/acsinfecdis.3c00673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/31/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024]
Abstract
Gram-negative bacteria possess a complex structural cell envelope that constitutes a barrier for antimicrobial peptides that neutralize the microbes by disrupting their cell membranes. Computational and experimental approaches were used to study a model outer membrane interaction with an antimicrobial peptide, melittin. The investigated membrane included di[3-deoxy-d-manno-octulosonyl]-lipid A (KLA) in the outer leaflet and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) in the inner leaflet. Molecular dynamics simulations revealed that the positively charged helical C-terminus of melittin anchors rapidly into the hydrophilic headgroup region of KLA, while the flexible N-terminus makes contacts with the phosphate groups of KLA, supporting melittin penetration into the boundary between the hydrophilic and hydrophobic regions of the lipids. Electrochemical techniques confirmed the binding of melittin to the model membrane. To probe the peptide conformation and orientation during interaction with the membrane, polarization modulation infrared reflection absorption spectroscopy was used. The measurements revealed conformational changes in the peptide, accompanied by reorientation and translocation of the peptide at the membrane surface. The study suggests that melittin insertion into the outer membrane affects its permeability and capacitance but does not disturb the membrane's bilayer structure, indicating a distinct mechanism of the peptide action on the outer membrane of Gram-negative bacteria.
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Affiliation(s)
- Justus
C. Stephani
- Institute
of Physics, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
| | - Luca Gerhards
- Institute
of Physics, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
| | - Bishoy Khairalla
- Department
of Chemistry, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
- Research
Center Neurosensory Science, Carl von Ossietzky
University of Oldenburg, 26111 Oldenburg, Germany
- CeNaD—Center
for Nanoscale Dynamics, Carl von Ossietzky
University of Oldenburg, 26111 Oldenburg, Germany
| | - Izabella Brand
- Department
of Chemistry, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
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3
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Daba GM, Elkhateeb WA. Ribosomally synthesized bacteriocins of lactic acid bacteria: Simplicity yet having wide potentials - A review. Int J Biol Macromol 2024; 256:128325. [PMID: 38007012 DOI: 10.1016/j.ijbiomac.2023.128325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/02/2023] [Accepted: 11/11/2023] [Indexed: 11/27/2023]
Abstract
Bacteriocins are ribosomally made bacterial peptides that have outstanding contributions in the field of food industry, as biopreservatives, and promising potentials in the medical field for improving human and animal health. Bacteriocins have many advantages over antibiotics such as being primary metabolites with relatively simpler biosynthetic mechanisms, which made their bioengineering for activity or specificity improving purposes much easier. Also, bacteriocins are degraded by proteolytic enzymes and do not stay in environment, which reduce chances of developing resistance. Bacteriocins can improve activity of some antibiotics, and some bacteriocins show potency against multidrug-resistant bacteria. Moreover, some potent bacteriocins have antiviral, antifungal, and antiprotozoal (antileishmanial) activities. On the other hand, bacteriocins have been introduced into the treatment of some ulcers and types of cancer. These potentials make bacteriocins attract extra attention as promising biotechnological tool. Hence, the history, characteristics, and classification of bacteriocins are described in this review. Furthermore, the main difference between bacteriocins and other antimicrobial peptides is clarified. Also, bacteriocins biosynthesis and identified modes of action are elucidated. Additionally, current and potential applications of bacteriocins in food and medical fields are highlighted. Finally, future perspectives concerning studying bacteriocins and their applications are discussed.
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Affiliation(s)
- Ghoson Mosbah Daba
- Chemistry of Natural and Microbial Products Department, Pharmaceutical Industries Researches Institute, National Research Centre, El Buhouth St., Egypt.
| | - Waill Ahmed Elkhateeb
- Chemistry of Natural and Microbial Products Department, Pharmaceutical Industries Researches Institute, National Research Centre, El Buhouth St., Egypt
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4
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Gu Y, Wu L, Hameed Y, Nabi-Afjadi M. Overcoming the challenge: cell-penetrating peptides and membrane permeability. BIOMATERIALS AND BIOSENSORS 2023; 2. [DOI: 10.58567/bab02010002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
<p>Cell-penetrating peptides (CPPs) have emerged as a promising strategy for enhancing the membrane permeability of bioactive molecules, particularly in the treatment of central nervous system diseases. CPPs possess the ability to deliver a diverse array of bioactive molecules into cells using either covalent or non-covalent approaches, with a preference for non-covalent methods to preserve the biological activity of the transported molecules. By effectively traversing various physiological barriers, CPPs have exhibited significant potential in preclinical and clinical drug development. The discovery of CPPs represents a valuable solution to the challenge of limited membrane permeability of bioactive molecules and will continue to exert a crucial influence on the field of biomedical science.</p>
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Affiliation(s)
- Yuan Gu
- The Statistics Department, The George Washington University, Washington, United States
| | - Long Wu
- Department of Surgery, University of Maryland, Baltimore, United States
| | - Yasir Hameed
- Department of Applied Biological Sciences, Tokyo University of Science, Tokyo, Japan
| | - Mohsen Nabi-Afjadi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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5
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Naito A, Kawamura I. Dynamic membrane interaction and amyloid fibril formation of glucagon, melittin and human calcitonin. Biophys Chem 2023; 298:107025. [PMID: 37127008 DOI: 10.1016/j.bpc.2023.107025] [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: 03/01/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/03/2023]
Abstract
Glucagon is a 29-amino acid peptide hormone secreted by pancreatic α-cells and interacts with specific receptors located in various organs. Glucagon tends to form gel-like fibril aggregates that are cytotoxic. It is important to reveal the glucagon-membrane interaction to understand activity and cytotoxicity of glucagon and glucagon oligomers. In this review, first glucagon-membrane interactions are described as morphological changes in dimyristoylphosphatidylcholine (DMPC) bilayers containing glucagon in acidic and neutral conditions as compared to the case of melittin. Second, fibril formation by glucagon in acidic solution is discussed in light of morphological and structural changes. Third, kinetic analysis of glucagon fibril formation was performed using a two-step autocatalytic reaction mechanism, as investigated in the case of human calcitonin. The first step is a nuclear formation, and the second step is an autocatalytic fibril elongation. Forth, fibril formation of glucagon inside glucagon-DMPC bilayers in neutral solution under near physiological condition is described.
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Affiliation(s)
- Akira Naito
- Graduate School of Engineering, Yokohama National University, Yokohama 240-8501, Japan.
| | - Izuru Kawamura
- Graduate School of Engineering, Yokohama National University, Yokohama 240-8501, Japan
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6
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Akbarzadeh-Khiavi M, Torabi M, Olfati AH, Rahbarnia L, Safary A. Bio-nano scale modifications of melittin for improving therapeutic efficacy. Expert Opin Biol Ther 2022; 22:895-909. [PMID: 35687355 DOI: 10.1080/14712598.2022.2088277] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Melittin (MLT), a natural membrane-active component, is the most prominent cytolytic peptide from bee venom. Remarkable biological properties of MLT, including anti-inflammatory, antimicrobial, anticancer, anti-protozoan, and antiarthritic activities, make it an up-and-coming therapeutic candidate for a wide variety of human diseases. Therapeutic applications of MLT may be hindered due to low stability, high toxicity, and weak tissue penetration. Different bio-nano scale modifications hold promise for improving its functionality and therapeutic efficacy. AREAS COVERED In the current review, we aimed to provide a comprehensive insight into strategies used for MLT conjugations and modifications, cellular delivery of modified forms, and their clinical perspectives by reviewing the published literature on PubMed, Scopus, and Google Scholar databases. We also emphasized the MLT structure modifications, mechanism of action, and cellular toxicity. EXPERT OPINION Developing new analogs and conjugates of MLT as a natural drug with improved functions and fewer side effects is crucial for the clinical translation of this approach worldwide, especially where the chemicals and synthetic drugs are more expensive or unavailable in the healthcare system. MLT-nanoconjugation may be one of the best-optimized strategies for improving peptide delivery, increasing its therapeutic efficacy, and providing minimal nonspecific cellular lytic activity. [Figure: see text].
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Affiliation(s)
- Mostafa Akbarzadeh-Khiavi
- Liver and Gastrointestinal Diseases Research Center Tabriz University of Medical Sciences, Tabriz, Iran.,Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mitra Torabi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir-Hossein Olfati
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leila Rahbarnia
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Azam Safary
- Connective Tissue Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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7
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Tichotová M, Ešnerová A, Tučková L, Bednárová L, Císařová I, Baszczyňski O, Procházková E. 31P NMR parameters may facilitate the stereochemical analysis of phosphorus-containing compounds. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 336:107149. [PMID: 35121491 DOI: 10.1016/j.jmr.2022.107149] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
Conventional Nuclear Magnetic Resonance (NMR) analysis relies on H-H/C-H interactions. However, these interactions are sometimes insufficient for an accurate and precise NMR analysis. In this study, we show that 31P NMR parameters can provide critical structural insights into the stereochemistry of phosphorus-containing compounds. For this purpose, we prepared a set of model phosphorus-based proline derivatives, separated diastereoisomers, and determined their absolute configuration by single-crystal X-ray diffraction. After supplementing these results by electronic circular dichroism (ECD) spectroscopy, we combined experimental data and DFT calculations from our model compounds to perform a detailed conformational analysis, thereby determining their relative configuration. Overall, our findings establish an experimental paradigm for combining 31P NMR spectroscopy with other optical methods to facilitate the stereochemical analysis of phosphorus-containing compounds.
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Affiliation(s)
- Markéta Tichotová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic; Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, 116 28 Prague, Czech Republic
| | - Aneta Ešnerová
- Department of Organic Chemistry, Faculty of Science, Charles University, 116 28 Prague, Czech Republic
| | - Lucie Tučková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic
| | - Ivana Císařová
- Department of Inorganic Chemistry, Faculty of Science, Charles University, 116 28 Prague, Czech Republic
| | - Ondřej Baszczyňski
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic; Department of Organic Chemistry, Faculty of Science, Charles University, 116 28 Prague, Czech Republic
| | - Eliška Procházková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
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8
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Yu L, Li K, Zhang J, Jin H, Saleem A, Song Q, Jia Q, Li P. Antimicrobial Peptides and Macromolecules for Combating Microbial Infections: From Agents to Interfaces. ACS APPLIED BIO MATERIALS 2022; 5:366-393. [PMID: 35072444 DOI: 10.1021/acsabm.1c01132] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bacterial resistance caused by the overuse of antibiotics and the shelter of biofilms has evolved into a global health crisis, which drives researchers to continuously explore antimicrobial molecules and strategies to fight against drug-resistant bacteria and biofilm-associated infections. Cationic antimicrobial peptides (AMPs) are considered to be a category of potential alternative for antibiotics owing to their excellent bactericidal potency and lesser likelihood of inducing drug resistance through their distinctive antimicrobial mechanisms. In this review, the hitherto reported plentiful action modes of AMPs are systematically classified into 15 types and three categories (membrane destructive, nondestructive membrane disturbance, and intracellular targeting mechanisms). Besides natural AMPs, cationic polypeptides, synthetic polymers, and biopolymers enable to achieve tunable antimicrobial properties by optimizing their structures. Subsequently, the applications of these cationic antimicrobial agents at the biointerface as contact-active surface coatings and multifunctional wound dressings are also emphasized here. At last, we provide our perspectives on the development of clinically significant cationic antimicrobials and related challenges in the translation of these materials.
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Affiliation(s)
- Luofeng Yu
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Kunpeng Li
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Jing Zhang
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Haoyu Jin
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Atif Saleem
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Qing Song
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Qingyan Jia
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Peng Li
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
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9
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Daba GM, Elnahas MO, Elkhateeb WA. Beyond biopreservatives, bacteriocins biotechnological applications: History, current status, and promising potentials. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2021.102248] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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10
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Zhao J, Sugihara K. Analysis of PDA Dose Curves for the Extraction of Antimicrobial Peptide Properties. J Phys Chem B 2021; 125:12206-12213. [PMID: 34706534 DOI: 10.1021/acs.jpcb.1c07533] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A mechanochromic polymer, polydiacetylene, changes color upon ligand binding, being a popular material in biosensing. However, whether it can also detect ligand functions in addition to binding is left understudied. In this work, we report that the polydiacetylene can be used to determine the net charges and the mode of actions (carpet model, toroidal pore model, etc.) of antimicrobial peptides and detergents via EC50 and Hill coefficients from the colorimetric response-dose curves. This opens a potential for high-throughput peptide screening by functions, which is difficult with the conventional methods.
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Affiliation(s)
- Jiangtao Zhao
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva, Switzerland
| | - Kaori Sugihara
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva, Switzerland.,Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba Meguro-Ku, Tokyo 153-8505, Japan
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11
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Aronica PGA, Reid LM, Desai N, Li J, Fox SJ, Yadahalli S, Essex JW, Verma CS. Computational Methods and Tools in Antimicrobial Peptide Research. J Chem Inf Model 2021; 61:3172-3196. [PMID: 34165973 DOI: 10.1021/acs.jcim.1c00175] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The evolution of antibiotic-resistant bacteria is an ongoing and troubling development that has increased the number of diseases and infections that risk going untreated. There is an urgent need to develop alternative strategies and treatments to address this issue. One class of molecules that is attracting significant interest is that of antimicrobial peptides (AMPs). Their design and development has been aided considerably by the applications of molecular models, and we review these here. These methods include the use of tools to explore the relationships between their structures, dynamics, and functions and the increasing application of machine learning and molecular dynamics simulations. This review compiles resources such as AMP databases, AMP-related web servers, and commonly used techniques, together aimed at aiding researchers in the area toward complementing experimental studies with computational approaches.
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Affiliation(s)
- Pietro G A Aronica
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Lauren M Reid
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,School of Chemistry, University of Southampton, Highfield Southampton, Hampshire, U.K. SO17 1BJ.,MedChemica Ltd, Alderley Park, Macclesfield, Cheshire, U.K. SK10 4TG
| | - Nirali Desai
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,Division of Biological and Life Sciences, Ahmedabad University, Central Campus, Ahmedabad, Gujarat, India 380009
| | - Jianguo Li
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,Singapore Eye Research Institute, 20 College Road Discovery Tower, Singapore 169856
| | - Stephen J Fox
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Shilpa Yadahalli
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Jonathan W Essex
- School of Chemistry, University of Southampton, Highfield Southampton, Hampshire, U.K. SO17 1BJ
| | - Chandra S Verma
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore.,School of Biological Sciences, Nanyang Technological University, 50 Nanyang Drive, 637551 Singapore
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12
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Lomize AL, Schnitzer KA, Todd SC, Pogozheva ID. Thermodynamics-Based Molecular Modeling of α-Helices in Membranes and Micelles. J Chem Inf Model 2021; 61:2884-2896. [PMID: 34029472 DOI: 10.1021/acs.jcim.1c00161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Folding of Membrane-Associated Peptides (FMAP) method was developed for modeling α-helix formation by linear peptides in micelles and lipid bilayers. FMAP 2.0 identifies locations of α-helices in the amino acid sequence, generates their three-dimensional models in planar bilayers or spherical micelles, and estimates their thermodynamic stabilities and tilt angles, depending on temperature and pH. The method was tested for 723 peptides (926 data points) experimentally studied in different environments and for 170 single-pass transmembrane (TM) proteins with available crystal structures. FMAP 2.0 detected more than 95% of experimentally observed α-helices with an average error in helix end determination of around 2, 3, 4, and 5 residues per helix for peptides in water, micelles, bilayers, and TM proteins, respectively. Helical and nonhelical residue states were predicted with an accuracy from 0.86 to 0.96, and the Matthews correlation coefficient was from 0.64 to 0.88 depending on the environment. Experimental micelle- and membrane-binding energies and tilt angles of peptides were reproduced with a root-mean-square deviation of around 2 kcal/mol and 7°, respectively. The TM and non-TM states of hydrophobic and pH-triggered α-helical peptides in various lipid bilayers were reproduced in more than 95% of cases. The FMAP 2.0 web server (https://membranome.org/fmap) is publicly available to explore the structural polymorphism of antimicrobial, cell-penetrating, fusion, and other membrane-binding peptides, which is important for understanding the mechanisms of their biological activities.
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Affiliation(s)
- Andrei L Lomize
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Kevin A Schnitzer
- Department of Electrical Engineering and Computer Science, College of Engineering, University of Michigan, 1221 Beal Avenue, Ann Arbor, Michigan 48109-2102, United States
| | - Spencer C Todd
- Department of Electrical Engineering and Computer Science, College of Engineering, University of Michigan, 1221 Beal Avenue, Ann Arbor, Michigan 48109-2102, United States
| | - Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
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13
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Grigolato F, Arosio P. The role of surfaces on amyloid formation. Biophys Chem 2021; 270:106533. [PMID: 33529995 DOI: 10.1016/j.bpc.2020.106533] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 01/02/2023]
Abstract
Interfaces can strongly accelerate or inhibit protein aggregation, destabilizing proteins that are stable in solution or, conversely, stabilizing proteins that are aggregation-prone. Although this behaviour is well-known, our understanding of the molecular mechanisms underlying surface-induced protein aggregation is still largely incomplete. A major challenge is represented by the high number of physico-chemical parameters involved, which are highly specific to the considered combination of protein, surface properties, and solution conditions. The key aspect determining the role of interfaces is the relative propensity of the protein to aggregate at the surface with respect to bulk. In this review, we discuss the multiple molecular determinants that regulate this balance. We summarize current experimental techniques aimed at characterizing protein aggregation at interfaces, and highlight the need to complement experimental analysis with theoretical modelling. In particular, we illustrate how chemical kinetic analysis can be combined with experimental methods to provide insights into the molecular mechanisms underlying surface-induced protein aggregation, under both stagnant and agitation conditions. We summarize recent progress in the study of important amyloids systems, focusing on selected relevant interfaces.
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Affiliation(s)
- Fulvio Grigolato
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich 8093, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich 8093, Switzerland.
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14
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Nguyen MHL, DiPasquale M, Rickeard BW, Yip CG, Greco KN, Kelley EG, Marquardt D. Time-resolved SANS reveals pore-forming peptides cause rapid lipid reorganization. NEW J CHEM 2021. [DOI: 10.1039/d0nj04717a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Time-resolved SANS showed alamethicin and melittin promote DMPC lipid vesicle mixing and perturb DMPC kinetics in similar ways.
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Affiliation(s)
| | | | - Brett W. Rickeard
- Department of Chemistry and Biochemistry
- University of Windsor
- Windsor
- Canada
| | - Caesar G. Yip
- Department of Chemistry and Biochemistry
- University of Windsor
- Windsor
- Canada
| | - Kaity N. Greco
- Department of Chemistry and Biochemistry
- University of Windsor
- Windsor
- Canada
| | - Elizabeth G. Kelley
- NIST Center for Neutron Research
- National Institute of Standards and Technology
- Gaithersburg
- USA
| | - Drew Marquardt
- Department of Chemistry and Biochemistry
- University of Windsor
- Windsor
- Canada
- Department of Physics
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15
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Naito A. Fibril Formation by Glucagon in Solution and in Membrane Environments. Mol Pharmacol 2020. [DOI: 10.5772/intechopen.91681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Glucagon is a 29-amino acid peptide hormone secreted by pancreatic α-cells and interacts with specific receptors located in various organs. Glucagon tends to form gel-like fibril aggregates that are cytotoxic because they activate apoptotic signaling pathways. First, fibril formation by glucagon in acidic solution is discussed in light of morphological and structural changes during elapsed time. Second, we provide kinetic analyses using a two-step autocatalytic reaction mechanism; the first step is a homogeneous nuclear formation process, and the second step is an autocatalytic heterogeneous fibril elongation process. Third, the processes of fibril formation by glucagon in a membrane environment are discussed based on the structural changes in the fibrils. In the presence of bicelles in acidic solution, glucagon interacts with the bicelles and forms fibril intermediates on the bicelle surface and grows into elongated fibrils. Glucagon-dimyristoylphosphatidylcholine (DMPC) bilayers in neutral solution mimic the environment for fibril formation by glucagon under near-physiological condition. Under these conditions, glucagon forms fibril intermediates that grow into elongated fibrils inside the lipid bilayer. Many days after preparing the glucagon-DMPC bilayer sample, the fibrils form networks inside and outside the bilayer. Furthermore, fibril intermediates strongly interact with lipid bilayers to form small particles.
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Haya K, Makino Y, Kikuchi-Kinoshita A, Kawamura I, Naito A. 31P and 13C solid-state NMR analysis of morphological changes of phospholipid bilayers containing glucagon during fibril formation of glucagon under neutral condition. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183290. [DOI: 10.1016/j.bbamem.2020.183290] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/25/2020] [Accepted: 03/23/2020] [Indexed: 02/07/2023]
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17
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Pandidan S, Mechler A. Membrane morphology effects in quartz crystal microbalance characterization of antimicrobial peptide activity. Biophys Chem 2020; 262:106381. [PMID: 32361097 DOI: 10.1016/j.bpc.2020.106381] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/15/2020] [Accepted: 04/19/2020] [Indexed: 10/24/2022]
Abstract
The mechanism of action of membrane disrupting antimicrobial peptides (AMPs) and the basis of their specificity and selectivity to pathogens are often studied by using biomimetic model membranes. It is often assumed that all model membrane morphologies, e.g. liposomes, supported bilayers, tethered bilayers etc. are equivalent. In this work the validity of this assumption was assessed. Melittin was used as the reference AMP as it can disrupt both bacterial and mammalian-mimetic membranes. Quartz crystal microbalance (QCM) viscoelastic fingerprints show characteristic differences between the three model morphologies: single bilayer membranes, multilamellar membrane stacks and unilamellar liposomes. In the second and third case, initial trends show material removal instead of material addition as in the single bilayer case, consistent with dissolution of some bilayers, and bursting liposomes, respectively. The latter is accompanied by a characteristic drop in the dissipation signal as the liposomes collapse. The results also highlight an important limitation of the QCM method, the need for a well established reference system for qualitative analysis of the viscoelastic fingerprints, and thus the importance of using the right model system, i.e. single bilayer membrane, for studies of the mechanism of action of AMPs.
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Affiliation(s)
- Sara Pandidan
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Adam Mechler
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia.
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18
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Effects of Peptide Charge, Orientation, and Concentration on Melittin Transmembrane Pores. Biophys J 2019; 114:2865-2874. [PMID: 29925023 DOI: 10.1016/j.bpj.2018.05.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 03/21/2018] [Accepted: 05/02/2018] [Indexed: 11/21/2022] Open
Abstract
Melittin is a short cationic peptide that exerts cytolytic effects on bacterial and eukaryotic cells. Experiments suggest that in zwitterionic membranes, melittin forms transmembrane toroidal pores supported by four to eight peptides. A recently constructed melittin variant with a reduced cationic charge, MelP5, is active at 10-fold lower concentrations. In previous work, we performed molecular dynamics simulations on the microsecond timescale to examine the supramolecular pore structure of a melittin tetramer in zwitterionic and partially anionic membranes. We now extend that study to include the effects of peptide charge, initial orientation, and number of monomers on the pore formation and stabilization processes. Our results show that parallel transmembrane orientations of melittin and MelP5 are more consistent with experimental data. Whereas a MelP5 parallel hexamer forms a large stable pore during the 5-μs simulation time, a melittin hexamer and an octamer are not fully stable, with several monomers dissociating during the simulation time. Interaction-energy analysis shows that this difference in behavior between melittin and MelP5 is not due to stronger electrostatic repulsion between neighboring melittin peptides but to peptide-lipid interactions that disfavor the isolated MelP5 transmembrane monomer. The ability of melittin monomers to diffuse freely in the 1,2-dimyristoyl-SN-glycero-3-phosphocholine membrane leads to dynamic pores with varying molecularity.
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19
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Pandidan S, Mechler A. Nano-viscosimetry analysis of the membrane disrupting action of the bee venom peptide melittin. Sci Rep 2019; 9:10841. [PMID: 31346251 PMCID: PMC6658469 DOI: 10.1038/s41598-019-47325-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/10/2019] [Indexed: 12/30/2022] Open
Abstract
Melittin is one of the most studied α-helical cationic membrane disrupting peptides. It is the main component of bee venom, however it is considered an antimicrobial peptide for its ability to kill bacteria. Melittin is believed to act by opening large toroidal pores in the plasma membrane of the targeted cells/bacteria, although this is questioned by some authors. Little is known, however, about the molecular mechanism leading to this activity. In this study the mechanism of action of melittin was studied by dye leakage and quartz crystal microbalance fingerprinting analysis in biomimetic model membranes. The results revealed the existence of multiple stages in the membrane disrupting action with characteristic differences between different membrane types. In bacterial-mimetic (charged) lipid mixtures the viscoelastic fingerprints suggest a surface-acting mechanism, whereas in mammalian-mimetic (neutral) membranes melittin appears to penetrate the bilayer already at low concentrations. In domain-forming mixed membranes melittin shows a preference for the domain containing predominantly zwitterionic lipids. The results confirm membrane poration but are inconsistent with the insertion-to-toroidal pore pathway. Therefore hypotheses of the two membrane disrupting pathways were developed, describing the membrane disruption as either surface tension modulation leading to toroidal pore formation, or linear aggregation leading to fissure formation in the membrane.
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Affiliation(s)
- Sara Pandidan
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Adam Mechler
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia.
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20
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A Comparative Study on Interactions of Antimicrobial Peptides L- and D-phenylseptin with 1,2-dimyristoyl-sn-glycero-3-phosphocholine. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9132601] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
L-phenylseptin (L-Phes) and D-phenylseptin (D-Phes) are amphibian antimicrobial peptides isolated from the skin secretion of Hypsiboas punctatus. In the N-termini, L-Phes and D-Phes contain three consecutive phenylalanine residues, l-Phe-l-Phe-l-Phe and l-Phe-d-Phe-l-Phe, respectively. They are known to exhibit antimicrobial activity against Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, and Xanthomonas axonopodis pv. Glycines. However, their mechanism of action and the role of the D-amino acid residue have not been elucidated yet. In this study, the interactions of both peptides with 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) were investigated by means of quartz crystal microbalance, circular dichroism, vibrational circular dichroism, 31P solid-state NMR, and molecular dynamics simulation. Both peptides have similar binding constants to the DMPC lipid bilayers, in the order of 106 M−1, and form an α-helix structure in the DMPC lipid bilayers. Both the peptides induce similar changes in the dynamics of DMPC lipids. Thus, in spite of the difference in the conformations caused by the chirality at the N-terminus, the peptides showed similar behavior in the membrane-bound state, experimentally and computationally.
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21
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Buck ZN, Torres J, Miskowiec A, Mamontov E, Kaiser H, Hansen FY, Taub H, Tyagi M, Collins L, Herwig KW. Effect of melittin on water diffusion and membrane structure in DMPC lipid bilayers. ACTA ACUST UNITED AC 2018. [DOI: 10.1209/0295-5075/123/18002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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Polido G, Shi X, Xu D, Guo C, Thai R, Patterson JP, Gianneschi NC, Suchyna TM, Sachs F, Holland GP. Investigating the interaction of Grammostola rosea venom peptides and model lipid bilayers with solid-state NMR and electron microscopy techniques. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1861:151-160. [PMID: 30463698 DOI: 10.1016/j.bbamem.2018.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/19/2018] [Accepted: 08/07/2018] [Indexed: 10/28/2022]
Abstract
Spider venom contains a number of small peptides that can control the gating properties of a wide range of ion channels with high affinity and specificity. These ion channels are responsible for coordination and control of many bodily functions such as transducing signals into sensory functions, smooth muscle contractions as well as serving as sensors in volume regulation. Hence, these peptides have been the topic of many research efforts in hopes that they can be used as biomedical therapeutics. Several peptides are known to control the gating properties of ion channels by involving the lipid membrane. GsMTx4, originally isolated from the Chilean Rose tarantula (Grammostola rosea), is known to selectively inhibit mechanosensitive ion channels by partitioning into the lipid bilayer. To further understand this indirect gating mechanism, we investigated the interactions between native GsAF2, VsTx1 and a synthetic form of GsMTx4 with model DMPC lipid bilayers using 31P solid-state NMR, 13C CP-MAS NMR, NS-TEM and cryo-TEM. The results reveal that these inhibitor cystine knot peptides perforate the DMPC lipid vesicles similarly with some subtle differences and ultimately create small spherical vesicles and anisotropic cylindrical and discoidal vesicles at concentrations near 1.0-1.5 mol% peptide. The anisotropic components align with their long axes along the NMR static B0 magnetic field, a property that should be useful in future NMR structural investigations of these systems. These findings move us forward in our understanding of how these peptides bind and interact with the lipid bilayer.
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Affiliation(s)
- Geraldine Polido
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA
| | - Xiangyan Shi
- Department of Chemistry and Biochemistry, Magnetic Resonance Research Center, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Dian Xu
- Department of Chemistry and Biochemistry, Magnetic Resonance Research Center, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Chengchen Guo
- Department of Chemistry and Biochemistry, Magnetic Resonance Research Center, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Rich Thai
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA
| | - Joseph P Patterson
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA
| | - Nathan C Gianneschi
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA
| | - Thomas M Suchyna
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY, USA
| | - Frederick Sachs
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY, USA
| | - Gregory P Holland
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA.
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23
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Naito A, Matsumori N, Ramamoorthy A. Dynamic membrane interactions of antibacterial and antifungal biomolecules, and amyloid peptides, revealed by solid-state NMR spectroscopy. Biochim Biophys Acta Gen Subj 2018; 1862:307-323. [PMID: 28599848 PMCID: PMC6384124 DOI: 10.1016/j.bbagen.2017.06.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 05/28/2017] [Accepted: 06/02/2017] [Indexed: 12/12/2022]
Abstract
A variety of biomolecules acting on the cell membrane folds into a biologically active structure in the membrane environment. It is, therefore, important to determine the structures and dynamics of such biomolecules in a membrane environment. While several biophysical techniques are used to obtain low-resolution information, solid-state NMR spectroscopy is one of the most powerful means for determining the structure and dynamics of membrane bound biomolecules such as antibacterial biomolecules and amyloidogenic proteins; unlike X-ray crystallography and solution NMR spectroscopy, applications of solid-state NMR spectroscopy are not limited by non-crystalline, non-soluble nature or molecular size of membrane-associated biomolecules. This review article focuses on the applications of solid-state NMR techniques to study a few selected antibacterial and amyloid peptides. Solid-state NMR studies revealing the membrane inserted bent α-helical structure associated with the hemolytic activity of bee venom melittin and the chemical shift oscillation analysis used to determine the transmembrane structure (with α-helix and 310-helix in the N- and C-termini, respectively) of antibiotic peptide alamethicin are discussed in detail. Oligomerization of an amyloidogenic islet amyloid polypeptide (IAPP, or also known as amylin) resulting from its aggregation in a membrane environment, molecular interactions of the antifungal natural product amphotericin B with ergosterol in lipid bilayers, and the mechanism of lipid raft formation by sphingomyelin studied using solid state NMR methods are also discussed in this review article. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Akira Naito
- Graduate School of Engineering, Yokohama National University, Yokohama 240-8501, Japan.
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109-1055, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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24
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Gomes B, Augusto MT, Felício MR, Hollmann A, Franco OL, Gonçalves S, Santos NC. Designing improved active peptides for therapeutic approaches against infectious diseases. Biotechnol Adv 2018; 36:415-429. [PMID: 29330093 DOI: 10.1016/j.biotechadv.2018.01.004] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 12/13/2017] [Accepted: 01/06/2018] [Indexed: 12/25/2022]
Abstract
Infectious diseases are one of the main causes of human morbidity and mortality. In the last few decades, pathogenic microorganisms' resistance to conventional drugs has been increasing, and it is now pinpointed as a major worldwide health concern. The need to search for new therapeutic options, as well as improved treatment outcomes, has therefore increased significantly, with biologically active peptides representing a new alternative. A substantial research effort is being dedicated towards their development, especially due to improved biocompatibility and target selectivity. However, the inherent limitations of peptide drugs are restricting their application. In this review, we summarize the current status of peptide drug development, focusing on antiviral and antimicrobial peptide activities, highlighting the design improvements needed, and those already being used, to overcome the drawbacks of the therapeutic application of biologically active peptides.
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Affiliation(s)
- Bárbara Gomes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Marcelo T Augusto
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Mário R Felício
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Axel Hollmann
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal; Laboratory of Molecular Microbiology, Institute of Basic and Applied Microbiology, National University of Quilmes, Bernal, Buenos Aires, Argentina; Laboratory of Biointerfaces and Biomimetic Systems, CITSE, National University of Santiago del Estero-CONICET, Santiago del Estero, Argentina
| | - Octávio L Franco
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, DF, Brazil; S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Sónia Gonçalves
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal.
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25
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Norisada K, Javkhlantugs N, Mishima D, Kawamura I, Saitô H, Ueda K, Naito A. Dynamic Structure and Orientation of Melittin Bound to Acidic Lipid Bilayers, As Revealed by Solid-State NMR and Molecular Dynamics Simulation. J Phys Chem B 2017; 121:1802-1811. [DOI: 10.1021/acs.jpcb.6b11207] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kazushi Norisada
- Graduate
School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Namsrai Javkhlantugs
- Graduate
School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
- School
of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia
| | - Daisuke Mishima
- Graduate
School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Izuru Kawamura
- Graduate
School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Hazime Saitô
- Department
of Life Science, University of Hyogo, Harima Science Garden City, Kamigori, Hyogo 678-1297, Japan
| | - Kazuyoshi Ueda
- Graduate
School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Akira Naito
- Graduate
School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
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26
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Characterization of antimicrobial activity against Listeria and cytotoxicity of native melittin and its mutant variants. Colloids Surf B Biointerfaces 2016; 143:194-205. [PMID: 27011349 DOI: 10.1016/j.colsurfb.2016.03.037] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 03/10/2016] [Accepted: 03/13/2016] [Indexed: 01/30/2023]
Abstract
Antimicrobial peptides (AMPs) are relatively short peptides that have the ability to penetrate the cell membrane, form pores leading to cell death. This study compares both antimicrobial activity and cytotoxicity of native melittin and its two mutants, namely, melittin I17K (GIGAVLKVLTTGLPALKSWIKRKRQQ) with a higher charge and lower hydrophobicity and mutant G1I (IIGAVLKVLTTGLPALISWIKRKRQQ) of higher hydrophobicity. The antimicrobial activity against different strains of Listeria was investigated by bioassay, viability studies, fluorescence and transmission electron microscopy. Cytotoxicity was examined by lactate dehydrogenase (LDH) assay on mammalian Caco-2 cells. The minimum inhibitory concentration of native, mutant I17K, mutant G1I against Listeria monocytogenes F4244 was 0.315±0.008, 0.814±0.006 and 0.494±0.037μg/ml respectively, whereas the minimum bactericidal concentration values were 3.263±0.0034, 7.412±0.017 and 5.366±0.019μg/ml respectively. Lag time for inactivation of L. monocytogenes F4244 was observed at concentrations below 0.20 and 0.78μg/ml for native and mutant melittin I17K respectively. The antimicrobial activity against L. monocytogenes F4244 was in the order native>G1I>I17K. Native melittin was cytotoxic to mammalian Caco-2 cells above concentration of 2μg/ml, whereas the two mutants exhibited negligible cytotoxicity up to a concentration of 8μg/ml. Pore formation in cell wall/membrane was observed by transmission electron microscopy. Molecular dynamics (MD) simulation of native and its mutants indicated that (i) surface native melittin and G1I exhibited higher tendency to penetrate a mimic of bacterial cell membrane and (ii) transmembrane native and I17K formed water channel in mimics of bacterial and mammalian cell membranes.
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27
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Leveritt JM, Pino-Angeles A, Lazaridis T. The structure of a melittin-stabilized pore. Biophys J 2016; 108:2424-2426. [PMID: 25992720 DOI: 10.1016/j.bpj.2015.04.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 04/07/2015] [Accepted: 04/09/2015] [Indexed: 11/30/2022] Open
Abstract
Melittin has been reported to form toroidal pores under certain conditions, but the atomic-resolution structure of these pores is unknown. A 9-μs all-atom molecular-dynamics simulation starting from a closely packed transmembrane melittin tetramer in DMPC shows formation of a toroidal pore after 1 μs. The pore remains stable with a roughly constant radius for the rest of the simulation. Surprisingly, one or two melittin monomers frequently transition between transmembrane and surface states. All four peptides are largely helical. A simulation in a DMPC/DMPG membrane did not lead to a stable pore, consistent with the experimentally observed lower activity of melittin on anionic membranes. The picture that emerges from this work is rather close to the classical toroidal pore, but more dynamic with respect to the configuration of the peptides.
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Affiliation(s)
- John M Leveritt
- Department of Chemistry, The City College of New York, New York, New York
| | | | - Themis Lazaridis
- Department of Chemistry, The City College of New York, New York, New York.
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28
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Nagao T, Mishima D, Javkhlantugs N, Wang J, Ishioka D, Yokota K, Norisada K, Kawamura I, Ueda K, Naito A. Structure and orientation of antibiotic peptide alamethicin in phospholipid bilayers as revealed by chemical shift oscillation analysis of solid state nuclear magnetic resonance and molecular dynamics simulation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2789-98. [PMID: 26248014 DOI: 10.1016/j.bbamem.2015.07.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/01/2015] [Accepted: 07/31/2015] [Indexed: 11/26/2022]
Abstract
The structure, topology and orientation of membrane-bound antibiotic alamethicin were studied using solid state nuclear magnetic resonance (NMR) spectroscopy. (13)C chemical shift interaction was observed in [1-(13)C]-labeled alamethicin. The isotropic chemical shift values indicated that alamethicin forms a helical structure in the entire region. The chemical shift anisotropy of the carbonyl carbon of isotopically labeled alamethicin was also analyzed with the assumption that alamethicin molecules rotate rapidly about the bilayer normal of the phospholipid bilayers. It is considered that the adjacent peptide planes form an angle of 100° or 120° when it forms α-helix or 310-helix, respectively. These properties lead to an oscillation of the chemical shift anisotropy with respect to the phase angle of the peptide plane. Anisotropic data were acquired for the 4 and 7 sites of the N- and C-termini, respectively. The results indicated that the helical axes for the N- and C-termini were tilted 17° and 32° to the bilayer normal, respectively. The chemical shift oscillation curves indicate that the N- and C-termini form the α-helix and 310-helix, respectively. The C-terminal 310-helix of alamethicin in the bilayer was experimentally observed and the unique bending structure of alamethicin was further confirmed by measuring the internuclear distances of [1-(13)C] and [(15)N] doubly-labeled alamethicin. Molecular dynamics simulation of alamethicin embedded into dimyristoyl phophatidylcholine (DMPC) bilayers indicates that the helical axes for α-helical N- and 310-helical C-termini are tilted 12° and 32° to the bilayer normal, respectively, which is in good agreement with the solid state NMR results.
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Affiliation(s)
- Takashi Nagao
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Daisuke Mishima
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Namsrai Javkhlantugs
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan; Center for Nanoscience and Nanotechnology, School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia
| | - Jun Wang
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Daisuke Ishioka
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Kiyonobu Yokota
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Kazushi Norisada
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Izuru Kawamura
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Kazuyoshi Ueda
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Akira Naito
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan.
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29
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Ashworth Briggs EL, Gomes RGB, Elhussein M, Collier W, Findlow IS, Khalid S, McCormick CJ, Williamson PTF. Interaction between the NS4B amphipathic helix, AH2, and charged lipid headgroups alters membrane morphology and AH2 oligomeric state--Implications for the Hepatitis C virus life cycle. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1671-7. [PMID: 25944559 PMCID: PMC4768108 DOI: 10.1016/j.bbamem.2015.04.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 02/27/2015] [Accepted: 04/25/2015] [Indexed: 01/27/2023]
Abstract
The non-structural protein 4B (NS4B) from Hepatitis C virus (HCV) plays a pivotal role in the remodelling of the host cell's membranes, required for the formation of the viral replication complex where genome synthesis occurs. NS4B is an integral membrane protein that possesses a number of domains vital for viral replication. Structural and biophysical studies have revealed that one of these, the second amphipathic N-terminal helix (AH2), plays a key role in these remodelling events. However, there is still limited understanding of the mechanism through which AH2 promotes these changes. Here we report on solid-state NMR and molecular dynamics studies that demonstrate that AH2 promotes the clustering of negatively charged lipids within the bilayer, a process that reduces the strain within the bilayer facilitating the remodelling of the lipid bilayer. Furthermore, the presence of negatively charged lipids within the bilayer appears to promote the disassociation of AH2 oligomers, highlighting a potential role for lipid recruitment in regulating NS protein interactions. Changes in membrane morphology studied by 2H and 31P Solid-state NMR. Bilayer charge influences the oligomeric state of the amphipathic helix AH2 from NS4B. Interaction of AH2 with charged lipid membranes reduces strain within bilayer. AH2 from NS4B is involved in membrane remodelling and membranous web formation. Lipid bilayer/NS4B interactions may regulate Hepatitis C virus lifecycle.
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Affiliation(s)
- Esther L Ashworth Briggs
- Centre for Biological Sciences/Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Rafael G B Gomes
- Centre for Biological Sciences/Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK; School of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Malaz Elhussein
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
| | - William Collier
- Centre for Biological Sciences/Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - I Stuart Findlow
- Centre for Biological Sciences/Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
| | - Chris J McCormick
- School of Medicine, University of Southampton, Southampton SO16 6YD, UK.
| | - Philip T F Williamson
- Centre for Biological Sciences/Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK.
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30
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Strandberg E, Ulrich AS. AMPs and OMPs: Is the folding and bilayer insertion of β-stranded outer membrane proteins governed by the same biophysical principles as for α-helical antimicrobial peptides? BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1944-54. [PMID: 25726906 DOI: 10.1016/j.bbamem.2015.02.019] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/13/2015] [Accepted: 02/18/2015] [Indexed: 11/24/2022]
Abstract
The folding and function of membrane proteins is controlled not only by specific but also by unspecific interactions with the constituent lipids. In this review, we focus on the influence of the spontaneous lipid curvature on the folding and insertion of peptides and proteins in membranes. Amphiphilic α-helical peptides, as represented by various antimicrobial sequences, are compared with β-barrel proteins, which are found in the outer membrane of Gram-negative bacteria. It has been shown that cationic amphiphilic peptides are always surface-bound in lipids with a negative spontaneous curvature like POPC, i.e. they are oriented parallel to the membrane plane. On the other hand, in lipids like DMPC with a positive curvature, these peptides can get tilted or completely inserted in a transmembrane state. Remarkably, the folding and spontaneous membrane insertion of β-barrel outer membrane proteins also proceeds more easily in lipids with a positive intrinsic curvature, while it is hampered by negative curvature. We therefore propose that a positive spontaneous curvature of the lipids promotes the ability of a surface-bound molecule to insert more deeply into the bilayer core, irrespective of the conformation, size, or shape of the peptide, protein, or folding intermediate. This article is part of a Special Issue entitled: Lipid-protein interactions.
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Affiliation(s)
- Erik Strandberg
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O.B. 3640, 76021 Karlsruhe, Germany
| | - Anne S Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O.B. 3640, 76021 Karlsruhe, Germany; KIT, Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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31
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Li W, Tailhades J, O'Brien-Simpson NM, Separovic F, Otvos L, Hossain MA, Wade JD. Proline-rich antimicrobial peptides: potential therapeutics against antibiotic-resistant bacteria. Amino Acids 2014; 46:2287-94. [PMID: 25141976 DOI: 10.1007/s00726-014-1820-1] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 07/28/2014] [Indexed: 02/06/2023]
Abstract
The increasing resistance of pathogens to antibiotics causes a huge clinical burden that places great demands on academic researchers and the pharmaceutical industry for resolution. Antimicrobial peptides, part of native host defense, have emerged as novel potential antibiotic alternatives. Among the different classes of antimicrobial peptides, proline-rich antimicrobial peptides, predominantly sourced from insects, have been extensively investigated to study their specific modes of action. In this review, we focus on recent developments in these peptides. They show a variety of modes of actions, including mechanism shift at high concentration, non-lytic mechanisms, as well as possessing different intracellular targets and lipopolysaccharide binding activity. Furthermore, proline-rich antimicrobial peptides display the ability to not only modulate the immune system via cytokine activity or angiogenesis but also possess properties of penetrating cell membranes and crossing the blood brain barrier suggesting a role as potential novel carriers. Ongoing studies of these peptides will likely lead to the development of more potent antimicrobial peptides that may serve as important additions to the armoury of agents against bacterial infection and drug delivery.
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Affiliation(s)
- Wenyi Li
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, 3010, Australia
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32
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Antimicrobial properties and membrane-active mechanism of a potential α-helical antimicrobial derived from cathelicidin PMAP-36. PLoS One 2014; 9:e86364. [PMID: 24466055 PMCID: PMC3897731 DOI: 10.1371/journal.pone.0086364] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 12/08/2013] [Indexed: 12/31/2022] Open
Abstract
Antimicrobial peptides (AMPs), which present in the non-specific immune system of organism, are amongst the most promising candidates for the development of novel antimicrobials. The modification of naturally occurring AMPs based on their residue composition and distribution is a simple and effective strategy for optimization of known AMPs. In this study, a series of truncated and residue-substituted derivatives of antimicrobial peptide PMAP-36 were designed and synthesized. The 24-residue truncated peptide, GI24, displayed antimicrobial activity comparable to the mother peptide PMAP-36 with MICs ranging from 1 to 4 µM, which is lower than the MICs of bee venom melittin. Although GI24 displayed high antimicrobial activity, its hemolytic activity was much lower than melittin, suggesting that GI24 have optimal cell selectivity. In addition, the crucial site of GI24 was identified through single site-mutation. An amino acid with high hydrophobicity at position 23 played an important role in guaranteeing the high antimicrobial activity of GI24. Then, lipid vesicles and whole bacteria were employed to investigate the membrane-active mechanisms. Membrane-simulating experiments showed that GI24 interacted strongly with negatively charged phospholipids and weakly with zwitterionic phospholipids, which corresponded well with the data of its biological activities. Membrane permeabilization and flow cytometry provide the evidence that GI24 killed microbial cells by permeabilizing the cell membrane and damaging membrane integrity. GI24 resulted in greater cell morphological changes and visible pores on cell membrane as determined using scanning electron microscopy (SEM) and transmission electron microscope (TEM). Taken together, the peptide GI24 may provide a promising antimicrobial agent for therapeutic applications against the frequently-encountered bacteria.
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33
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Burton MG, Huang QM, Hossain MA, Wade JD, Clayton AHA, Gee ML. Long-time-scale interaction dynamics between a model antimicrobial peptide and giant unilamellar vesicles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:14613-14621. [PMID: 24168523 DOI: 10.1021/la403083m] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The interaction dynamics between a lytic peptide and a biomembrane was studied using time-lapse fluorescence lifetime imaging microscopy. The model membrane was 1,2-dipalmitoyl-sn-glycero-3-phosphochloine giant unilamellar vesicles (GUVs), and the peptide was the K14 derivative of melittin, to which the polarity-sensitive fluorescent probe AlexaFluor 430 was grafted. The interaction of the peptide with the GUVs resulted in a progressive quenching of the fluorescence lifetime over a period of minutes. From previous photophysics characterization of the peptide, we were able to deconvolve the contribution of three distinct peptide states to the lifetime trajectory and use this data to develop a kinetics model for the interaction process. It was found that the peptide-membrane interaction was well described by a two-step mechanism: peptide monomer adsorption followed by membrane surface migration, assembly, and insertion to form membrane pores. There was an equilibrium exchange between pore and surface monomers at all lipid/peptide (L/P) concentration ratios, suggesting that the fully inserted phase was reached, even at low peptide concentrations. In contrast to previous studies, there was no evidence of critical behavior; irrespective of L/P ratio, lytic pores were the dominant peptide state at equilibrium and were formed even at very low peptide concentrations. We suggest that this behavior is seen in GUVs because their low curvature means low Laplace pressure. Membrane elasticity is therefore relatively ineffective at damping the thermal fluctuations of lipid molecules that lead to random molecular-level lipid protrusions and membrane undulations. The transient local membrane deformations that result from these thermal fluctuations create the conditions necessary for facile peptide insertion.
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Affiliation(s)
- Matthew G Burton
- School of Chemistry and ‡Florey Department of Neuroscience and Mental Health, Centre for Neuroscience Research Chemistry, University of Melbourne , Parkville, Victoria 3010, Australia
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34
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Irudayam SJ, Pobandt T, Berkowitz ML. Free Energy Barrier for Melittin Reorientation from a Membrane-Bound State to a Transmembrane State. J Phys Chem B 2013; 117:13457-63. [DOI: 10.1021/jp406328d] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Sheeba J. Irudayam
- Department
of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599 United States
| | - Tobias Pobandt
- Max Planck Institute of Colloids, Interfaces, Theory, Bio-Systems, Potsdam, D-14424 Germany
| | - Max L. Berkowitz
- Department
of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599 United States
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35
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Khatun UL, Mukhopadhyay C. Interaction of bee venom toxin melittin with ganglioside GM1 bicelle. Biophys Chem 2013; 180-181:66-75. [DOI: 10.1016/j.bpc.2013.06.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 06/14/2013] [Accepted: 06/17/2013] [Indexed: 12/11/2022]
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36
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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: 63] [Impact Index Per Article: 5.7] [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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37
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Ueno R, Yao H. On the surface structure of 1,3-dithiol-protected gold nanoparticles interpreted by the size effect of IR absorption properties. Colloids Surf A Physicochem Eng Asp 2013. [DOI: 10.1016/j.colsurfa.2013.03.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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38
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Multiple membrane interactions and versatile vesicle deformations elicited by melittin. Toxins (Basel) 2013; 5:637-64. [PMID: 23594437 PMCID: PMC3705284 DOI: 10.3390/toxins5040637] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 04/02/2013] [Accepted: 04/10/2013] [Indexed: 01/11/2023] Open
Abstract
Melittin induces various reactions in membranes and has been widely studied as a model for membrane-interacting peptide; however, the mechanism whereby melittin elicits its effects remains unclear. Here, we observed melittin-induced changes in individual giant liposomes using direct real-time imaging by dark-field optical microscopy, and the mechanisms involved were correlated with results obtained using circular dichroism, cosedimentation, fluorescence quenching of tryptophan residues, and electron microscopy. Depending on the concentration of negatively charged phospholipids in the membrane and the molecular ratio between lipid and melittin, melittin induced the “increasing membrane area”, “phased shrinkage”, or “solubilization” of liposomes. In phased shrinkage, liposomes formed small particles on their surface and rapidly decreased in size. Under conditions in which the increasing membrane area, phased shrinkage, or solubilization were mainly observed, the secondary structure of melittin was primarily estimated as an α-helix, β-like, or disordered structure, respectively. When the increasing membrane area or phased shrinkage occurred, almost all melittin was bound to the membranes and reached more hydrophobic regions of the membranes than when solubilization occurred. These results indicate that the various effects of melittin result from its ability to adopt various structures and membrane-binding states depending on the conditions.
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39
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Tsutsumi A, Javkhlantugs N, Kira A, Umeyama M, Kawamura I, Nishimura K, Ueda K, Naito A. Structure and orientation of bovine lactoferrampin in the mimetic bacterial membrane as revealed by solid-state NMR and molecular dynamics simulation. Biophys J 2012; 103:1735-43. [PMID: 23083717 DOI: 10.1016/j.bpj.2012.09.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 09/05/2012] [Accepted: 09/10/2012] [Indexed: 10/27/2022] Open
Abstract
Bovine lactoferrampin (LFampinB) is a newly discovered antimicrobial peptide found in the N1-domain of bovine lactoferrin (268-284), and consists of 17 amino-acid residues. It is important to determine the orientation and structure of LFampinB in bacterial membranes to reveal the antimicrobial mechanism. We therefore performed (13)C and (31)P NMR, (13)C-(31)P rotational echo double resonance (REDOR), potassium ion-selective electrode, and quartz-crystal microbalance measurements for LFampinB with mimetic bacterial membrane and molecular-dynamics simulation in acidic membrane. (31)P NMR results indicated that LFampinB caused a defect in mimetic bacterial membranes. Ion-selective electrode measurements showed that ion leakage occurred for the mimetic bacterial membrane containing cardiolipin. Quartz-crystal microbalance measurements revealed that LFampinB had greater affinity to acidic phospholipids than that to neutral phospholipids. (13)C DD-MAS and static NMR spectra showed that LFampinB formed an α-helix in the N-terminus region and tilted 45° to the bilayer normal. REDOR dephasing patterns between carbonyl carbon nucleus in LFampinB and phosphorus nuclei in lipid phosphate groups were measured by (13)C-(31)P REDOR and the results revealed that LFampinB is located in the interfacial region of the membrane. Molecular-dynamics simulation showed the tilt angle to be 42° and the rotation angle to be 92.5° for Leu(3), which are in excellent agreement with the experimental values.
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Affiliation(s)
- Atsushi Tsutsumi
- Graduate School of Engineering, Yokohama National University, Yokohama, Kanagawa, Japan
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40
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Irudayam SJ, Berkowitz ML. Binding and reorientation of melittin in a POPC bilayer: computer simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2975-81. [PMID: 22877705 DOI: 10.1016/j.bbamem.2012.07.026] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 07/26/2012] [Accepted: 07/27/2012] [Indexed: 11/26/2022]
Abstract
We performed, using an all-atom force field, molecular dynamics computer simulations to study the binding of melittin to the POPC bilayer and its subsequent reorientation in this bilayer. The binding process involves a simultaneous folding and adsorption of the peptide to the bilayer, followed by the creation of a "U shaped" conformation. The reorientation of melittin from the parallel to the perpendicular conformation requires charged residues to cross the hydrophobic core of the bilayer. This is accomplished by a creation of defects in the bilayer that are filled out with water. The defects are caused by peptide charged residues dragging the lipid headgroup atoms along with them, as they reorient. With increased concentration of melittin water defects form stable pores; this makes it easier for the peptide N-terminus to reorient. Our results complement experimental and computational observations of the melittin/lipid bilayer interaction.
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Affiliation(s)
- Sheeba J Irudayam
- Department of Chemistry, University of North Carolina at Chapel Hill, North Carolina, NC 27599, USA.
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41
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Kokot G, Mally M, Svetina S. The dynamics of melittin-induced membrane permeability. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2012; 41:461-74. [DOI: 10.1007/s00249-012-0800-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 02/24/2012] [Accepted: 03/06/2012] [Indexed: 10/28/2022]
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42
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Javkhlantugs N, Naito A, Ueda K. Molecular dynamics simulation of Bombolitin II in the dipalmitoylphosphatidylcholine membrane bilayer. Biophys J 2011; 101:1212-20. [PMID: 21889459 DOI: 10.1016/j.bpj.2011.07.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Revised: 06/15/2011] [Accepted: 07/12/2011] [Indexed: 11/29/2022] Open
Abstract
The orientation behavior of Bombolitin II (BLT2) in the dipalmitoylphosphatidylcholine membrane bilayer was investigated by using molecular-dynamics simulation. During the 20-ns simulation, the BLT2 began to tilt and finally reached the angle of 51° from the membrane-normal. The structure of the peptide formed the amphipathic α-helical structure during the entire simulation time. The peptide tilts with its hydrophobic side faced to the hydrophobic core of the bilayer. We analyzed the mechanism of the tilting behavior of the peptide associated with the membrane in detail. The analysis showed that the hydrogen-bond interaction and the electrostatic interaction were found to exist between Lys(12) and a lipid molecule. These interactions are considered to work as an important factor in tilting the peptide to the membrane-normal.
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43
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Lin CH, Tzen JTC, Shyu CL, Yang MJ, Tu WC. Structural and biological characterization of mastoparans in the venom of Vespa species in Taiwan. Peptides 2011; 32:2027-36. [PMID: 21884742 DOI: 10.1016/j.peptides.2011.08.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 08/15/2011] [Accepted: 08/15/2011] [Indexed: 11/30/2022]
Abstract
Mastoparans, a family of small peptides, are isolated from the wasp venom. In this study, six mastoparans were identified in the venom of six Vespa species in Taiwan. The precursors of these mastoparans are composed of N-terminal signal sequence, prosequence, mature mastoparan, and appendix glycine at C-terminus. These mature mastoparans all have characteristic features of linear cationic peptides rich in hydrophobic and basic amino acids without disulfide bond. Therefore, these peptides could be predicted to adopt an amphipathic α-helical secondary structure. In fact, the CD (circular dichroism) spectra of these peptides show a high content α-helical conformation in the presence of 8 mM SDS or 40% 2,2,2-trifluoroethanol (TFE). All mastoparans exhibit mast cell degranulation activity, antimicrobial activity against both Gram-positive and -negative bacteria tested, various degree of hemolytic activity on chicken, human, and sheep erythrocytes as well as membrane permeabilization on Escherichia coli BL21. Our results also show that the hemolytic activity of mastoparans is correlated to mean hydrophobicity and mean hydrophobic moment.
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Affiliation(s)
- Chun-Hsien Lin
- Department of Entomology, National Chung Hsing University, Taichung, Taiwan, ROC
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44
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Hall K, Lee TH, Aguilar MI. The role of electrostatic interactions in the membrane binding of melittin. J Mol Recognit 2011; 24:108-18. [PMID: 21194121 DOI: 10.1002/jmr.1032] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The binding of melittin and the C-terminally truncated analogue of melittin (21Q) to a range of phospholipid bilayers was studied using surface plasmon resonance (SPR). The phospholipid model membranes included zwitterionic dimyristylphosphatidylcholine (DMPC) and dimyristylphosphatidylethanolamine (DMPE), together with mixtures DMPC/dimyristylphosphatidylglycerol (DMPG), DMPC/DMPG/cholesterol and DMPE/DMPG. Melittin bound rapidly to all membrane mixtures, whereas 21Q, which has a reduced charge, bound much more slowly on the DMPC and DMPC/DMPG mixtures reflecting the role of the initial electrostatic interaction. The loss of the cationic residues also significantly decreased the binding of 21Q with DMPC/DMPG/Cholesterol, DMPE and DMPE/DMPG. The role of electrostatics was also highlighted with NaCl in the buffer, which affected the way melittin bound to the different membranes, causing a more uniform, concentration dependant increase in response. The biosensor results were correlated with the conformation of the peptides determined by circular dichroism analysis, which indicated that high α-helicity was associated with high binding affinity. Overall, the results demonstrate that the positively charged residues at the C-terminus of melittin play an essential role in membrane binding, that modulation of peptide charge influences selectivity of binding to different phospholipids and that manipulation of the cationic regions of antimicrobial peptides can be used to modulate membrane selectivity.
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Affiliation(s)
- Kristopher Hall
- Department of Biochemistry & Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
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45
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Butterfield SM, Lashuel HA. Amyloidogenic protein-membrane interactions: mechanistic insight from model systems. Angew Chem Int Ed Engl 2011; 49:5628-54. [PMID: 20623810 DOI: 10.1002/anie.200906670] [Citation(s) in RCA: 483] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The toxicity of amyloid-forming proteins is correlated with their interactions with cell membranes. Binding events between amyloidogenic proteins and membranes result in mutually disruptive structural perturbations, which are associated with toxicity. Membrane surfaces promote the conversion of amyloid-forming proteins into toxic aggregates, and amyloidogenic proteins, in turn, compromise the structural integrity of the cell membrane. Recent studies with artificial model membranes have highlighted the striking resemblance of the mechanisms of membrane permeabilization of amyloid-forming proteins to those of pore-forming toxins and antimicrobial peptides.
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Affiliation(s)
- Sara M Butterfield
- Laboratory of Molecular Neurobiology and Neuroproteomics, Swiss Federal Institute of Technology Lausanne (EPFL), SV-BMI-LMNN AI2351, 1015 Lausanne, Switzerland
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46
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Florance HV, Stopford AP, Kalapothakis JM, McCullough BJ, Bretherick A, Barran PE. Evidence for α-helices in the gas phase: A case study using Melittin from honey bee venom. Analyst 2011; 136:3446-52. [DOI: 10.1039/c1an15291b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Toraya S, Javkhlantugs N, Mishima D, Nishimura K, Ueda K, Naito A. Dynamic structure of bombolitin II bound to lipid bilayers as revealed by solid-state NMR and molecular-dynamics simulation. Biophys J 2010; 99:3282-9. [PMID: 21081076 PMCID: PMC2980745 DOI: 10.1016/j.bpj.2010.09.060] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2010] [Revised: 09/15/2010] [Accepted: 09/20/2010] [Indexed: 01/19/2023] Open
Abstract
Bombolitin II (BLT2) is one of the hemolytic heptadecapeptides originally isolated from the venom of a bumblebee. Structure and orientation of BLT2 bound to 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) membranes were determined by solid-state (31)P and (13)C NMR spectroscopy. (31)P NMR spectra showed that BLT2-DPPC membranes were disrupted into small particles below the gel-to-liquid crystalline phase transition temperature (T(c)) and fused to form a magnetically oriented vesicle system where the membrane surface is parallel to the magnetic fields above the T(c). (13)C NMR spectra of site-specifically (13)C-labeled BLT2 at the carbonyl carbons were observed and the chemical shift anisotropies were analyzed to determine the dynamic structure of BLT2 bound to the magnetically oriented vesicle system. It was revealed that the membrane-bound BLT2 adopted an α-helical structure, rotating around the membrane normal with the tilt angle of the helical axis at 33°. Interatomic distances obtained from rotational-echo double-resonance experiments further showed that BLT2 adopted a straight α-helical structure. Molecular dynamics simulation performed in the BLT2-DPPC membrane system showed that the BLT2 formed a straight α-helix and that the C-terminus was inserted into the membrane. The α-helical axis is tilted 30° to the membrane normal, which is almost the same as the value obtained from solid-state NMR. These results suggest that the membrane disruption induced by BLT2 is attributed to insertion of BLT2 into the lipid bilayers.
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Affiliation(s)
- Shuichi Toraya
- Faculty of Engineering, Yokohama National University, Yokohama, Japan
| | | | - Daisuke Mishima
- Faculty of Engineering, Yokohama National University, Yokohama, Japan
| | | | - Kazuyoshi Ueda
- Faculty of Engineering, Yokohama National University, Yokohama, Japan
| | - Akira Naito
- Faculty of Engineering, Yokohama National University, Yokohama, Japan
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Saitô H, Ando I, Ramamoorthy A. Chemical shift tensor - the heart of NMR: Insights into biological aspects of proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 57:181-228. [PMID: 20633363 PMCID: PMC2905606 DOI: 10.1016/j.pnmrs.2010.04.005] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 04/26/2010] [Indexed: 05/19/2023]
Affiliation(s)
- Hazime Saitô
- Department of Life Science, Himeji Institute of Technology, University of Hyogo, Kamigori, Hyog, 678-1297, Japan
| | - Isao Ando
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, 152-0033, Japan
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA
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Butterfield S, Lashuel H. Wechselwirkungen zwischen amyloidogenen Proteinen und Membranen: Modellsysteme liefern mechanistische Einblicke. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906670] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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50
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Liu Z, Zhou Q, Mao X, Zheng X, Guo J, Zhang F, Wen T, Pang H. Crystallization and preliminary X-ray analysis of cecropin B from Bombyx mori. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:851-3. [PMID: 20606290 PMCID: PMC2898478 DOI: 10.1107/s1744309110020130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 05/27/2010] [Indexed: 11/10/2022]
Abstract
Cecropin B is a 37-residue cationic antimicrobial peptide derived from the haemolymph of Bombyx mori. The precise mechanism by which cecropins exert their antimicrobial and cytolytic activities is not well understood. Crystals of cecropin B were obtained by the hanging-drop vapour-diffusion method using polyethylene glycol as a precipitant at 289 K. The crystal diffracted to 1.43 A resolution using X-ray radiation and belonged to the orthorhombic space group P1, with unit-cell parameters a = 15.08, b = 22.75, c = 30.20 A, alpha = 96.9, beta = 103.1, gamma = 96.5 degrees. The asymmetric unit contained only one molecule of cecropin B, with a calculated Matthews coefficient of 2.48 A(3) Da(-1) and a solvent content of 50.4%.
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Affiliation(s)
- Zhongyuan Liu
- School of Medicine, Tsinghua University, Hai’dian District, Beijing 100084, People’s Republic of China
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, Xinjiang University, Urumqi 830046, People’s Republic of China
| | - Qiangjun Zhou
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Xinfang Mao
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, Xinjiang University, Urumqi 830046, People’s Republic of China
| | - Xiangdong Zheng
- School of Medicine, Tsinghua University, Hai’dian District, Beijing 100084, People’s Republic of China
| | - Jiubiao Guo
- School of Medicine, Tsinghua University, Hai’dian District, Beijing 100084, People’s Republic of China
| | - Fuchun Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, Xinjiang University, Urumqi 830046, People’s Republic of China
| | - Tingyi Wen
- Department of Industrial Microbiology and Biotechnology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Hai Pang
- School of Medicine, Tsinghua University, Hai’dian District, Beijing 100084, People’s Republic of China
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