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Peng Z, Iwabuchi S, Izumi K, Takiguchi S, Yamaji M, Fujita S, Suzuki H, Kambara F, Fukasawa G, Cooney A, Di Michele L, Elani Y, Matsuura T, Kawano R. Lipid vesicle-based molecular robots. LAB ON A CHIP 2024; 24:996-1029. [PMID: 38239102 PMCID: PMC10898420 DOI: 10.1039/d3lc00860f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
A molecular robot, which is a system comprised of one or more molecular machines and computers, can execute sophisticated tasks in many fields that span from nanomedicine to green nanotechnology. The core parts of molecular robots are fairly consistent from system to system and always include (i) a body to encapsulate molecular machines, (ii) sensors to capture signals, (iii) computers to make decisions, and (iv) actuators to perform tasks. This review aims to provide an overview of approaches and considerations to develop molecular robots. We first introduce the basic technologies required for constructing the core parts of molecular robots, describe the recent progress towards achieving higher functionality, and subsequently discuss the current challenges and outlook. We also highlight the applications of molecular robots in sensing biomarkers, signal communications with living cells, and conversion of energy. Although molecular robots are still in their infancy, they will unquestionably initiate massive change in biomedical and environmental technology in the not too distant future.
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Affiliation(s)
- Zugui Peng
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Shoji Iwabuchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Kayano Izumi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Sotaro Takiguchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Misa Yamaji
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Shoko Fujita
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Harune Suzuki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Fumika Kambara
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Genki Fukasawa
- School of Life Science and Technology, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan
| | - Aileen Cooney
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Lorenzo Di Michele
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- FabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Yuval Elani
- Department of Chemical Engineering, Imperial College London, South Kensington, London SW7 2AZ, UK
- FabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Tomoaki Matsuura
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
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Salnikov E, Bechinger B. Effect of lipid saturation on the topology and oligomeric state of helical membrane polypeptides. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184001. [PMID: 35817122 DOI: 10.1016/j.bbamem.2022.184001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Natural liquid crystalline membranes are made up of many different lipids carrying a mixture of saturated and unsaturated fatty acyl chains. Whereas in the past considerable attention has been paid to cholesterol content, the phospholipid head groups and the membrane surface charge the detailed fatty acyl composition was often considered less important. However, recent investigations indicate that the detailed fatty acyl chain composition has pronounced effects on the oligomerization of the transmembrane helical anchoring domains of the MHC II receptor or the membrane alignment of the cationic antimicrobial peptide PGLa. In contrast the antimicrobial peptides magainin 2 and alamethicin are less susceptible to lipid saturation. Using histidine-rich LAH4 designer peptides the high energetic contributions of lipid saturation in stabilizing transmembrane helical alignments are quantitatively evaluated. These observations can have important implications for the biological regulation of membrane proteins and should be taken into considerations during biophysical or structural experiments.
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Affiliation(s)
- Evgeniy Salnikov
- University of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics and NMR, Strasbourg, France
| | - Burkhard Bechinger
- University of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics and NMR, Strasbourg, France; Institut Universitaire de France, France.
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3
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A Peptide from Budding Yeast GAPDH Serves as a Promising Antifungal against Cryptococcus neoformans. Microbiol Spectr 2022; 10:e0082621. [PMID: 35019693 PMCID: PMC8754130 DOI: 10.1128/spectrum.00826-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Infection of Cryptococcus neoformans is one of the leading causes of morbidity and mortality, particularly among immunocompromised patients. However, currently available drugs for the treatment of C. neoformans infection are minimal. Here, we report SP1, a peptide derived from glyceraldehyde-3-phosphate dehydrogenase (GAPDH) of Saccharomyces cerevisiae, efficiently kills C. neoformans and Cryptococcus gattii. SP1 causes damages to the capsule. Unlike many antimicrobial peptides, SP1 does not form pores on the cell membrane of C. neoformans. It interacts with membrane ergosterol and enters vacuole possibly through membrane trafficking. C. neoformans treated with SP1 show the apoptotic phenotypes such as imbalance of calcium ion homeostasis, reactive oxygen increment, phosphatidylserine exposure, and nuclear fragmentation. Our data imply that SP1 has the potential to be developed into a treatment option for cryptococcosis. IMPORTANCE Cryptococcus neoformans and Cryptococcus gattii can cause cryptococcosis, which has a high mortality rate. To treat the disease, amphotericin B and fluconazole are often used in clinic. However, amphotericin B has rather high renal toxicity, and tolerance to these drugs are quicky developed. The peptide SP1 derived from baker's yeast GAPDH shows antifungal function to kill Cryptococcus neoformans and Cryptococcus gattii efficiently with a high specificity, even for the drug-resistant strains. Our data demonstrate that SP1 induces the apoptosis-like death of Cryptococcus neoformans at low concentrations. The finding of this peptide may shed light on a new direction to treat cryptococcosis.
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Juhl DW, Glattard E, Aisenbrey C, Bechinger B. Antimicrobial peptides: mechanism of action and lipid-mediated synergistic interactions within membranes. Faraday Discuss 2021; 232:419-434. [PMID: 34533138 DOI: 10.1039/d0fd00041h] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Biophysical and structural studies of peptide-lipid interactions, peptide topology and dynamics have changed our view of how antimicrobial peptides insert and interact with membranes. Clearly, both peptides and lipids are highly dynamic, and change and mutually adapt their conformation, membrane penetration and detailed morphology on a local and a global level. As a consequence, peptides and lipids can form a wide variety of supramolecular assemblies in which the more hydrophobic sequences preferentially, but not exclusively, adopt transmembrane alignments and have the potential to form oligomeric structures similar to those suggested by the transmembrane helical bundle model. In contrast, charged amphipathic sequences tend to stay intercalated at the membrane interface. Although the membranes are soft and can adapt, at increasing peptide density they cause pronounced disruptions of the phospholipid fatty acyl packing. At even higher local or global concentrations the peptides cause transient membrane openings, rupture and ultimately lysis. Interestingly, mixtures of peptides such as magainin 2 and PGLa, which are stored and secreted naturally as a cocktail, exhibit considerably enhanced antimicrobial activities when investigated together in antimicrobial assays and also in pore forming experiments applied to biophysical model systems. Our most recent investigations reveal that these peptides do not form stable complexes but act by specific lipid-mediated interactions and the nanoscale properties of phospholipid bilayers.
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Affiliation(s)
- Dennis W Juhl
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, 4, rue Blaise Pascal, 67070 Strasbourg, France.
| | - Elise Glattard
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, 4, rue Blaise Pascal, 67070 Strasbourg, France.
| | - Christopher Aisenbrey
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, 4, rue Blaise Pascal, 67070 Strasbourg, France.
| | - Burkhard Bechinger
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, 4, rue Blaise Pascal, 67070 Strasbourg, France. .,Institut Universitaire de France, France
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5
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Birdsall ER, Petti MK, Saraswat V, Ostrander JS, Arnold MS, Zanni MT. Structure Changes of a Membrane Polypeptide under an Applied Voltage Observed with Surface-Enhanced 2D IR Spectroscopy. J Phys Chem Lett 2021; 12:1786-1792. [PMID: 33576633 PMCID: PMC8162810 DOI: 10.1021/acs.jpclett.0c03706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The structures of many membrane-bound proteins and polypeptides depend on the membrane potential. However, spectroscopically studying their structures under an applied field is challenging, because a potential is difficult to generate across more than a few bilayers. We study the voltage-dependent structures of the membrane-bound polypeptide, alamethicin, using a spectroelectrochemical cell coated with a rough, gold film to create surface plasmons. The plasmons sufficiently enhance the 2D IR signal to measure a single bilayer. The film is also thick enough to conduct current and thereby apply a potential. The 2D IR spectra resolve features from both 310- and α-helical structures and cross-peaks connecting the two. We observe changes in the peak intensity, not their frequencies, upon applying a voltage. A similar change occurs with pH, which is known to alter the angle of alamethicin relative to the surface normal. The spectra are modeled using a vibrational exciton Hamiltonian, and the voltage-dependent spectra are consistent with a change in angle of the 310- and α-helices in the membrane from 55 to 44°and from 31 to 60°, respectively. The 310- and α-helices are coupled by approximately 10 cm-1. These experiments provide new structural information about alamethicin under a potential difference and demonstrate a technique that might be applied to voltage-gated membrane proteins and compared to molecular dynamics structures.
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Affiliation(s)
- Erin R Birdsall
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Megan K Petti
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Vivek Saraswat
- Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua S Ostrander
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, Indiana Wesleyan University, Marion, Indiana 46953, United States
| | - Michael S Arnold
- Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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6
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Ivanova N, Ivanova A. Influence of the dimensionality of the periodic boundary conditions on the transport of a drug-peptide complex across model cell membranes. J Biomol Struct Dyn 2021; 40:5345-5356. [PMID: 33416039 DOI: 10.1080/07391102.2020.1870157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Many research efforts are devoted to improving the efficiency of chemotherapy. One of the aspects is to facilitate the transport of drugs across the cell membranes by attaching the therapeutics to a carrier molecule. The current study focuses on computational investigation of such a system with doxorubicin as the model drug, which is covalently bound to a cell-penetrating peptide. The correct description of its membrane translocation at the molecular level requires proper choice of the model membrane and of the simulation parameters. For the purpose, two phospholipid bilayers are built, one containing solely DPPC and another with mixed lipid content mimicking the composition of a human erythrocyte membrane. Atomistic molecular dynamics simulations are carried out in two types of periodic boundary conditions (2D and 3D PBC), in order to assess the effect of the periodicity dimensionality on the intermolecular interactions. The evolution of some basic characteristics of the bilayers and of the drug-peptide complex is tracked: mass density profiles, electrostatic potentials, lateral diffusion coefficients and areas per lipid, lipid-complex radial distribution functions, secondary structure of the peptide and orientation of the drug relative to the membrane. Thus, the influence of the periodic boundary conditions is quantified and it shows that the mixed system in 3D PBC is the most suitable for analysis of the translocation of the transporting moiety across cell membranes.
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Affiliation(s)
- Nikoleta Ivanova
- Department of Physical Chemistry, Laboratory of Quantum and Computational Chemistry, Faculty of Chemistry and Pharmacy, University of Sofia, Sofia, Bulgaria
| | - Anela Ivanova
- Department of Physical Chemistry, Laboratory of Quantum and Computational Chemistry, Faculty of Chemistry and Pharmacy, University of Sofia, Sofia, Bulgaria
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7
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Sancho-Vaello E, Gil-Carton D, François P, Bonetti EJ, Kreir M, Pothula KR, Kleinekathöfer U, Zeth K. The structure of the antimicrobial human cathelicidin LL-37 shows oligomerization and channel formation in the presence of membrane mimics. Sci Rep 2020; 10:17356. [PMID: 33060695 PMCID: PMC7562864 DOI: 10.1038/s41598-020-74401-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 09/26/2020] [Indexed: 12/22/2022] Open
Abstract
The human cathelicidin LL-37 serves a critical role in the innate immune system defending bacterial infections. LL-37 can interact with molecules of the cell wall and perforate cytoplasmic membranes resulting in bacterial cell death. To test the interactions of LL-37 and bacterial cell wall components we crystallized LL-37 in the presence of detergents and obtained the structure of a narrow tetrameric channel with a strongly charged core. The formation of a tetramer was further studied by cross-linking in the presence of detergents and lipids. Using planar lipid membranes a small but defined conductivity of this channel could be demonstrated. Molecular dynamic simulations underline the stability of this channel in membranes and demonstrate pathways for the passage of water molecules. Time lapse studies of E. coli cells treated with LL-37 show membrane discontinuities in the outer membrane followed by cell wall damage and cell death. Collectively, our results open a venue to the understanding of a novel AMP killing mechanism and allows the rational design of LL-37 derivatives with enhanced bactericidal activity.
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Affiliation(s)
- Enea Sancho-Vaello
- Unidad de Biofisica, Centro Mixto Consejo Superior de Investigaciones Cientificas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia, Spain.,Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - David Gil-Carton
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160, Derio, Spain
| | - Patrice François
- Genomic Research Laboratory, Department of Medical Specialities, Geneva University Hospitals, University of Geneva, Genève, Switzerland
| | - Eve-Julie Bonetti
- Genomic Research Laboratory, Department of Medical Specialities, Geneva University Hospitals, University of Geneva, Genève, Switzerland
| | - Mohamed Kreir
- Nanion Technologies GmbH, Gabrielenstraße 9, 80636, Munich, Germany.,Janssen Pharmaceutica NV, Janssen R&D, Nonclinical Safety, Beerse, Belgium
| | - Karunakar Reddy Pothula
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany
| | - Kornelius Zeth
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000, Roskilde, Denmark.
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8
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Mayer SF, Ducrey J, Dupasquier J, Haeni L, Rothen-Rutishauser B, Yang J, Fennouri A, Mayer M. Targeting specific membranes with an azide derivative of the pore-forming peptide ceratotoxin A. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:183023. [DOI: 10.1016/j.bbamem.2019.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 07/01/2019] [Accepted: 07/09/2019] [Indexed: 10/26/2022]
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9
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Brukhno AV, Grant J, Underwood TL, Stratford K, Parker SC, Purton JA, Wilding NB. DL_MONTE: a multipurpose code for Monte Carlo simulation. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1569760] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- A. V. Brukhno
- Scientific Computing Department, STFC, Daresbury Laboratory, Warrington, UK
| | - J. Grant
- Department of Chemistry, University of Bath, Bath, UK
- Computing Services, University of Bath, Bath, UK
| | | | | | - S. C. Parker
- Department of Chemistry, University of Bath, Bath, UK
| | - J. A. Purton
- Scientific Computing Department, STFC, Daresbury Laboratory, Warrington, UK
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10
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Aisenbrey C, Marquette A, Bechinger B. The Mechanisms of Action of Cationic Antimicrobial Peptides Refined by Novel Concepts from Biophysical Investigations. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1117:33-64. [PMID: 30980352 DOI: 10.1007/978-981-13-3588-4_4] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Even 30 years after the discovery of magainins, biophysical and structural investigations on how these peptides interact with membranes can still bear surprises and add new interesting detail to how these peptides exert their antimicrobial action. Early on, using oriented solid-state NMR spectroscopy, it was found that the amphipathic helices formed by magainins are active when being oriented parallel to the membrane surface. More recent investigations indicate that this in-planar alignment is also found when PGLa and magainin in combination exert synergistic pore-forming activities, where studies on the mechanism of synergistic interaction are ongoing. In a related manner, the investigation of dimeric antimicrobial peptide sequences has become an interesting topic of research which bears promise to refine our views how antimicrobial action occurs. The molecular shape concept has been introduced to explain the effects of lipids and peptides on membrane morphology, locally and globally, and in particular of cationic amphipathic helices that partition into the membrane interface. This concept has been extended in this review to include more recent ideas on soft membranes that can adapt to external stimuli including membrane-disruptive molecules. In this manner, the lipids can change their shape in the presence of low peptide concentrations, thereby maintaining the bilayer properties. At higher peptide concentrations, phase transitions occur which lead to the formation of pores and membrane lytic processes. In the context of the molecular shape concept, the properties of lipopeptides, including surfactins, are shortly presented, and comparisons with the hydrophobic alamethicin sequence are made.
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Affiliation(s)
| | - Arnaud Marquette
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, Strasbourg, France
| | - Burkhard Bechinger
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, Strasbourg, France. .,Faculté de chimie, Institut le Bel, Strasbourg, France.
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11
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Abbasi F, Alvarez-Malmagro J, Su Z, Leitch JJ, Lipkowski J. Pore Forming Properties of Alamethicin in Negatively Charged Floating Bilayer Lipid Membranes Supported on Gold Electrodes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:13754-13765. [PMID: 30265810 DOI: 10.1021/acs.langmuir.8b02554] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Electrochemical impedance spectroscopy (EIS), atomic force microscopy (AFM), and photon polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) were employed to investigate the formation of alamethicin pores in negatively charged bilayers composed of a mixture of 1,2-dimyristoyl- sn-glycero-3-phosphocholine (DMPC) and egg-PG floating at gold (111) electrode surfaces modified by self-assembled monolayers of 1-thio-β-d-glucose (β-Tg). The EIS data showed that the presence of alamethicin decreases the membrane resistivity by about 1 order of magnitude. PM-IRRAS measurements provided information about the tilt angles of peptide helical axis with respect to the bilayer normal. The small tilt angles obtained for the peptide helical axis prove that the alamethicin molecules were inserted into the DMPC/egg-PG membranes. The tilt angles decreased when negative potentials were applied, which correlates with the observed decrease in membrane resistivity, indicating that ion pore formation is assisted by the transmembrane potential. Molecular resolution AFM images provided visual evidence that alamethicin molecules aggregate forming hexagonal porous 2D lattices with periodicities of 2.0 ± 0.2 nm. The pore formation by alamethicin in the negatively charged membrane was compared with the interaction of this peptide with a bilayer formed by zwitterionic lipids. The comparison of these results showed that alamethicin preferentially forms ion translocating pores in negatively charged phospholipid membranes.
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Affiliation(s)
- Fatemeh Abbasi
- Department of Chemistry , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
| | | | - ZhangFei Su
- Department of Chemistry , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
| | - J Jay Leitch
- Department of Chemistry , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
| | - Jacek Lipkowski
- Department of Chemistry , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
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12
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Das S, Ben Haj Salah K, Djibo M, Inguimbert N. Peptaibols as a model for the insertions of chemical modifications. Arch Biochem Biophys 2018; 658:16-30. [DOI: 10.1016/j.abb.2018.09.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/05/2018] [Accepted: 09/18/2018] [Indexed: 12/13/2022]
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13
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Marquette A, Bechinger B. Biophysical Investigations Elucidating the Mechanisms of Action of Antimicrobial Peptides and Their Synergism. Biomolecules 2018; 8:E18. [PMID: 29670065 PMCID: PMC6023007 DOI: 10.3390/biom8020018] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 01/30/2023] Open
Abstract
Biophysical and structural investigations are presented with a focus on the membrane lipid interactions of cationic linear antibiotic peptides such as magainin, PGLa, LL37, and melittin. Observations made with these peptides are distinct as seen from data obtained with the hydrophobic peptide alamethicin. The cationic amphipathic peptides predominantly adopt membrane alignments parallel to the bilayer surface; thus the distribution of polar and non-polar side chains of the amphipathic helices mirror the environmental changes at the membrane interface. Such a membrane partitioning of an amphipathic helix has been shown to cause considerable disruptions in the lipid packing arrangements, transient openings at low peptide concentration, and membrane disintegration at higher peptide-to-lipid ratios. The manifold supramolecular arrangements adopted by lipids and peptides are represented by the 'soft membranes adapt and respond, also transiently' (SMART) model. Whereas molecular dynamics simulations provide atomistic views on lipid membranes in the presence of antimicrobial peptides, the biophysical investigations reveal interesting details on a molecular and supramolecular level, and recent microscopic imaging experiments delineate interesting sequences of events when bacterial cells are exposed to such peptides. Finally, biophysical studies that aim to reveal the mechanisms of synergistic interactions of magainin 2 and PGLa are presented, including unpublished isothermal titration calorimetry (ITC), circular dichroism (CD) and dynamic light scattering (DLS) measurements that suggest that the peptides are involved in liposome agglutination by mediating intermembrane interactions. A number of structural events are presented in schematic models that relate to the antimicrobial and synergistic mechanism of amphipathic peptides when they are aligned parallel to the membrane surface.
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Affiliation(s)
- Arnaud Marquette
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, 4, rue Blaise Pascal, 67070 Strasbourg, France.
| | - Burkhard Bechinger
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, 4, rue Blaise Pascal, 67070 Strasbourg, France.
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14
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Abbasi F, Leitch JJ, Su Z, Szymanski G, Lipkowski J. Direct visualization of alamethicin ion pores formed in a floating phospholipid membrane supported on a gold electrode surface. Electrochim Acta 2018. [DOI: 10.1016/j.electacta.2018.02.057] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Sekiya Y, Sakashita S, Shimizu K, Usui K, Kawano R. Channel current analysis estimates the pore-formation and the penetration of transmembrane peptides. Analyst 2018; 143:3540-3543. [DOI: 10.1039/c8an00243f] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We measured the current signal of the transmembrane model peptides using the barrel-stave, toroidal pore, and penetration models in order to establish a precise assignment of the channel signals.
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Affiliation(s)
- Yusuke Sekiya
- Department of Biotechnology and Life Science
- Tokyo University of Agriculture and Technology
- Tokyo 184-8588
- Japan
| | - Shungo Sakashita
- FIRST (Faculty of Frontiers of Innovative Research in Science and Technology)
- Konan University
- Kobe 650-0047
- Japan
| | - Keisuke Shimizu
- Department of Biotechnology and Life Science
- Tokyo University of Agriculture and Technology
- Tokyo 184-8588
- Japan
| | - Kenji Usui
- FIRST (Faculty of Frontiers of Innovative Research in Science and Technology)
- Konan University
- Kobe 650-0047
- Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science
- Tokyo University of Agriculture and Technology
- Tokyo 184-8588
- Japan
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16
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Syryamina VN, De Zotti M, Toniolo C, Formaggio F, Dzuba SA. Alamethicin self-assembling in lipid membranes: concentration dependence from pulsed EPR of spin labels. Phys Chem Chem Phys 2018; 20:3592-3601. [DOI: 10.1039/c7cp07298h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The antimicrobial action of the peptide antibiotic alamethicin (Alm) is commonly related to peptide self-assembling resulting in the formation of voltage-dependent channels in bacterial membranes, which induces ion permeation.
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Affiliation(s)
- Victoria N. Syryamina
- Institute of Chemical Kinetics and Combustion
- RAS
- Novosibirsk 630090
- Russian Federation
- Novosibirsk State University
| | - Marta De Zotti
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
| | - Claudio Toniolo
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
- Institute of Biomolecular Chemistry
| | - Fernando Formaggio
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
- Institute of Biomolecular Chemistry
| | - Sergei A. Dzuba
- Institute of Chemical Kinetics and Combustion
- RAS
- Novosibirsk 630090
- Russian Federation
- Novosibirsk State University
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17
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Sun L, Mao J, Zhao Y, Quan C, Zhong M, Fan S. Coarse-grained molecular dynamics simulation of interactions between cyclic lipopeptide Bacillomycin D and cell membranes. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1384632] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Liang Sun
- College of Life Science, Dalian Minzu University, Dalian, China
| | - Jiashun Mao
- College of Mechanical and Electronic Engineering, Dalian Minzu University, Dalian, China
| | - Ying Zhao
- School of Physics and Materials Engineering, Key Laboratory of Photosensitive Material & Device of Liaoning Province, Key Laboratory of New Energy & Rare Earth Resource Utilization of State Ethnic Affairs Commission, Dalian Minzu University, Dalian, China
| | - Chunshan Quan
- College of Life Science, Dalian Minzu University, Dalian, China
| | - Meiling Zhong
- College of Life Science, Dalian Minzu University, Dalian, China
| | - Shengdi Fan
- College of Life Science, Dalian Minzu University, Dalian, China
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18
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Structural Behavior of the Peptaibol Harzianin HK VI in a DMPC Bilayer: Insights from MD Simulations. Biophys J 2017. [PMID: 28636916 DOI: 10.1016/j.bpj.2017.05.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Microsecond molecular dynamics simulations of harzianin HK VI (HZ) interacting with a dimyristoylphosphatidylcholine bilayer were performed at the condition of low peptide-to-lipid ratio. Two orientations of HZ molecule in the bilayer were found and characterized. In the orientation perpendicular to the bilayer surface, HZ induces a local thinning of the bilayer. When inserted into the bilayer parallel to its surface, HZ is located nearly completely within the hydrophobic region of the bilayer. A combination of solid-state NMR and circular dichroism experiments found the latter orientation to be dominant. An extended sampling simulation provided qualitative results and showed the same orientation to be a global minimum of free energy. The secondary structure of HZ was characterized, and it was found to be located in the 310-helical family. The specific challenges of computer simulation of nonpolar peptides are discussed briefly.
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19
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Salnikov ES, Raya J, De Zotti M, Zaitseva E, Peggion C, Ballano G, Toniolo C, Raap J, Bechinger B. Alamethicin Supramolecular Organization in Lipid Membranes from 19F Solid-State NMR. Biophys J 2017; 111:2450-2459. [PMID: 27926846 DOI: 10.1016/j.bpj.2016.09.048] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 09/10/2016] [Accepted: 09/29/2016] [Indexed: 11/24/2022] Open
Abstract
Alamethicins (ALMs) are antimicrobial peptides of fungal origin. Their sequences are rich in hydrophobic amino acids and strongly interact with lipid membranes, where they cause a well-defined increase in conductivity. Therefore, the peptides are thought to form transmembrane helical bundles in which the more hydrophilic residues line a water-filled pore. Whereas the peptide has been well characterized in terms of secondary structure, membrane topology, and interactions, much fewer data are available regarding the quaternary arrangement of the helices within lipid bilayers. A new, to our knowledge, fluorine-labeled ALM derivative was prepared and characterized when reconstituted into phospholipid bilayers. As a part of these studies, C19F3-labeled compounds were characterized and calibrated for the first time, to our knowledge, for 19F solid-state NMR distance and oligomerization measurements by centerband-only detection of exchange (CODEX) experiments, which opens up a large range of potential labeling schemes. The 19F-19F CODEX solid-state NMR experiments performed with ALM in POPC lipid bilayers and at peptide/lipid ratios of 1:13 are in excellent agreement with molecular-dynamics calculations of dynamic pentameric assemblies. When the peptide/lipid ratio was lowered to 1:30, ALM was found in the dimeric form, indicating that the supramolecular organization is tuned by equilibria that can be shifted by changes in environmental conditions.
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Affiliation(s)
- Evgeniy S Salnikov
- Institute of Chemistry, University of Strasbourg/CNRS, UMR7177, Strasbourg, France
| | - Jesus Raya
- Institute of Chemistry, University of Strasbourg/CNRS, UMR7177, Strasbourg, France
| | - Marta De Zotti
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, Padova, Italy
| | - Ekaterina Zaitseva
- Department of Membrane Physiology and Technology, Institute of Physiology, University of Freiburg, Freiburg, Germany
| | - Cristina Peggion
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, Padova, Italy
| | - Gema Ballano
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, Padova, Italy
| | - Claudio Toniolo
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, Padova, Italy
| | - Jan Raap
- Leiden Institute of Chemistry, Gorlaeus Laboratories, University of Leiden, Leiden, the Netherlands
| | - Burkhard Bechinger
- Institute of Chemistry, University of Strasbourg/CNRS, UMR7177, Strasbourg, France.
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20
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Bera I, Marathe MV, Payghan PV, Ghoshal N. Identification of novel hits as highly prospective dual agonists for mu and kappa opioid receptors: an integrated in silico approach. J Biomol Struct Dyn 2017; 36:279-301. [DOI: 10.1080/07391102.2016.1275810] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Indrani Bera
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology , Kolkata 700032, India
| | | | - Pavan V. Payghan
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology , Kolkata 700032, India
| | - Nanda Ghoshal
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology , Kolkata 700032, India
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21
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Kratz EG, Duke RE, Cisneros GA. Long-range electrostatic corrections in multipolar/polarizable QM/MM simulations. Theor Chem Acc 2016; 135:166. [PMID: 28367078 PMCID: PMC5373107 DOI: 10.1007/s00214-016-1923-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 06/04/2016] [Indexed: 10/21/2022]
Abstract
Taking long-range electrostatic effects into account in classical and hybrid quantum mechanics-molecular mechanics (QM/MM) simulations is necessary for an accurate description of the system under study. We have recently developed a method, termed long-range electrostatic corrections (LREC), for monopolar QM/MM calculations. Here, we present an extension of LREC for multipolar/polarizable QM/MM simulations within the LICHEM software package. Reaction barriers and QM-MM interaction energies converge with a LREC cutoff between 20 and 25 Å, in agreement with our previous results. Additionally, the LREC approach for the QM-MM interactions can be smoothly combined with standard shifting or Ewald summation methods in the MM calculations. We recommend the use of QM(LREC)/MM(PME), where the QM region is treated with LREC and the MM region is treated with particle mesh Ewald (PME) summation. This combination is an excellent compromise between simplicity, speed, and accuracy for large QM/MM simulations.
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Affiliation(s)
- Eric G Kratz
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - Robert E Duke
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - G Andrés Cisneros
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
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22
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Li ZL, Ding HM, Ma YQ. Interaction of peptides with cell membranes: insights from molecular modeling. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:083001. [PMID: 26828575 DOI: 10.1088/0953-8984/28/8/083001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The investigation of the interaction of peptides with cell membranes is the focus of active research. It can enhance the understanding of basic membrane functions such as membrane transport, fusion, and signaling processes, and it may shed light on potential applications of peptides in biomedicine. In this review, we will present current advances in computational studies on the interaction of different types of peptides with the cell membrane. Depending on the properties of the peptide, membrane, and external environment, the peptide-membrane interaction shows a variety of different forms. Here, on the basis of recent computational progress, we will discuss how different peptides could initiate membrane pores, translocate across the membrane, induce membrane endocytosis, produce membrane curvature, form fibrils on the membrane surface, as well as interact with functional membrane proteins. Finally, we will present a conclusion summarizing recent progress and providing some specific insights into future developments in this field.
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Affiliation(s)
- Zhen-lu Li
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, People's Republic of China
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23
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Wong-Ekkabut J, Karttunen M. Molecular dynamics simulation of water permeation through the alpha-hemolysin channel. J Biol Phys 2016; 42:133-46. [PMID: 26264478 PMCID: PMC4713412 DOI: 10.1007/s10867-015-9396-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 07/21/2015] [Indexed: 02/05/2023] Open
Abstract
The alpha-hemolysin (AHL) nanochannel is a non-selective channel that allows for uncontrolled transport of small molecules across membranes leading to cell death. Although it is a bacterial toxin, it has promising applications, ranging from drug delivery systems to nano-sensing devices. This study focuses on the transport of water molecules through an AHL nanochannel using molecular dynamics (MD) simulations. Our results show that AHL can quickly transport water across membranes. The first-passage time approach was used to estimate the diffusion coefficient and the mean exit time. To study the energetics of transport, the potential of mean force (PMF) of a water molecule along the AHL nanochannel was calculated. The results show that the energy barriers of water permeation across a nanopore are always positive along the channel and the values are close to thermal energy (kBT). These findings suggest that the observed quick permeation of water is due to small energy barriers and a hydrophobic inner channel surface resulting in smaller friction. We speculate that these physical mechanisms are important in how AHL causes cell death.
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Affiliation(s)
- Jirasak Wong-Ekkabut
- Department of Physics, Faculty of Science, Kasetsart University, 50 Phahon Yothin Rd, Chatuchak, Bangkok, Thailand, 10900.
| | - Mikko Karttunen
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, Canada, N2L 3G1.
- Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, MetaForum, 5600 MB, Eindhoven, The Netherlands.
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24
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Freeman EC, Farimani AB, Aluru NR, Philen MK. Multiscale modeling of droplet interface bilayer membrane networks. BIOMICROFLUIDICS 2015; 9:064101. [PMID: 26594262 PMCID: PMC4644148 DOI: 10.1063/1.4935382] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 10/28/2015] [Indexed: 05/17/2023]
Abstract
Droplet interface bilayer (DIB) networks are considered for the development of stimuli-responsive membrane-based materials inspired by cellular mechanics. These DIB networks are often modeled as combinations of electrical circuit analogues, creating complex networks of capacitors and resistors that mimic the biomolecular structures. These empirical models are capable of replicating data from electrophysiology experiments, but these models do not accurately capture the underlying physical phenomena and consequently do not allow for simulations of material functionalities beyond the voltage-clamp or current-clamp conditions. The work presented here provides a more robust description of DIB network behavior through the development of a hierarchical multiscale model, recognizing that the macroscopic network properties are functions of their underlying molecular structure. The result of this research is a modeling methodology based on controlled exchanges across the interfaces of neighboring droplets. This methodology is validated against experimental data, and an extension case is provided to demonstrate possible future applications of droplet interface bilayer networks.
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Affiliation(s)
- Eric C Freeman
- College of Engineering, University of Georgia , Athens, Georgia 30602, USA
| | - Amir B Farimani
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, USA
| | - Narayana R Aluru
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, USA
| | - Michael K Philen
- Department of Aerospace and Ocean Engineering, Virginia Tech , Blacksburg, Virginia 24061, USA
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25
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Fanelli R, Salah KBH, Inguimbert N, Didierjean C, Martinez J, Cavelier F. Access to α,α-Disubstituted Disilylated Amino Acids and Their Use in Solid-Phase Peptide Synthesis. Org Lett 2015; 17:4498-501. [DOI: 10.1021/acs.orglett.5b02175] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Roberto Fanelli
- Institut
des Biomolécules Max Mousseron, IBMM, UMR-5247, CNRS, Université Montpellier, ENSCM, Place Eugène Bataillon, Montpellier34095 Cedex 5, France
| | - Khoubaib Ben Haj Salah
- Université de Perpignan Via Domitia, CRIOBE USR
3278, 58 avenue P. Alduy Bât T, 66860 Perpignan, France
| | - Nicolas Inguimbert
- Université de Perpignan Via Domitia, CRIOBE USR
3278, 58 avenue P. Alduy Bât T, 66860 Perpignan, France
| | - Claude Didierjean
- CRM2
(UMR UL-CNRS 7036) Faculté des Sciences et Technologies, Université de Lorraine, 70239 Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
| | - Jean Martinez
- Institut
des Biomolécules Max Mousseron, IBMM, UMR-5247, CNRS, Université Montpellier, ENSCM, Place Eugène Bataillon, Montpellier34095 Cedex 5, France
| | - Florine Cavelier
- Institut
des Biomolécules Max Mousseron, IBMM, UMR-5247, CNRS, Université Montpellier, ENSCM, Place Eugène Bataillon, Montpellier34095 Cedex 5, France
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26
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Fang D, Duke RE, Cisneros GA. A new smoothing function to introduce long-range electrostatic effects in QM/MM calculations. J Chem Phys 2015; 143:044103. [PMID: 26233103 PMCID: PMC4514725 DOI: 10.1063/1.4926652] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 07/01/2015] [Indexed: 12/23/2022] Open
Abstract
A new method to account for long range electrostatic contributions is proposed and implemented for quantum mechanics/molecular mechanics long range electrostatic correction (QM/MM-LREC) calculations. This method involves the use of the minimum image convention under periodic boundary conditions and a new smoothing function for energies and forces at the cutoff boundary for the Coulomb interactions. Compared to conventional QM/MM calculations without long-range electrostatic corrections, the new method effectively includes effects on the MM environment in the primary image from its replicas in the neighborhood. QM/MM-LREC offers three useful features including the avoidance of calculations in reciprocal space (k-space), with the concomitant avoidance of having to reproduce (analytically or approximately) the QM charge density in k-space, and the straightforward availability of analytical Hessians. The new method is tested and compared with results from smooth particle mesh Ewald (PME) for three systems including a box of neat water, a double proton transfer reaction, and the geometry optimization of the critical point structures for the rate limiting step of the DNA dealkylase AlkB. As with other smoothing or shifting functions, relatively large cutoffs are necessary to achieve comparable accuracy with PME. For the double-proton transfer reaction, the use of a 22 Å cutoff shows a close reaction energy profile and geometries of stationary structures with QM/MM-LREC compared to conventional QM/MM with no truncation. Geometry optimization of stationary structures for the hydrogen abstraction step by AlkB shows some differences between QM/MM-LREC and the conventional QM/MM. These differences underscore the necessity of the inclusion of the long-range electrostatic contribution.
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Affiliation(s)
- Dong Fang
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - Robert E Duke
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - G Andrés Cisneros
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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27
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Han E, Lee H. Structural effects of tachyplesin I and its linear derivative on their aggregation and mobility in lipid bilayers. J Mol Graph Model 2015; 59:123-8. [DOI: 10.1016/j.jmgm.2015.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 04/09/2015] [Accepted: 04/17/2015] [Indexed: 10/23/2022]
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28
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Laner M, Hünenberger PH. Phase-transition properties of glycerol–dipalmitate lipid bilayers investigated using molecular dynamics simulation. J Mol Graph Model 2015; 59:136-47. [DOI: 10.1016/j.jmgm.2015.04.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 11/29/2022]
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29
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Effect of methanol on the phase-transition properties of glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulations: In quest of the biphasic effect. J Mol Graph Model 2015; 55:85-104. [DOI: 10.1016/j.jmgm.2014.10.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/29/2014] [Accepted: 10/30/2014] [Indexed: 11/21/2022]
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30
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Reif MM, Oostenbrink C. Toward the correction of effective electrostatic forces in explicit-solvent molecular dynamics simulations: restraints on solvent-generated electrostatic potential and solvent polarization. Theor Chem Acc 2015; 134:2. [PMID: 26097404 PMCID: PMC4470580 DOI: 10.1007/s00214-014-1600-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 11/19/2014] [Indexed: 11/26/2022]
Abstract
Despite considerable advances in computing power, atomistic simulations under nonperiodic boundary conditions, with Coulombic electrostatic interactions and in systems large enough to reduce finite-size associated errors in thermodynamic quantities to within the thermal energy, are still not affordable. As a result, periodic boundary conditions, systems of microscopic size and effective electrostatic interaction functions are frequently resorted to. Ensuing artifacts in thermodynamic quantities are nowadays routinely corrected a posteriori, but the underlying configurational sampling still descends from spurious forces. The present study addresses this problem through the introduction of on-the-fly corrections to the physical forces during an atomistic molecular dynamics simulation. Two different approaches are suggested, where the force corrections are derived from special potential energy terms. In the first approach, the solvent-generated electrostatic potential sampled at a given atom site is restrained to a target value involving corrections for electrostatic artifacts. In the second approach, the long-range regime of the solvent polarization around a given atom site is restrained to the Born polarization, i.e., the solvent polarization corresponding to the ideal situation of a macroscopic system under nonperiodic boundary conditions and governed by Coulombic electrostatic interactions. The restraints are applied to the explicit-water simulation of a hydrated sodium ion, and the effect of the restraints on the structural and energetic properties of the solvent is illustrated. Furthermore, by means of the calculation of the charging free energy of a hydrated sodium ion, it is shown how the electrostatic potential restraint translates into the on-the-fly consideration of the corresponding free-energy correction terms. It is discussed how the restraints can be generalized to situations involving several solute particles. Although the present study considers a very simple system only, it is an important step toward the on-the-fly elimination of finite-size and approximate-electrostatic artifacts during atomistic molecular dynamics simulations.
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Affiliation(s)
- Maria M. Reif
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
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31
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Hong H. Role of Lipids in Folding, Misfolding and Function of Integral Membrane Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 855:1-31. [DOI: 10.1007/978-3-319-17344-3_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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32
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Abstract
The rapid spread of drug-resistant pathogenic microbial strains has created an urgent need for the development of new anti-infective molecules, having different mechanism of action in comparison to existing drugs. Natural antimicrobial peptides (AMPs) represent a novel class of molecules with a broad spectrum of activity and a low rate in inducing bacterial resistance. In particular, linear alpha-helical cationic antimicrobial peptides are among the most widespread membrane-disruptive AMPs in nature, representing a particularly successful structural arrangement of the innate defense against microbes. However, until now, many AMPs have failed in clinical trials because of several drawbacks that strongly limit their applicability such as degradation, cytotoxicity, and high production cost. Thus, to overcome the limitations of native peptides, a rational in silico approach to AMPs design becomes a promising strategy that drastically reduce production costs and the time required for evaluation of activity and toxicity. This chapter focuses on the strategies and methods for de novo design of potentially active AMPs. In particular, statistical-based design strategies and MD methods for modelling AMPs are elucidated.
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Affiliation(s)
- Giuseppe Maccari
- Center for Nanotechnology Innovation @NEST, Istituto Italiano di Tecnologia, Pisa, Italy
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33
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Laner M, Horta BAC, Hünenberger PH. Long-timescale motions in glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulation. J Mol Graph Model 2014; 55:48-64. [PMID: 25437095 DOI: 10.1016/j.jmgm.2014.10.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 10/24/2022]
Abstract
The occurrence of long-timescale motions in glycerol-1-monopalmitate (GMP) lipid bilayers is investigated based on previously reported 600 ns molecular dynamics simulations of a 2×8×8 GMP bilayer patch in the temperature range 302-338 K, performed at three different hydration levels, or in the presence of the cosolutes methanol or trehalose at three different concentrations. The types of long-timescale motions considered are: (i) the possible phase transitions; (ii) the precession of the relative collective tilt-angle of the two leaflets in the gel phase; (iii) the trans-gauche isomerization of the dihedral angles within the lipid aliphatic tails; and (iv) the flipping of single lipids across the two leaflets. The results provide a picture of GMP bilayers involving a rich spectrum of events occurring on a wide range of timescales, from the 100-ps range isomerization of single dihedral angles, via the 100-ns range of tilt precession motions, to the multi-μs range of phase transitions and lipid-flipping events.
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Affiliation(s)
- Monika Laner
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Bruno A C Horta
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland; Dpto. de Engenharia Elétrica, PUC-Rio, Rio de Janeiro, Brazil; Dpto. de Ciências Biológicas, UEZO, Rio de Janeiro, Brazil.
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34
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Protein arcs may form stable pores in lipid membranes. Biophys J 2014; 106:154-61. [PMID: 24411247 DOI: 10.1016/j.bpj.2013.11.4490] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 11/04/2013] [Accepted: 11/22/2013] [Indexed: 01/22/2023] Open
Abstract
Electron microscopy and atomic force microscopy images of cholesterol-dependent cytolysins and related proteins that form large pores in lipid membranes have revealed the presence of incomplete rings, or arcs. Some evidence indicates that these arcs are inserted into the membrane and induce membrane leakage, but other experiments seem to refute that. Could such pores, only partially lined by protein, be kinetically and thermodynamically stable? How would the lipids be structured in such a pore? Using the antimicrobial peptide protegrin-1 as a model, we test the stability of pores only partially lined by peptide using all-atom molecular dynamics simulations in POPC and POPE/POPG membranes. The data show that, whereas pure lipid pores close rapidly, pores partially lined by protegrin arcs are stable for at least 300 ns. Estimates of the thermodynamic stability of these arcs using line tension data and implicit solvent calculations show that these arcs can be marginally stable in both zwitterionic and anionic membranes. Arcs provide an explanation for the observed ion selectivity in protegrin electrophysiology experiments and could possibly be involved in other membrane permeabilization processes where lipids are thought to participate, such as those induced by antimicrobial peptides and colicins, as well as the Bax apoptotic pore.
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35
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Effect of the cosolutes trehalose and methanol on the equilibrium and phase-transition properties of glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulations. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2014; 43:517-44. [DOI: 10.1007/s00249-014-0982-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 07/16/2014] [Accepted: 07/24/2014] [Indexed: 10/24/2022]
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36
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Castro TG, Micaêlo NM. Conformational and thermodynamic properties of non-canonical α,α-dialkyl glycines in the peptaibol Alamethicin: molecular dynamics studies. J Phys Chem B 2014; 118:9861-70. [PMID: 25091499 DOI: 10.1021/jp505400q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, we investigate the structure, dynamic and thermodynamic properties of noncanonical disubstituted amino acids (α,α-dialkyl glycines), also known as non-natural amino acids, in the peptaibol Alamethicin. The amino acids under study are Aib (α-amino isobutyric acid or α-methyl alanine), Deg (α,α-diethyl glycine), Dpg (α,α-dipropyl glycine), Dibg (α,α-di-isobutyl glycine), Dhg (α,α-dihexyl glycine), DΦg (α,α-diphenyl glycine), Dbzg (α,α-dibenzyl glycine), Ac6c (α,α-cyclohexyl glycine), and Dmg (α,α-dihydroxymethyl glycine). It is hypothesized that these amino acids are able to induce well-defined secondary structure in peptidomimetics. To test this hypothesis, new peptidomimetics of Alamethicin were constructed by replacing the native Aib positions of Alamethicin by one or more new α,α-dialkyl glycines. Dhg and Ac6c demonstrated the capacity to induce well-defined α-helical structures. Dhg and Ac6c also promote the thermodynamic stabilization of these peptides in a POPC model membrane and are better alternatives to the Aib in Alamethicin. These noncanonical amino acids also improved secondary structure properties, revealing preorganization in water and maintenance of α helical structure in POPC. We show that it is possible to optimize the helicity and thermodynamic properties of native Alamethicin, and we suggest that these amino acids could be incorporated in other peptides with similar structural effect.
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Affiliation(s)
- Tarsila G Castro
- Departamento de Química, Escola de Ciências, Universidade do Minho , Largo do Paço, Braga 4704-553, Portugal
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Rahaman A, Lazaridis T. A thermodynamic approach to alamethicin pore formation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014. [DOI: 10.1016/j.bbamem.2014.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Di Luca M, Maccari G, Nifosì R. Treatment of microbial biofilms in the post-antibiotic era: prophylactic and therapeutic use of antimicrobial peptides and their design by bioinformatics tools. Pathog Dis 2014; 70:257-70. [PMID: 24515391 DOI: 10.1111/2049-632x.12151] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 01/22/2014] [Accepted: 01/30/2014] [Indexed: 12/14/2022] Open
Abstract
The treatment for biofilm infections is particularly challenging because bacteria in these conditions become refractory to antibiotic drugs. The reduced effectiveness of current therapies spurs research for the identification of novel molecules endowed with antimicrobial activities and new mechanisms of antibiofilm action. Antimicrobial peptides (AMPs) have been receiving increasing attention as potential therapeutic agents, because they represent a novel class of antibiotics with a wide spectrum of activity and a low rate in inducing bacterial resistance. Over the past decades, a large number of naturally occurring AMPs have been identified or predicted from various organisms as effector molecules of the innate immune system playing a crucial role in the first line of defense. Recent studies have shown the ability of some AMPs to act against microbial biofilms, in particular during early phases of biofilm development. Here, we provide a review of the antimicrobial peptides tested on biofilms, highlighting their advantages and disadvantages for prophylactic and therapeutic applications. In addition, we describe the strategies and methods for de novo design of potentially active AMPs and discuss how informatics and computational tools may be exploited to improve antibiofilm effectiveness.
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Cisneros GA, Karttunen M, Ren P, Sagui C. Classical electrostatics for biomolecular simulations. Chem Rev 2014; 114:779-814. [PMID: 23981057 PMCID: PMC3947274 DOI: 10.1021/cr300461d] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Biomimetic Membrane Supported at a Metal Electrode Surface. ADVANCES IN PLANAR LIPID BILAYERS AND LIPOSOMES 2014. [DOI: 10.1016/b978-0-12-418698-9.00001-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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Han E, Lee H. Effects of PEGylation on the binding interaction of magainin 2 and tachyplesin I with lipid bilayer surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:14214-14221. [PMID: 24160865 DOI: 10.1021/la4036985] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Poly(ethylene glycol) (PEG)-grafted magainin 2 and tachyplesin I were simulated with lipid bilayers. In the simulations of PEGylated magainin 2 and tachyplesin I in water, both peptides are wrapped by PEG chains. The α-helical structure of PEGylated magainin 2 is broken in water, while the β-sheet of PEGylated tachyplesin I keeps stable, similar to the structural behavior of unPEGylated peptides, in agreement with experiments. Simulations of PEGylated peptides with lipid bilayers show that PEG chains block the electrostatic interaction between cationic residues of peptides and anionic phosphates of lipids, leading to the less binding of the peptide to the bilayer surface, which is observed more significantly for magainin 2 than for tachyplesin I. Since the random-coiled magainin 2 can be more completely covered by PEGs than does the β-sheet tachyplesin I, the PEGylation effect on the decreased binding is larger for magainin 2, showing the dependence of PEGylation on the peptide structure. These simulation findings qualitatively support the experimental observation of the different extents of the reduced membrane-permeabilizing activity for PEGylated magainin 2 and tachyplesin I.
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Affiliation(s)
- Eol Han
- Department of Chemical Engineering, Dankook University , Yongin 448-701, South Korea
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Bortolus M, De Zotti M, Formaggio F, Maniero AL. Alamethicin in bicelles: Orientation, aggregation, and bilayer modification as a function of peptide concentration. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2620-7. [DOI: 10.1016/j.bbamem.2013.07.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 05/24/2013] [Accepted: 07/08/2013] [Indexed: 10/26/2022]
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Rahaman A, Lazaridis T. A thermodynamic approach to alamethicin pore formation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:98-105. [PMID: 24071593 DOI: 10.1016/j.bbamem.2013.09.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 09/10/2013] [Accepted: 09/17/2013] [Indexed: 12/15/2022]
Abstract
The structure and energetics of alamethicin Rf30 monomer to nonamer in cylindrical pores of 5 to 11Å radius are investigated using molecular dynamics simulations in an implicit membrane model that includes the free energy cost of acyl chain hydrophobic area exposure. Stable, low energy pores are obtained for certain combinations of radius and oligomeric number. The trimer and the tetramer formed 6Å pores that appear closed while the larger oligomers formed open pores at their optimal radius. The hexamer in an 8Å pore and the octamer in an 11Å pore give the lowest effective energy per monomer. However, all oligomers beyond the pentamer have comparable energies, consistent with the observation of multiple conductance levels. The results are consistent with the widely accepted "barrel-stave" model. The N terminal portion of the molecule exhibits smaller tilt with respect to the membrane normal than the C terminal portion, resulting in a pore shape that is a hybrid between a funnel and an hourglass. Transmembrane voltage has little effect on the structure of the oligomers but enhances or decreases their stability depending on its orientation. Antiparallel bundles are lower in energy than the commonly accepted parallel ones and could be present under certain experimental conditions. Dry aggregates (without an aqueous pore) have lower average effective energy than the corresponding aggregates in a pore, suggesting that alamethicin pores may be excited states that are stabilized in part by voltage and in part by the ion flow itself.
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Affiliation(s)
- Asif Rahaman
- Department of Chemistry, City College of New York, 160 Convent Avenue, New York, NY 10031, USA
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He Y, Prieto L, Lazaridis T. Modeling peptide binding to anionic membrane pores. J Comput Chem 2013; 34:1463-75. [PMID: 23580260 DOI: 10.1002/jcc.23282] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 02/14/2013] [Accepted: 03/04/2013] [Indexed: 02/04/2023]
Abstract
Peptide-induced pore formation in membranes can be dissected into two steps: pore formation and peptide binding to the pore. A computational method is proposed to study the second step in anionic membranes. The electrostatic potential is obtained from numerical solutions to the Poisson-Boltzmann equation and is then used in conjunction with IMM1 (implicit membrane model 1). A double charge layer model is used to incorporate the effects of the membrane dipole potential. Inhomogeneity of the charge density in the pore, characterized by explicit membrane simulations of toroidal pores, is included in the model. This approach was applied to two extensively studied peptides, magainin and melittin. In agreement with previous work, binding to toroidal pores is more favorable than binding to the flat membrane. The dependence of binding energy on anionic content exhibits different patterns for the two peptides, in correlation with the different lipid selectivity that has been observed experimentally.
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Affiliation(s)
- Yi He
- Department of Chemistry, City College of New York, New York, New York 10031, USA
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Lama D, Modi V, Sankararamakrishnan R. Behavior of solvent-exposed hydrophobic groove in the anti-apoptotic Bcl-XL protein: clues for its ability to bind diverse BH3 ligands from MD simulations. PLoS One 2013; 8:e54397. [PMID: 23468841 PMCID: PMC3585337 DOI: 10.1371/journal.pone.0054397] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 12/13/2012] [Indexed: 11/19/2022] Open
Abstract
Bcl-XL is a member of Bcl-2 family of proteins involved in the regulation of intrinsic pathway of apoptosis. Its overexpression in many human cancers makes it an important target for anti-cancer drugs. Bcl-XL interacts with the BH3 domain of several pro-apoptotic Bcl-2 partners. This helical bundle protein has a pronounced hydrophobic groove which acts as a binding region for the BH3 domains. Eight independent molecular dynamics simulations of the apo/holo forms of Bcl-XL were carried out to investigate the behavior of solvent-exposed hydrophobic groove. The simulations used either a twin-range cut-off or particle mesh Ewald (PME) scheme to treat long-range interactions. Destabilization of the BH3 domain-containing helix H2 was observed in all four twin-range cut-off simulations. Most of the other major helices remained stable. The unwinding of H2 can be related to the ability of Bcl-XL to bind diverse BH3 ligands. The loss of helical character can also be linked to the formation of homo- or hetero-dimers in Bcl-2 proteins. Several experimental studies have suggested that exposure of BH3 domain is a crucial event before they form dimers. Thus unwinding of H2 seems to be functionally very important. The four PME simulations, however, revealed a stable helix H2. It is possible that the H2 unfolding might occur in PME simulations at longer time scales. Hydrophobic residues in the hydrophobic groove are involved in stable interactions among themselves. The solvent accessible surface areas of bulky hydrophobic residues in the groove are significantly buried by the loop LB connecting the helix H2 and subsequent helix. These observations help to understand how the hydrophobic patch in Bcl-XL remains stable in the solvent-exposed state. We suggest that both the destabilization of helix H2 and the conformational heterogeneity of loop LB are important factors for binding of diverse ligands in the hydrophobic groove of Bcl-XL.
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Affiliation(s)
- Dilraj Lama
- Department of Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur, Kanpur, India
| | - Vivek Modi
- Department of Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur, Kanpur, India
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Direct visualization of the alamethicin pore formed in a planar phospholipid matrix. Proc Natl Acad Sci U S A 2012; 109:21223-7. [PMID: 23236158 DOI: 10.1073/pnas.1201559110] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present direct visualization of pores formed by alamethicin (Alm) in a matrix of phospholipids using electrochemical scanning tunneling microscopy (EC-STM). High-resolution EC-STM images show individual peptide molecules forming channels. The channels are not dispersed randomly in the monolayer but agglomerate forming 2D nanocrystals with a hexagonal lattice in which the average channel-channel distance is 1.90 ± 0.1 nm. The STM images suggest that each Alm is shared between the two adjacent channels. Every channel consists of six Alm molecules. Three or four of these molecules have the hydrophilic group oriented toward the center of the channel allowing for water column formation inside the channel. The dimensions of the central pore in the images are consistent with the dimension of the water column in a model of hexameric pore proposed in the literature. The images obtained in this work validate the barrel-stave model of the pore formed in phospholipid membranes by amphiphatic peptides. They also provide direct evidence for cluster formation by such pores.
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Chandler DE, Penin F, Schulten K, Chipot C. The p7 protein of hepatitis C virus forms structurally plastic, minimalist ion channels. PLoS Comput Biol 2012; 8:e1002702. [PMID: 23028296 PMCID: PMC3447957 DOI: 10.1371/journal.pcbi.1002702] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 07/27/2012] [Indexed: 12/20/2022] Open
Abstract
Hepatitis C virus (HCV) p7 is a membrane-associated oligomeric protein harboring ion channel activity. It is essential for effective assembly and release of infectious HCV particles and an attractive target for antiviral intervention. Yet, the self-assembly and molecular mechanism of p7 ion channelling are currently only partially understood. Using molecular dynamics simulations (aggregate time 1.2 µs), we show that p7 can form stable oligomers of four to seven subunits, with a bias towards six or seven subunits, and suggest that p7 self-assembles in a sequential manner, with tetrameric and pentameric complexes forming as intermediate states leading to the final hexameric or heptameric assembly. We describe a model of a hexameric p7 complex, which forms a transiently-open channel capable of conducting ions in simulation. We investigate the ability of the hexameric model to flexibly rearrange to adapt to the local lipid environment, and demonstrate how this model can be reconciled with low-resolution electron microscopy data. In the light of these results, a view of p7 oligomerization is proposed, wherein hexameric and heptameric complexes may coexist, forming minimalist, yet robust functional ion channels. In the absence of a high-resolution p7 structure, the models presented in this paper can prove valuable as a substitute structure in future studies of p7 function, or in the search for p7-inhibiting drugs.
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Affiliation(s)
- Danielle E. Chandler
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - François Penin
- Bases Moléculaires et Structurales des Systèmes Infectieux, IBCP, Université Lyon 1, Univ Lyon, France; CNRS, UMR 5086, Lyon, France
| | - Klaus Schulten
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Christophe Chipot
- Beckman Institute, University of Illinois at Urbana-Champaign Urbana, Illinois, United States of America
- Équipe de Dynamique des Assemblages Membranaires UMR 7565, Université de Lorraine, Vanduvre-lès-Nancy, France
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Hjørringgaard CU, Vad BS, Matchkov VV, Nielsen SB, Vosegaard T, Nielsen NC, Otzen DE, Skrydstrup T. Cyclodextrin-scaffolded alamethicin with remarkably efficient membrane permeabilizing properties and membrane current conductance. J Phys Chem B 2012; 116:7652-9. [PMID: 22676384 DOI: 10.1021/jp2098679] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Bacterial resistance to classical antibiotics is a serious medical problem, which continues to grow. Small antimicrobial peptides represent a potential solution and are increasingly being developed as novel therapeutic agents. Many of these peptides owe their antibacterial activity to the formation of trans-membrane ion-channels resulting in cell lysis. However, to further develop the field of peptide antibiotics, a thorough understanding of their mechanism of action is needed. Alamethicin belongs to a class of peptides called peptaibols and represents one of these antimicrobial peptides. To examine the dynamics of assembly and to facilitate a thorough structural evaluation of the alamethicin ion-channels, we have applied click chemistry for the synthesis of templated alamethicin multimers covalently attached to cyclodextrin-scaffolds. Using oriented circular dichroism, calcein release assays, and single-channel current measurements, the α-helices of the templated multimers were demonstrated to insert into lipid bilayers forming highly efficient and remarkably stable ion-channels.
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Affiliation(s)
- Claudia U Hjørringgaard
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
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Mihajlovic M, Lazaridis T. Charge distribution and imperfect amphipathicity affect pore formation by antimicrobial peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:1274-83. [PMID: 22290189 DOI: 10.1016/j.bbamem.2012.01.016] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 01/14/2012] [Accepted: 01/17/2012] [Indexed: 10/14/2022]
Abstract
Antimicrobial peptides often permeabilize biological membranes via a pore mechanism. Two pore types have been proposed: toroidal, where the pore is partly lined by lipid, and barrel-stave, where a cylindrical pore is completely lined by peptides. What drives the preference of antimicrobial peptides for a certain pore type is not yet fully understood. According to neutron scattering and oriented circular dichroism, melittin and MG-H2 induce toroidal pores whereas alamethicin forms barrel-stave pores. In previous work we found that indeed melittin seems to favor toroidal pores whereas alamethicin favors cylindrical pores. Here we designed mutants of these two peptides and the magainin analog MG-H2, aimed to probe how the distribution of charges along the helix and its imperfectly amphipathic structure influence pore formation. Molecular dynamics (MD) simulations of the peptides in a pre-formed cylindrical pore have been performed. The duration of the simulations was 136ns to 216ns. We found that a melittin mutant with lysine 7 neutralized favors cylindrical pores whereas a MG-H2 mutant with lysines in the N-terminal half of these peptides neutralized and an alamethicin mutant with a positive charge at the position 7 form semitoroidal pores. These results suggest that charged residues within the N-terminal half are important for toroidal pore formation. Toroidal pores produced by MG-H2 are more disordered than the melittin pores, likely because of the charged residues located in the middle of the MG-H2 helix (K11 and K14). Imperfect amphipathicity of melittin seems to play a role in its preference for toroidal pores since the substitutions of charged residues located within the nonpolar face by hydrophobic residues suppress evolution of a toroidal pore. The mutations change the position of lysine 7 near the N-terminus, relative to the lower leaflet headgroups. The MD simulations also show that the melittin P14A mutant forms a toroidal pore, but its configuration diverges from that of melittin and it is probably metastable.
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Affiliation(s)
- Maja Mihajlovic
- Department of Chemistry, The City College of New York, 160 Convent Ave. New York, NY 10031, USA.
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Wilson MA, Wei C, Bjelkmar P, Wallace BA, Pohorille A. Molecular dynamics simulation of the antiamoebin ion channel: linking structure and conductance. Biophys J 2011; 100:2394-402. [PMID: 21575573 DOI: 10.1016/j.bpj.2011.03.054] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 03/21/2011] [Accepted: 03/24/2011] [Indexed: 11/19/2022] Open
Abstract
Molecular-dynamics simulations were carried out to ascertain which of the potential multimeric forms of the transmembrane peptaibol channel, antiamoebin, is consistent with its measured conductance. Estimates of the conductance obtained through counting ions that cross the channel and by solving the Nernst-Planck equation yield consistent results, indicating that the motion of ions inside the channel can be satisfactorily described as diffusive. The calculated conductance of octameric channels is markedly higher than the conductance measured in single channel recordings, whereas the tetramer appears to be nonconducting. The conductance of the hexamer was estimated to be 115 ± 34 pS and 74 ± 20 pS, at 150 mV and 75 mV, respectively, in satisfactory agreement with the value of 90 pS measured at 75 mV. On this basis, we propose that the antiamoebin channel consists of six monomers. Its pore is large enough to accommodate K⁺ and Cl⁻ with their first solvation shells intact. The free energy barrier encountered by K⁺ is only 2.2 kcal/mol whereas Cl⁻ encounters a substantially higher barrier of nearly 5 kcal/mol. This difference makes the channel selective for cations. Ion crossing events are shown to be uncorrelated and follow Poisson statistics.
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Affiliation(s)
- Michael A Wilson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, USA
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