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Conde-Torres D, Calvelo M, Rovira C, Piñeiro Á, Garcia-Fandino R. Unlocking the specificity of antimicrobial peptide interactions for membrane-targeted therapies. Comput Struct Biotechnol J 2024; 25:61-74. [PMID: 38695015 PMCID: PMC11061258 DOI: 10.1016/j.csbj.2024.04.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 04/06/2024] [Accepted: 04/07/2024] [Indexed: 05/04/2024] Open
Abstract
Antimicrobial peptides (AMPs) are increasingly recognized as potent therapeutic agents, with their selective affinity for pathological membranes, low toxicity profile, and minimal resistance development making them particularly attractive in the pharmaceutical landscape. This study offers a comprehensive analysis of the interaction between specific AMPs, including magainin-2, pleurocidin, CM15, LL37, and clavanin, with lipid bilayer models of very different compositions that have been ordinarily used as biological membrane models of healthy mammal, cancerous, and bacterial cells. Employing unbiased molecular dynamics simulations and metadynamics techniques, we have deciphered the intricate mechanisms by which these peptides recognize pathogenic and pathologic lipid patterns and integrate into lipid assemblies. Our findings reveal that the transverse component of the peptide's hydrophobic dipole moment is critical for membrane interaction, decisively influencing the molecule's orientation and expected therapeutic efficacy. Our approach also provides insight on the kinetic and dynamic dependence on the peptide orientation in the axial and azimuthal angles when coming close to the membrane. The aim is to establish a robust framework for the rational design of peptide-based, membrane-targeted therapies, as well as effective quantitative descriptors that can facilitate the automated design of novel AMPs for these therapies using machine learning methods.
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Affiliation(s)
- Daniel Conde-Torres
- Center for Research in Biological Chemistry and Molecular Materials, Departamento de Química Orgánica, Universidade de Santiago de Compostela, Campus Vida s/n, 15782 Santiago de Compostela, Spain
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Martín Calvelo
- Departament de Química Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, Spain
| | - Carme Rovira
- Departament de Química Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Ángel Piñeiro
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Rebeca Garcia-Fandino
- Center for Research in Biological Chemistry and Molecular Materials, Departamento de Química Orgánica, Universidade de Santiago de Compostela, Campus Vida s/n, 15782 Santiago de Compostela, Spain
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2
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Park P, Matsubara DK, Barzotto DR, Lima FS, Chaimovich H, Marrink SJ, Cuccovia IM. Vesicle protrusion induced by antimicrobial peptides suggests common carpet mechanism for short antimicrobial peptides. Sci Rep 2024; 14:9701. [PMID: 38678109 PMCID: PMC11055889 DOI: 10.1038/s41598-024-60601-w] [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: 09/30/2023] [Accepted: 04/25/2024] [Indexed: 04/29/2024] Open
Abstract
Short-cationic alpha-helical antimicrobial peptides (SCHAMPs) are promising candidates to combat the growing global threat of antimicrobial resistance. They are short-sequenced, selective against bacteria, and have rapid action by destroying membranes. A full understanding of their mechanism of action will provide key information to design more potent and selective SCHAMPs. Molecular Dynamics (MD) simulations are invaluable tools that provide detailed insights into the peptide-membrane interaction at the atomic- and meso-scale level. We use atomistic and coarse-grained MD to look into the exact steps that four promising SCHAMPs-BP100, Decoralin, Neurokinin-1, and Temporin L-take when they interact with membranes. Following experimental set-ups, we explored the effects of SCHAMPs on anionic membranes and vesicles at multiple peptide concentrations. Our results showed all four peptides shared similar binding steps, initially binding to the membrane through electrostatic interactions and then flipping on their axes, dehydrating, and inserting their hydrophobic moieties into the membrane core. At higher concentrations, fully alpha-helical peptides induced membrane budding and protrusions. Our results suggest the carpet mode of action is fit for the description of SCHAMPs lysis activity and discuss the importance of large hydrophobic residues in SCHAMPs design and activity.
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Affiliation(s)
- Peter Park
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9747 AG, Groningen, the Netherlands
| | - Danilo K Matsubara
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Domenico R Barzotto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Filipe S Lima
- Departamento de Química Fundamental, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco, Recife, Brazil
| | - Hernan Chaimovich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9747 AG, Groningen, the Netherlands.
| | - Iolanda M Cuccovia
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
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3
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Frigini EN, Porasso RD, Beke-Somfai T, López Cascales JJ, Enriz RD, Pantano S. The Mechanism of Antimicrobial Small-Cationic Peptides from Coarse-Grained Simulations. J Chem Inf Model 2023; 63:6877-6889. [PMID: 37905818 DOI: 10.1021/acs.jcim.3c01348] [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: 11/02/2023]
Abstract
Antimicrobial cationic peptides (AMPs) are excellent candidates for use as therapeutic antimicrobial agents. Among them, short peptides possessing sequences of 9-11 amino acids have some advantages over long-sequence peptides. However, one of the main limitations of short peptides is that their mechanism of action at the molecular level is not well-known. In this article, we report a model based on multiscale molecular dynamics simulations of short peptides interacting with vesicles containing palmitoyl-oleoyl-phosphatidylglycerol (POPG)/palmitoyl-oleoyl-phosphatidylethanolamine (POPE). Simulations using this approach have allowed us to understand the different behaviors of peptides with antimicrobial activity with respect to those that do not produce this effect. We found remarkable agreement with a series of experimental results directly supporting our model. Moreover, these results allow us to understand the mechanism of action at the molecular level of these short peptides. Our simulations suggest that mechanical inhomogeneities appear in the membrane, promoting membrane rupture when a threshold concentration of peptides adsorbed on the membrane is achieved. These results explain the high structural demand for these peptides to maintain a delicate balance between the affinity for the bilayer surface, a low peptide-peptide repulsion (in order to reach the threshold concentration), and an acceptable tendency to penetrate into the bilayer. This mechanism is different from those proposed for peptides with long amino acid sequences. Such information is very useful from the medicinal chemistry point of view for the design of new small antimicrobial peptides.
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Affiliation(s)
- Ezequiel N Frigini
- Facultad de Química, Bioquímica y Farmacia, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Universidad Nacional de San Luis, Ejército de los Andes 950, San Luis 5700, Argentina
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
| | - Rodolfo D Porasso
- Instituto de Matemáticas Aplicada San Luis (IMASL), CONICET, Facultad de Ciencias Físico Matemáticas y Naturales, Universidad Nacional de San Luis, Av. Ejército de los Andes 950, San Luis 5700, Argentina
| | - Tamás Beke-Somfai
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, H-1117 Budapest, Hungary
| | - José Javier López Cascales
- Universidad Politécnica de Cartagena, Grupo de Bioinformática y Macromoleculas (BioMac), Area de Química Física, Aulario II, Campus de Alfonso XIII, 30203 Cartagena, Murcia, Spain
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Universidad Nacional de San Luis, Ejército de los Andes 950, San Luis 5700, Argentina
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
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4
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Poruthoor AJ, Sharma A, Grossfield A. Understanding the free-energy landscape of phase separation in lipid bilayers using molecular dynamics. Biophys J 2023; 122:4144-4159. [PMID: 37742069 PMCID: PMC10645549 DOI: 10.1016/j.bpj.2023.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/28/2023] [Accepted: 09/19/2023] [Indexed: 09/25/2023] Open
Abstract
Liquid-liquid phase separation inside the cell often results in biological condensates that can critically affect cell homeostasis. Such phase separation events occur in multiple parts of cells, including the cell membranes, where the "lipid raft" hypothesis posits the formation of ordered domains floating in a sea of disordered lipids. The resulting lipid domains often have functional roles. However, the thermodynamics of lipid phase separation and their resulting mechanistic effects on cell function and dysfunction are poorly understood. Understanding such complex phenomena in cell membranes, with their diverse lipid compositions, is exceptionally difficult. For these reasons, simple model systems that can recapitulate similar behavior are widely used to study this phenomenon. Despite these simplifications, the timescale and length scales of domain formation pose a challenge for molecular dynamics (MD) simulations. Thus, most MD studies focus on spontaneous lipid phase separation-essentially measuring the sign (but not the amplitude) of the free-energy change upon separation-rather than directly interrogating the thermodynamics. Here, we propose a proof-of-concept pipeline that can directly measure this free energy by combining coarse-grained MD with enhanced sampling protocols using a novel collective variable. This approach will be a useful tool to help connect the thermodynamics of phase separation with the mechanistic insights already available from MD simulations.
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Affiliation(s)
- Ashlin J Poruthoor
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York
| | - Akshara Sharma
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York
| | - Alan Grossfield
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.
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5
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Borges-Araújo L, Patmanidis I, Singh AP, Santos LHS, Sieradzan AK, Vanni S, Czaplewski C, Pantano S, Shinoda W, Monticelli L, Liwo A, Marrink SJ, Souza PCT. Pragmatic Coarse-Graining of Proteins: Models and Applications. J Chem Theory Comput 2023; 19:7112-7135. [PMID: 37788237 DOI: 10.1021/acs.jctc.3c00733] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The molecular details involved in the folding, dynamics, organization, and interaction of proteins with other molecules are often difficult to assess by experimental techniques. Consequently, computational models play an ever-increasing role in the field. However, biological processes involving large-scale protein assemblies or long time scale dynamics are still computationally expensive to study in atomistic detail. For these applications, employing coarse-grained (CG) modeling approaches has become a key strategy. In this Review, we provide an overview of what we call pragmatic CG protein models, which are strategies combining, at least in part, a physics-based implementation and a top-down experimental approach to their parametrization. In particular, we focus on CG models in which most protein residues are represented by at least two beads, allowing these models to retain some degree of chemical specificity. A description of the main modern pragmatic protein CG models is provided, including a review of the most recent applications and an outlook on future perspectives in the field.
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Affiliation(s)
- Luís Borges-Araújo
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Ilias Patmanidis
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Akhil P Singh
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
| | - Lucianna H S Santos
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, Inserm, CNRS, 06560 Valbonne, France
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Wataru Shinoda
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita, Okayama 700-8530, Japan
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Adam Liwo
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
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6
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Rainsford P, Rylandsholm FG, Jakubec M, Silk M, Juskewitz E, Ericson JU, Svendsen JS, Engh RA, Isaksson J. Label-free measurement of antimicrobial peptide interactions with lipid vesicles and nanodiscs using microscale thermophoresis. Sci Rep 2023; 13:12619. [PMID: 37537266 PMCID: PMC10400562 DOI: 10.1038/s41598-023-39785-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023] Open
Abstract
One strategy to combat antimicrobial resistance is the discovery of new classes of antibiotics. Most antibiotics will at some point interact with the bacterial membrane to either interfere with its integrity or to cross it. Reliable and efficient tools for determining the dissociation constant for membrane binding (KD) and the partitioning coefficient between the aqueous- and membrane phases (KP) are therefore important tools for discovering and optimizing antimicrobial hits. Here we demonstrate that microscale thermophoresis (MST) can be used for label-free measurement of KD by utilising the intrinsic fluorescence of tryptophan and thereby removing the need for chromophore labelling. As proof of principle, we have used the method to measure the binding of a set of small cyclic AMPs to large unilamellar vesicles (LUVs) and two types of lipid nanodiscs assembled by styrene maleic acid (SMA) and quaternary ammonium SMA (SMA-QA). The measured KD values correlate well with the corresponding measurements using surface plasmon resonance (SPR), also broadly reflecting the tested AMPs' minimal inhibition concentration (MIC) towards S. aureus and E. coli. We conclude that MST is a promising method for fast and cost-efficient detection of peptide-lipid interactions or mapping of sample conditions in preparation for more advanced studies that rely on expensive sample preparation, labelling and/or instrument time.
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Affiliation(s)
- Philip Rainsford
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019, Tromsø, Norway
| | - Fredrik G Rylandsholm
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019, Tromsø, Norway
| | - Martin Jakubec
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019, Tromsø, Norway
| | - Mitchell Silk
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019, Tromsø, Norway
| | - Eric Juskewitz
- Research Group for Host Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, 9019, Tromsø, Norway
| | - Johanna U Ericson
- Research Group for Host Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, 9019, Tromsø, Norway
| | - John-Sigurd Svendsen
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019, Tromsø, Norway
| | - Richard A Engh
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019, Tromsø, Norway
| | - Johan Isaksson
- Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, 9019, Tromsø, Norway.
- Natural Products and Medicinal Chemistry, Department of Pharmacy, Faculty of Health Sciences, UiT the Arctic University of Norway, 9037, Tromsø, Norway.
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7
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Makowski M, Almendro-Vedia VG, Domingues MM, Franco OL, López-Montero I, Melo MN, Santos NC. Activity modulation of the Escherichia coli F 1F O ATP synthase by a designed antimicrobial peptide via cardiolipin sequestering. iScience 2023; 26:107004. [PMID: 37416464 PMCID: PMC10320169 DOI: 10.1016/j.isci.2023.107004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 02/13/2023] [Accepted: 05/26/2023] [Indexed: 07/08/2023] Open
Abstract
Most antimicrobial peptides (AMPs) exert their microbicidal activity through membrane permeabilization. The designed AMP EcDBS1R4 has a cryptic mechanism of action involving the membrane hyperpolarization of Escherichia coli, suggesting that EcDBS1R4 may hinder processes involved in membrane potential dissipation. We show that EcDBS1R4 can sequester cardiolipin, a phospholipid that interacts with several respiratory complexes of E. coli. Among these, F1FO ATP synthase uses membrane potential to fuel ATP synthesis. We found that EcDBS1R4 can modulate the activity of ATP synthase upon partition to membranes containing cardiolipin. Molecular dynamics simulations suggest that EcDBS1R4 alters the membrane environment of the transmembrane FO motor, impairing cardiolipin interactions with the cytoplasmic face of the peripheral stalk that binds the catalytic F1 domain to the FO domain. The proposed mechanism of action, targeting membrane protein function through lipid reorganization may open new venues of research on the mode of action and design of other AMPs.
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Affiliation(s)
- Marcin Makowski
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Víctor G. Almendro-Vedia
- Instituto Pluridisciplinar, Universidad Complutense de Madrid, Ps Juan XXIII 1, 28040 Madrid, Spain
- Universidad Complutense de Madrid, Departamento de Química Física, 28040 Madrid, Spain
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
| | - Marco M. Domingues
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Octavio L. Franco
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, 71966-700 Federal District, Brazil
- S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, 79117-900 Mato Grosso do Sul, Brazil
| | - Iván López-Montero
- Instituto Pluridisciplinar, Universidad Complutense de Madrid, Ps Juan XXIII 1, 28040 Madrid, Spain
- Universidad Complutense de Madrid, Departamento de Química Física, 28040 Madrid, Spain
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Nuno C. Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
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8
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Puelles JS, Ghorbani M, Tuck B, Machuca LL, Ackland ML, Chen F, Somers AE, Forsyth M. Effect of cetrimonium carrier micelles on bacterial membranes and extracellular DNA, an in silico study. Sci Rep 2023; 13:8041. [PMID: 37198168 DOI: 10.1038/s41598-023-32475-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/28/2023] [Indexed: 05/19/2023] Open
Abstract
Microorganisms do not live as dispersed single cells but rather they form aggregates with extracellular polymeric substances at interfaces. Biofilms are considered efficient life forms because they shield bacteria from biocides and collect dilute nutrients. This is a big concern in industry since the microorganisms can colonize a wide range of surfaces, accelerating material deterioration, colonizing medical devices, contaminating ultrapure drinking water, increasing energy costs and creating focus of infection. Conventional biocides that target a specific component of the bacteria are not effective in the presence of biofilms. Efficient biofilm inhibitors are based on a multitarget approach interacting with the bacteria and the biofilm matrix. Their rationale design requires a thorough understanding of inhibitory mechanisms that are still largely lacking today. Herein we uncover via molecular modelling the inhibition mechanism of cetrimonium 4-OH cinnamate (CTA-4OHcinn). Simulations show that CTA-4OH micelles can disrupt symmetric and asymmetric bilayers, representative of inner and outer bacterial membranes, following three stages: adsorption, assimilation, and defect formation. The main driving force for micellar attack is electrostatic interactions. In addition to disrupting the bilayers, the micelles work as carriers facilitating the trapping of 4OH cinnamate anions within the bilayer upper leaflet and overcoming electrostatic repulsion. The micelles also interact with extracellular DNA (e-DNA), which is one of the main components of biofilms. It is observed that CTA-4OHcinn forms spherical micelles on the DNA backbone; which hinders their ability to pack. This is demonstrated by modelling the DNA along the hbb histone-like protein, showing that in the presence of CTA-4OHcinn, DNA does not pack properly around hbb. The abilities of CTA-4OHcinn to cause cell death through membrane disruption and to disperse a mature, multi-species biofilm are also confirmed experimentally.
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Affiliation(s)
| | - Mahdi Ghorbani
- Institute for Frontier Materials, Deakin University, Geelong, VIC, 3217, Australia
| | - Benjamin Tuck
- Curtin Corrosion Centre, WA School of Mines: Minerals, Energy and Chemical Engineering, Curtin University, Kent Street, Bentley, WA, 6102, Australia
| | - Laura L Machuca
- Curtin Corrosion Centre, WA School of Mines: Minerals, Energy and Chemical Engineering, Curtin University, Kent Street, Bentley, WA, 6102, Australia
| | - M Leigh Ackland
- ARC Centre of Excellence for Electromaterials Science (ACES), Deakin University, Burwood, 3125, Australia
- School of Life and Environmental Sciences, Deakin University, Burwood, Victoria, 3125, Australia
| | - Fangfang Chen
- Institute for Frontier Materials, Deakin University, Geelong, VIC, 3217, Australia.
- ARC Centre of Excellence for Electromaterials Science (ACES), Deakin University, Burwood, 3125, Australia.
| | - Anthony E Somers
- Institute for Frontier Materials, Deakin University, Geelong, VIC, 3217, Australia.
| | - Maria Forsyth
- Institute for Frontier Materials, Deakin University, Geelong, VIC, 3217, Australia.
- ARC Centre of Excellence for Electromaterials Science (ACES), Deakin University, Burwood, 3125, Australia.
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9
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Spinti JK, Neiva Nunes F, Melo MN. Room for improvement in the initial martini 3 parameterization of peptide interactions. Chem Phys Lett 2023. [DOI: 10.1016/j.cplett.2023.140436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
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10
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MacDermott-Opeskin HI, Wilson KA, O'Mara ML. The Impact of Antimicrobial Peptides on the Acinetobacter baumannii Inner Membrane Is Modulated by Lipid Polyunsaturation. ACS Infect Dis 2023; 9:815-826. [PMID: 36920795 DOI: 10.1021/acsinfecdis.2c00530] [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: 03/16/2023]
Abstract
The Gram-negative pathogen Acinetobacter baumannii is a primary contributor to nosocomial multi-drug-resistant (MDR) infections. To combat the rise of MDR infections, novel features of A. baumannii need to be considered for the development of new treatment options. One such feature is the preferential scavenging of exogenous lipids, including host-derived polyunsaturated fatty acids (PUFAs), for membrane phospholipid synthesis. These alterations in membrane composition impact both the lipid chemistry and the membrane biophysical properties. In this work we examine how antimicrobial peptides (AMPs) interact with the inner membranes of A. baumannii in the presence and absence of polyunsaturated phospholipids. Using coarse-grained molecular dynamics simulations of complex A. baumannii inner membrane models derived from lipidomes of bacteria grown in the presence and absence of PUFAs, we examine the impact of the adsorption of four prototypical AMPs (CAMEL, LL-37, pexiganan, and magainin-2) on the membrane biophysical properties. Our simulations reveal that the impact of AMP adsorption on the membrane biophysical properties was dependent on both the membrane composition and the specific AMP involved. Both lipid headgroup charge and tail unsaturation played important roles in driving the interactions that occurred both within the membrane and between the membrane and AMPs. The changes to the membrane biophysical properties also showed a complex relationship with the AMP's physical properties, such as AMP charge, chain length, and charge-to-mass ratio. Cumulatively, this work highlights the importance of studying AMPs using a complex membrane environment and provides insights into the mechanistic action of AMPs in polyunsaturated lipid-rich bacterial membranes.
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Affiliation(s)
- Hugo I MacDermott-Opeskin
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Katie A Wilson
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia.,Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL A1C 5S7 Canada
| | - Megan L O'Mara
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
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11
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Takahashi H, Sovadinova I, Yasuhara K, Vemparala S, Caputo GA, Kuroda K. Biomimetic antimicrobial polymers—Design, characterization, antimicrobial, and novel applications. WIRES NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 15:e1866. [PMID: 36300561 DOI: 10.1002/wnan.1866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 09/15/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022]
Abstract
Biomimetic antimicrobial polymers have been an area of great interest as the need for novel antimicrobial compounds grows due to the development of resistance. These polymers were designed and developed to mimic naturally occurring antimicrobial peptides in both physicochemical composition and mechanism of action. These antimicrobial peptide mimetic polymers have been extensively investigated using chemical, biophysical, microbiological, and computational approaches to gain a deeper understanding of the molecular interactions that drive function. These studies have helped inform SARs, mechanism of action, and general physicochemical factors that influence the activity and properties of antimicrobial polymers. However, there are still lingering questions in this field regarding 3D structural patterning, bioavailability, and applicability to alternative targets. In this review, we present a perspective on the development and characterization of several antimicrobial polymers and discuss novel applications of these molecules emerging in the field. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease.
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Affiliation(s)
- Haruko Takahashi
- Graduate School of Integrated Sciences for Life Hiroshima University Higashi‐Hiroshima Hiroshima Japan
| | - Iva Sovadinova
- RECETOX, Faculty of Science Masaryk University Brno Czech Republic
| | - Kazuma Yasuhara
- Division of Materials Science, Graduate School of Science and Technology Nara Institute of Science and Technology Nara Japan
- Center for Digital Green‐Innovation Nara Institute of Science and Technology Nara Japan
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences CIT Campus Chennai India
- Homi Bhabha National Institute Training School Complex Mumbai India
| | - Gregory A. Caputo
- Department of Chemistry & Biochemistry Rowan University Glassboro New Jersey USA
| | - Kenichi Kuroda
- Department of Biologic and Materials Sciences & Prosthodontics, School of Dentistry University of Michigan Ann Arbor Michigan USA
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12
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Amphiphilic Gold Nanoparticles: A Biomimetic Tool to Gain Mechanistic Insights into Peptide-Lipid Interactions. MEMBRANES 2022; 12:membranes12070673. [PMID: 35877876 PMCID: PMC9324301 DOI: 10.3390/membranes12070673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 02/04/2023]
Abstract
Functional peptides are now widely used in a myriad of biomedical and clinical contexts, from cancer therapy and tumor targeting to the treatment of bacterial and viral infections. Underlying this diverse range of applications are the non-specific interactions that can occur between peptides and cell membranes, which, in many contexts, result in spontaneous internalization of the peptide within cells by avoiding energy-driven endocytosis. For this to occur, the amphipathicity and surface structural flexibility of the peptides play a crucial role and can be regulated by the presence of specific molecular residues that give rise to precise molecular events. Nevertheless, most of the mechanistic details regulating the encounter between peptides and the membranes of bacterial or animal cells are still poorly understood, thus greatly limiting the biomimetic potential of these therapeutic molecules. In this arena, finely engineered nanomaterials—such as small amphiphilic gold nanoparticles (AuNPs) protected by a mixed thiol monolayer—can provide a powerful tool for mimicking and investigating the physicochemical processes underlying peptide-lipid interactions. Within this perspective, we present here a critical review of membrane effects induced by both amphiphilic AuNPs and well-known amphiphilic peptide families, such as cell-penetrating peptides and antimicrobial peptides. Our discussion is focused particularly on the effects provoked on widely studied model cell membranes, such as supported lipid bilayers and lipid vesicles. Remarkable similarities in the peptide or nanoparticle membrane behavior are critically analyzed. Overall, our work provides an overview of the use of amphiphilic AuNPs as a highly promising tailor-made model to decipher the molecular events behind non-specific peptide-lipid interactions and highlights the main affinities observed both theoretically and experimentally. The knowledge resulting from this biomimetic approach could pave the way for the design of synthetic peptides with tailored functionalities for next-generation biomedical applications, such as highly efficient intracellular delivery systems.
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13
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Marrink SJ, Monticelli L, Melo MN, Alessandri R, Tieleman DP, Souza PCT. Two decades of Martini: Better beads, broader scope. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials University of Groningen Groningen The Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras Portugal
| | - Riccardo Alessandri
- Pritzker School of Molecular Engineering University of Chicago Chicago Illinois USA
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences University of Calgary Alberta Canada
| | - Paulo C. T. Souza
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
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14
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Patra P, Banerjee R, Chakrabarti J. Effect of biphosphate salt on dipalmitoylphosphatidylcholine bilayer deformation by Tat polypeptide. Biopolymers 2022; 113:e23518. [PMID: 35621373 DOI: 10.1002/bip.23518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/06/2022]
Abstract
Translocation of positively charged cell penetrating peptides (CPP) through cell membrane is important in drug delivery. Here we report all-atom molecular dynamics simulations to investigate how a biphosphate salt in a solvent affects the interaction of a CPP, HIV-1 Tat peptide with model dipalmitoylphosphatidylcholine (DPPC) lipid bilayer. Tat peptide has a large number of basic arginines and a couple of polar glutamines. We observe that in absence of salt, the basic residues of the polypeptide get localized in the vicinity of the membrane without altering the bilayer properties much; polypeptide induce local thinning of the bilayer membrane at the area of localization. In presence of biphosphate salt, the basic residues, dressed by the biphosphate ions, are repelled by the phosphate head groups of the lipid molecules. However, polar glutamine prefers to stay in the vicinity of the bilayer. This leads to larger local bilayer thickness at the contact point by the polar residue and non-uniform bilayer thickness profile. The thickness deformation of bilayer structure disappears upon mutating the polar residue, suggesting importance of the polar residue in bilayer deformation. Our studies point to control bilayer deformation by appropriate peptide sequence and solvent conditions.
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Affiliation(s)
- Piya Patra
- Maulana Abul Kalam Azad University of Technology, West Bengal, Haringhata, Nadia, West Bengal, India
| | - Raja Banerjee
- Maulana Abul Kalam Azad University of Technology, West Bengal, Haringhata, Nadia, West Bengal, India
| | - Jaydeb Chakrabarti
- Department of Chemical, Biological and Macro-Molecular Sciences, Thematic Unit of Excellence on Computational Materials Science and Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Salt Lake, Kolkata, West Bengal, India
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15
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Lata K, Singh M, Chatterjee S, Chattopadhyay K. Membrane Dynamics and Remodelling in Response to the Action of the Membrane-Damaging Pore-Forming Toxins. J Membr Biol 2022; 255:161-173. [PMID: 35305136 DOI: 10.1007/s00232-022-00227-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/02/2022] [Indexed: 12/11/2022]
Abstract
Pore-forming protein toxins (PFTs) represent a diverse class of membrane-damaging proteins that are produced by a wide variety of organisms. PFT-mediated membrane perforation is largely governed by the chemical composition and the physical properties of the plasma membranes. The interaction between the PFTs with the target membranes is critical for the initiation of the pore-formation process, and can lead to discrete membrane reorganization events that further aids in the process of pore-formation. Punching holes on the plasma membranes by the PFTs interferes with the cellular homeostasis by disrupting the ion-balance inside the cells that in turn can turn on multiple signalling cascades required to restore membrane integrity and cellular homeostasis. In this review, we discuss the physicochemical attributes of the plasma membranes associated with the pore-formation processes by the PFTs, and the subsequent membrane remodelling events that may start off the membrane-repair mechanisms.
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Affiliation(s)
- Kusum Lata
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, 140306, India
| | - Mahendra Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, 140306, India
| | - Shamaita Chatterjee
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, 140306, India
| | - Kausik Chattopadhyay
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, 140306, India.
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16
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MacDermott-Opeskin HI, Gupta V, O’Mara ML. Lipid-mediated antimicrobial resistance: a phantom menace or a new hope? Biophys Rev 2022; 14:145-162. [PMID: 35251360 PMCID: PMC8880301 DOI: 10.1007/s12551-021-00912-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/14/2021] [Indexed: 02/06/2023] Open
Abstract
Abstract The proposition of a post-antimicrobial era is all the more realistic with the continued rise of antimicrobial resistance. The development of new antimicrobials is failing to counter the ever-increasing rates of bacterial antimicrobial resistance. This necessitates novel antimicrobials and drug targets. The bacterial cell membrane is an essential and highly conserved cellular component in bacteria and acts as the primary barrier for entry of antimicrobials into the cell. Although previously under-exploited as an antimicrobial target, the bacterial cell membrane is attractive for the development of novel antimicrobials due to its importance in pathogen viability. Bacterial cell membranes are diverse assemblies of macromolecules built around a central lipid bilayer core. This lipid bilayer governs the overall membrane biophysical properties and function of its membrane-embedded proteins. This mini-review will outline the mechanisms by which the bacterial membrane causes and controls resistance, with a focus on alterations in the membrane lipid composition, chemical modification of constituent lipids, and the efflux of antimicrobials by membrane-embedded efflux systems. Thorough insight into the interplay between membrane-active antimicrobials and lipid-mediated resistance is needed to enable the rational development of new antimicrobials. In particular, the union of computational approaches and experimental techniques for the development of innovative and efficacious membrane-active antimicrobials is explored.
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Affiliation(s)
- Hugo I. MacDermott-Opeskin
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601 Australia
| | - Vrinda Gupta
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601 Australia
| | - Megan L. O’Mara
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601 Australia
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17
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Gupta A, Dey S, Bhowmik D, Maiti S. Coexisting Ordered and Disordered Membrane Phases Have Distinct Modes of Interaction with Disease-Associated Oligomers. J Phys Chem B 2022; 126:1016-1023. [PMID: 35104126 DOI: 10.1021/acs.jpcb.1c09421] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ordered membrane domains are thought to influence the attachment and insertion of toxic amyloid oligomers, and consequently, their toxicity. However, if and how the molecular aspects of this interaction depend on the membrane order is poorly understood. Here we measure the affinity, location, and degree of insertion of the small oligomers of hIAPP (human Islet Amyloid Polypeptide, associated with Type II diabetes) at near-physiological concentrations to adjacent domains of a biphasic lipid bilayer. Using simultaneous atomic force, confocal and fluorescence lifetime microscopy (AFM-FLIM), we find that hIAPP oligomers have a nearly 8-fold higher affinity to the disordered domains over the ordered domains. To probe whether this difference indicates different modes of interaction, we measure the change of lifetime of peptide-attached fluorescent labels induced by soluble fluorescence quenchers and also measure the kinetics of localized photobleaching. We find that in the raft-like ordered domains, the oligomers primarily lie on the aqueous interface with limited membrane penetration. However, in the neighboring disordered domains, their C-termini penetrate deeper into the lipid bilayer. We conclude that local membrane order determines not only the affinity but also the mode of interaction of amyloid oligomers, which may have significant implications for disease mechanisms.
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Affiliation(s)
- Ankur Gupta
- Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Simli Dey
- Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Debanjan Bhowmik
- Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Sudipta Maiti
- Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
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18
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Franco LR, Park P, Chaimovich H, Coutinho K, Cuccovia IM, Lima FS. Simulations reveal that antimicrobial BP100 induces local membrane thinning, slows lipid dynamics and favors water penetration. RSC Adv 2022; 12:4573-4588. [PMID: 35425494 PMCID: PMC8981376 DOI: 10.1039/d1ra06267k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/26/2022] [Indexed: 11/21/2022] Open
Abstract
MD simulations reveal that BP100 peptide induces local membrane thinning and negative curvature, slows lipid dynamics and increases the water life time in the lipid hydrophobic core and transmembrane water transport in the direction of the peptide.
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Affiliation(s)
| | - Peter Park
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Hernan Chaimovich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, São Paulo, Brazil
| | - Iolanda M. Cuccovia
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Filipe S. Lima
- Departamento de Química Fundamental, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco, Recife, Brazil
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19
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Melo MN. Coarse-Grain Simulations of Membrane-Adsorbed Helical Peptides. Methods Mol Biol 2022; 2405:137-150. [PMID: 35298812 DOI: 10.1007/978-1-0716-1855-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The amphipathic α-helix is a common motif for peptide adsorption to membranes. Many physiologically relevant events involving membrane-adsorbed peptides occur over time and size scales readily accessible to coarse-grain molecular dynamics simulations. This methodological suitability, however, comes with a number of pitfalls. Here, I exemplify a multi-step adsorption equilibration procedure on the antimicrobial peptide Magainin 2. It involves careful control of peptide freedom to promote optimal membrane adsorption before other interactions are allowed. This shortens preparation times prior to production simulations while avoiding divergence into unrealistic or artifactual configurations.
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Affiliation(s)
- Manuel N Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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20
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Koneru JK, Prakashchand DD, Dube N, Ghosh P, Mondal J. Spontaneous transmembrane pore formation by short-chain synthetic peptide. Biophys J 2021; 120:4557-4574. [PMID: 34478698 DOI: 10.1016/j.bpj.2021.08.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 08/14/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022] Open
Abstract
Amphiphilic β-peptides, which are synthetically designed short-chain helical foldamers of β-amino acids, are established potent biomimetic alternatives of natural antimicrobial peptides. An intriguing question is how the distinct molecular architecture of these short-chain and rigid synthetic peptides translates to its potent membrane-disruption ability. Here, we address this question via a combination of all-atom and coarse-grained molecular dynamics simulations of the interaction of mixed phospholipid bilayer with an antimicrobial 10-residue globally amphiphilic helical β-peptide at a wide range of concentrations. The simulation demonstrates that multiple copies of this synthetic peptide, initially placed in aqueous solution, readily self-assemble and adsorb at membrane interface. Subsequently, beyond a threshold peptide/lipid ratio, the surface-adsorbed oligomeric aggregate moves inside the membrane and spontaneously forms stable water-filled transmembrane pores via a cooperative mechanism. The defects induced by these pores lead to the dislocation of interfacial lipid headgroups, membrane thinning, and substantial water leakage inside the hydrophobic core of the membrane. A molecular analysis reveals that despite having a short architecture, these synthetic peptides, once inside the membrane, would stretch themselves toward the distal leaflet in favor of potential contact with polar headgroups and interfacial water layer. The pore formed in coarse-grained simulation was found to be resilient upon structural refinement. Interestingly, the pore-inducing ability was found to be elusive in a non-globally amphiphilic sequence isomer of the same β-peptide, indicating strong sequence dependence. Taken together, this work puts forward key perspectives of membrane activity of minimally designed synthetic biomimetic oligomers relative to the natural antimicrobial peptides.
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Affiliation(s)
- Jaya Krishna Koneru
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad, Telangana, India
| | - Dube Dheeraj Prakashchand
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad, Telangana, India
| | - Namita Dube
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad, Telangana, India
| | - Pushpita Ghosh
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad, Telangana, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad, Telangana, India.
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21
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Shen H, Wu Z, Lu C. Extension of the CAVS model to the simulation of helical peptides in a membrane environment. Phys Chem Chem Phys 2021; 23:12850-12863. [PMID: 34060579 DOI: 10.1039/d1cp01238j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Considering the effect of peptide insertion on the dipole potential of the lipid membrane, we extend the CAVS coarse-grained (CG) model to the simulation of helical peptides in a membrane environment. In this approach, the CG scheme for a peptide backbone is similar to the treatment in the united-atom model, while we treated the side chain of an amino acid by grouping 1-3 heavy atoms into a CG unit. The CAVS CG force field for peptides is optimized by reproducing the experimental results for the backbone (φ, ψ) distribution and predicting the PMF profiles of transferring organic molecules in a lipid bilayer membrane obtained from all-atom simulations. The CAVS simulation of a helical peptide in a phosphatidylcholine (PC) lipid bilayer revealed that the insertion of a peptide increases the dipole potential of the PC lipid bilayer, in which the peptide and its neutralized ions make a significant contribution. Finally, we carried out the CAVS simulation for five different helical peptides in the PC lipid bilayer to explore the behavior of peptide tilt, showing excellent agreement with the all-atom simulations. Our work suggests that the peptide tilt should relieve the deformation stress from the lipid bilayer, and the peptide aggregation could reduce the peptide tilt by resisting the deformation stress from the surrounding lipids.
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Affiliation(s)
- Hujun Shen
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Education University, Guiyang, Guizhou 550018, P. R. China.
| | - Zhenhua Wu
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, P. R. China
| | - Chan Lu
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Education University, Guiyang, Guizhou 550018, P. R. China.
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22
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Pirtskhalava M, Vishnepolsky B, Grigolava M, Managadze G. Physicochemical Features and Peculiarities of Interaction of AMP with the Membrane. Pharmaceuticals (Basel) 2021; 14:471. [PMID: 34067510 PMCID: PMC8156082 DOI: 10.3390/ph14050471] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/25/2021] [Accepted: 04/29/2021] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial peptides (AMPs) are anti-infectives that have the potential to be used as a novel and untapped class of biotherapeutics. Modes of action of antimicrobial peptides include interaction with the cell envelope (cell wall, outer- and inner-membrane). A comprehensive understanding of the peculiarities of interaction of antimicrobial peptides with the cell envelope is necessary to perform a rational design of new biotherapeutics, against which working out resistance is hard for microbes. In order to enable de novo design with low cost and high throughput, in silico predictive models have to be invoked. To develop an efficient predictive model, a comprehensive understanding of the sequence-to-function relationship is required. This knowledge will allow us to encode amino acid sequences expressively and to adequately choose the accurate AMP classifier. A shared protective layer of microbial cells is the inner, plasmatic membrane. The interaction of AMP with a biological membrane (native and/or artificial) has been comprehensively studied. We provide a review of mechanisms and results of interactions of AMP with the cell membrane, relying on the survey of physicochemical, aggregative, and structural features of AMPs. The potency and mechanism of AMP action are presented in terms of amino acid compositions and distributions of the polar and apolar residues along the chain, that is, in terms of the physicochemical features of peptides such as hydrophobicity, hydrophilicity, and amphiphilicity. The survey of current data highlights topics that should be taken into account to come up with a comprehensive explanation of the mechanisms of action of AMP and to uncover the physicochemical faces of peptides, essential to perform their function. Many different approaches have been used to classify AMPs, including machine learning. The survey of knowledge on sequences, structures, and modes of actions of AMP allows concluding that only possessing comprehensive information on physicochemical features of AMPs enables us to develop accurate classifiers and create effective methods of prediction. Consequently, this knowledge is necessary for the development of design tools for peptide-based antibiotics.
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Affiliation(s)
- Malak Pirtskhalava
- Ivane Beritashvili Center of Experimental Biomedicine, Tbilisi 0160, Georgia; (B.V.); (M.G.); (G.M.)
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23
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Risselada HJ, Grubmüller H. How proteins open fusion pores: insights from molecular simulations. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 50:279-293. [PMID: 33340336 PMCID: PMC8071795 DOI: 10.1007/s00249-020-01484-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023]
Abstract
Fusion proteins can play a versatile and involved role during all stages of the fusion reaction. Their roles go far beyond forcing the opposing membranes into close proximity to drive stalk formation and fusion. Molecular simulations have played a central role in providing a molecular understanding of how fusion proteins actively overcome the free energy barriers of the fusion reaction up to the expansion of the fusion pore. Unexpectedly, molecular simulations have revealed a preference of the biological fusion reaction to proceed through asymmetric pathways resulting in the formation of, e.g., a stalk-hole complex, rim-pore, or vertex pore. Force-field based molecular simulations are now able to directly resolve the minimum free-energy path in protein-mediated fusion as well as quantifying the free energies of formed reaction intermediates. Ongoing developments in Graphics Processing Units (GPUs), free energy calculations, and coarse-grained force-fields will soon gain additional insights into the diverse roles of fusion proteins.
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Affiliation(s)
- H Jelger Risselada
- Department of Theoretical Physics, Georg-August University of Göttingen, Göttingen, Germany. .,Leiden University, Leiden Institute of Chemistry (LIC), Leiden, The Netherlands.
| | - Helmut Grubmüller
- Max Planck Institute for Biophysical Chemistry, Theoretical and Computational Biophysics Department, Göttingen, Germany
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24
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Benfield AH, Henriques ST. Mode-of-Action of Antimicrobial Peptides: Membrane Disruption vs. Intracellular Mechanisms. FRONTIERS IN MEDICAL TECHNOLOGY 2020; 2:610997. [PMID: 35047892 PMCID: PMC8757789 DOI: 10.3389/fmedt.2020.610997] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/20/2020] [Indexed: 12/28/2022] Open
Abstract
Antimicrobial peptides are an attractive alternative to traditional antibiotics, due to their physicochemical properties, activity toward a broad spectrum of bacteria, and mode-of-actions distinct from those used by current antibiotics. In general, antimicrobial peptides kill bacteria by either disrupting their membrane, or by entering inside bacterial cells to interact with intracellular components. Characterization of their mode-of-action is essential to improve their activity, avoid resistance in bacterial pathogens, and accelerate their use as therapeutics. Here we review experimental biophysical tools that can be employed with model membranes and bacterial cells to characterize the mode-of-action of antimicrobial peptides.
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