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Sánchez-Lozano I, Muñoz-Cruz LC, Hellio C, Band-Schmidt CJ, Cruz-Narváez Y, Becerra-Martínez E, Hernández-Guerrero CJ. Metabolomic Insights of Biosurfactant Activity from Bacillus niabensis against Planktonic Cells and Biofilm of Pseudomonas stutzeri Involved in Marine Biofouling. Int J Mol Sci 2023; 24:ijms24044249. [PMID: 36835662 PMCID: PMC9965525 DOI: 10.3390/ijms24044249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/03/2023] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
In marine environments, biofilm can cause negative impacts, including the biofouling process. In the search for new non-toxic formulations that inhibit biofilm, biosurfactants (BS) produced by the genus Bacillus have demonstrated considerable potential. To elucidate the changes that BS from B. niabensis promote in growth inhibition and biofilm formation, this research performed a nuclear magnetic resonance (NMR) metabolomic profile analysis to compare the metabolic differences between planktonic cells and biofilms of Pseudomonas stutzeri, a pioneer fouling bacteria. The multivariate analysis showed a clear separation between groups with a higher concentration of metabolites in the biofilm than in planktonic cells of P. stutzeri. When planktonic and biofilm stages were treated with BS, some differences were found among them. In planktonic cells, the addition of BS had a minor effect on growth inhibition, but at a metabolic level, NADP+, trehalose, acetone, glucose, and betaine were up-regulated in response to osmotic stress. When the biofilm was treated with the BS, a clear inhibition was observed and metabolites such as glucose, acetic acid, histidine, lactic acid, phenylalanine, uracil, and NADP+ were also up-regulated, while trehalose and histamine were down-regulated in response to the antibacterial effect of the BS.
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Affiliation(s)
- Ilse Sánchez-Lozano
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. Instituto Politécnico Nacional S/N, Col. Playa Palo de Santa Rita, La Paz 23096, Mexico
| | - Luz Clarita Muñoz-Cruz
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. Instituto Politécnico Nacional S/N, Col. Playa Palo de Santa Rita, La Paz 23096, Mexico
| | - Claire Hellio
- CNRS, IRD, Ifremer, LEMAR, Univ. Brest, Institut Universitaire Européen de la Mer, F-29280 Plouzané, France
| | - Christine J. Band-Schmidt
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. Instituto Politécnico Nacional S/N, Col. Playa Palo de Santa Rita, La Paz 23096, Mexico
| | - Yair Cruz-Narváez
- Laboratorio de Posgrado de Operaciones Unitarias, Instituto Politécnico Nacional-ESIQIE-UPALM, Unidad Profesional Adolfo López Mateos, Edificio 7, 1.er Piso, Sección A, Av. Luis Enrique Erro S/N, Zacatenco, Delegación Gustavo A. Madero, Mexico City 07738, Mexico
| | - Elvia Becerra-Martínez
- Centro de Nanociencias y Micro y Nanotecnologías, Instituto Politécnico Nacional, Unidad Profesional Adolfo López Mateos, Av. Luis Enrique Erro S/N, Zacatenco, Delegación Gustavo A. Madero, Mexico City 07738, Mexico
- Correspondence: (E.B.-M.); (C.J.H.-G.)
| | - Claudia J. Hernández-Guerrero
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. Instituto Politécnico Nacional S/N, Col. Playa Palo de Santa Rita, La Paz 23096, Mexico
- Correspondence: (E.B.-M.); (C.J.H.-G.)
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2
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Englerová K, Bedlovičová Z, Nemcová R, Király J, Maďar M, Hajdučková V, Styková E, Mucha R, Reiffová K. Bacillus amyloliquefaciens-Derived Lipopeptide Biosurfactants Inhibit Biofilm Formation and Expression of Biofilm-Related Genes of Staphylococcus aureus. Antibiotics (Basel) 2021; 10:1252. [PMID: 34680832 PMCID: PMC8532693 DOI: 10.3390/antibiotics10101252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/05/2021] [Accepted: 10/13/2021] [Indexed: 11/24/2022] Open
Abstract
Biosurfactants (BSs) are surface-active compounds produced by diverse microorganisms, including the genus Bacillus. These bioactive compounds possess biological activities such as antiadhesive, antimicrobial and antibiofilm effects that can lead to important applications in combating many infections. Based on these findings, we decided to investigate the antibiofilm activity of BSs from the marine Bacillus amyloliquefaciens against Staphylococcus aureus CCM 4223. Expression of biofilm-related genes was also evaluated using qRT-PCR. Isolated and partially purified BSs were identified and characterized by molecular tools and by UHPLC-DAD and MALDI-TOF/MS. Bacillus amyloliquefaciens 3/22, that exhibited surfactant activity evaluated by oil spreading assay, was characterized using the 16S rRNA sequencing method. Screening by PCR detected the presence of the sfp, srfAA, fenD and ituD genes, suggesting production of the lipopeptides (LPs) surfactin, fengycin and iturin. The above findings were further supported by the results of UHPLC-DAD and MALDI-TOF/MS. As quantified by the crystal violet method, the LPs significantly (p < 0.001) reduced biofilm formation of S. aureus in a dose-dependent manner and decreased expression of biofilm-related genes fnbA, fnbB, sortaseA and icaADBC operon. Data from our investigation indicate a promising therapeutic application for LPs isolated from B. amyloliquefaciens toward prevention of S. aureus biofilm infections.
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Affiliation(s)
- Karolína Englerová
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (K.E.); (R.N.); (J.K.); (M.M.); (V.H.)
| | - Zdenka Bedlovičová
- Department of Chemistry, Biochemistry and Biophysics, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia
| | - Radomíra Nemcová
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (K.E.); (R.N.); (J.K.); (M.M.); (V.H.)
| | - Ján Király
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (K.E.); (R.N.); (J.K.); (M.M.); (V.H.)
| | - Marián Maďar
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (K.E.); (R.N.); (J.K.); (M.M.); (V.H.)
| | - Vanda Hajdučková
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (K.E.); (R.N.); (J.K.); (M.M.); (V.H.)
| | - Eva Styková
- Equine Clinic, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia;
| | - Rastislav Mucha
- Institute of Neurobiology BMC, Slovak Academy of Sciences, Šoltésovej 4-6, 040 01 Košice, Slovakia;
| | - Katarína Reiffová
- Department of Analytical Chemistry, Institute of Chemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Moyzesová 11, 041 54 Košice, Slovakia;
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Ceresa C, Fracchia L, Fedeli E, Porta C, Banat IM. Recent Advances in Biomedical, Therapeutic and Pharmaceutical Applications of Microbial Surfactants. Pharmaceutics 2021; 13:466. [PMID: 33808361 PMCID: PMC8067001 DOI: 10.3390/pharmaceutics13040466] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 12/19/2022] Open
Abstract
The spread of antimicrobial-resistant pathogens typically existing in biofilm formation and the recent COVID-19 pandemic, although unrelated phenomena, have demonstrated the urgent need for methods to combat such increasing threats. New avenues of research for natural molecules with desirable properties to alleviate this situation have, therefore, been expanding. Biosurfactants comprise a group of unique and varied amphiphilic molecules of microbial origin capable of interacting with lipidic membranes/components of microorganisms and altering their physicochemical properties. These features have encouraged closer investigations of these microbial metabolites as new pharmaceutics with potential applications in clinical, hygiene and therapeutic fields. Mounting evidence has indicated that biosurfactants have antimicrobial, antibiofilm, antiviral, immunomodulatory and antiproliferative activities that are exploitable in new anticancer treatments and wound healing applications. Some biosurfactants have already been approved for use in clinical, food and environmental fields, while others are currently under investigation and development as antimicrobials or adjuvants to antibiotics for microbial suppression and biofilm eradication strategies. Moreover, due to the COVID-19 pandemic, biosurfactants are now being explored as an alternative to current products or procedures for effective cleaning and handwash formulations, antiviral plastic and fabric surface coating agents for shields and masks. In addition, biosurfactants have shown promise as drug delivery systems and in the medicinal relief of symptoms associated with SARS-CoV-2 acute respiratory distress syndrome.
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Affiliation(s)
- Chiara Ceresa
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale “A. Avogadro”, 28100 Novara, Italy; (C.C.); (E.F.); (C.P.)
| | - Letizia Fracchia
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale “A. Avogadro”, 28100 Novara, Italy; (C.C.); (E.F.); (C.P.)
| | - Emanuele Fedeli
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale “A. Avogadro”, 28100 Novara, Italy; (C.C.); (E.F.); (C.P.)
| | - Chiara Porta
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale “A. Avogadro”, 28100 Novara, Italy; (C.C.); (E.F.); (C.P.)
- Center for Translational Research on Autoimmune & Allergic Diseases (CAAD), Università del Piemonte Orientale “A. Avogadro”, 28100 Novara, Italy
| | - Ibrahim M. Banat
- Pharmaceutical Science Research Group, Biomedical Science Research Institute, Ulster University, Coleraine, Northern Ireland BT52 1SA, UK;
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Matamoros-Recio A, Franco-Gonzalez JF, Forgione RE, Torres-Mozas A, Silipo A, Martín-Santamaría S. Understanding the Antibacterial Resistance: Computational Explorations in Bacterial Membranes. ACS OMEGA 2021; 6:6041-6054. [PMID: 33718695 PMCID: PMC7948216 DOI: 10.1021/acsomega.0c05590] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/09/2021] [Indexed: 05/05/2023]
Affiliation(s)
- Alejandra Matamoros-Recio
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Research Margarita Salas, CIB-CSIC, C/Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Juan Felipe Franco-Gonzalez
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Research Margarita Salas, CIB-CSIC, C/Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Rosa Ester Forgione
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Research Margarita Salas, CIB-CSIC, C/Ramiro de Maeztu, 9, 28040 Madrid, Spain
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant’Angelo, Università di Napoli Federico II, Via Cintia 4, 80126 Napoli, Italy
| | - Angel Torres-Mozas
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Research Margarita Salas, CIB-CSIC, C/Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Alba Silipo
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant’Angelo, Università di Napoli Federico II, Via Cintia 4, 80126 Napoli, Italy
| | - Sonsoles Martín-Santamaría
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Research Margarita Salas, CIB-CSIC, C/Ramiro de Maeztu, 9, 28040 Madrid, Spain
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5
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Rani G, Kuroda K, Vemparala S. Towards designing globular antimicrobial peptide mimics: role of polar functional groups in biomimetic ternary antimicrobial polymers. SOFT MATTER 2021; 17:2090-2103. [PMID: 33439212 DOI: 10.1039/d0sm01896a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Using atomistic molecular dynamics simulations, we study the interaction of ternary methacrylate polymers, composed of charged cationic, hydrophobic and neutral polar groups, with model bacterial membrane. Our simulation data shows that the random ternary polymers can penetrate deep into the membrane interior and partitioning of even a single polymer has a pronounced effect on the membrane structure. Lipid reorganization, on polymer binding, shows a strong affinity of the ternary polymer for anionic POPG lipids and the same is compared with the control case of binary polymers (only cationic and hydrophobic groups). While binary polymers exhibit strong propensity of acquired amphiphilic conformations upon membrane insertion, our results strongly suggest that such amphiphilic conformations are absent in the case of random ternary polymers. The ternary polymers adopt a more folded conformation, staying aligned in the direction of the membrane normal and subsequently penetrating deeper into the membrane interior suggesting a novel membrane partitioning mechanism without amphiphilic conformations. Finally, we also examine the interactions of ternary polymer aggregates with model bacterial membranes, which show that replacing some of the hydrophobic groups by polar groups leads to weakly held ternary aggregates enabling them to undergo rapid partitioning and insertion into membrane interior. Our work thus underscores the role of inclusion of polar groups into the framework of traditional binary biomimetic antimicrobial polymers and suggests different mode of partitioning into bacterial membranes, mimicking antimicrobial mechanism of globular antimicrobial peptides like Defensin.
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Affiliation(s)
- Garima Rani
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India. and Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Kenichi Kuroda
- Department of Biologic and Materials Sciences, School of Dentistry, University of Michigan, Ann Arbor, Michigan 48109, USA.
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India. and Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
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6
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Simcock PW, Bublitz M, Cipcigan F, Ryadnov MG, Crain J, Stansfeld PJ, Sansom MSP. Membrane Binding of Antimicrobial Peptides Is Modulated by Lipid Charge Modification. J Chem Theory Comput 2021; 17:1218-1228. [PMID: 33395285 DOI: 10.1021/acs.jctc.0c01025] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptide interactions with lipid bilayers play a key role in a range of biological processes and depend on electrostatic interactions between charged amino acids and lipid headgroups. Antimicrobial peptides (AMPs) initiate the killing of bacteria by binding to and destabilizing their membranes. The multiple peptide resistance factor (MprF) provides a defense mechanism for bacteria against a broad range of AMPs. MprF reduces the negative charge of bacterial membranes through enzymatic conversion of the anionic lipid phosphatidyl glycerol (PG) to either zwitterionic alanyl-phosphatidyl glycerol (Ala-PG) or cationic lysyl-phosphatidyl glycerol (Lys-PG). The resulting change in the membrane charge is suggested to reduce the binding of AMPs to membranes, thus impeding downstream AMP activity. Using coarse-grained molecular dynamics to investigate the effects of these modified lipids on AMP binding to model membranes, we show that AMPs have substantially reduced affinity for model membranes containing Ala-PG or Lys-PG. More than 5000 simulations in total are used to define the relationship between lipid bilayer composition, peptide sequence (using five different membrane-active peptides), and peptide binding to membranes. The degree of interaction of a peptide with a membrane correlates with the membrane surface charge density. Free energy profile (potential of mean force) calculations reveal that the lipid modifications due to MprF alter the energy barrier to peptide helix penetration of the bilayer. These results will offer a guide to the design of novel peptides, which addresses the issue of resistance via MprF-mediated membrane modification.
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Affiliation(s)
- Patrick W Simcock
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
| | - Maike Bublitz
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
| | | | - Maxim G Ryadnov
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Jason Crain
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
- IBM Research UK, Hartree Centre, Daresbury WA4 4AD, U.K
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
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Rani G, Kuroda K, Vemparala S. Aggregation of methacrylate-based ternary biomimetic antimicrobial polymers in solution. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 33:064003. [PMID: 33105118 DOI: 10.1088/1361-648x/abc4c9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Using detailed atomistic simulations, we explore the morphological characteristics of aggregates formed in solution phase by ternary biomimetic antimicrobial (AM) methacrylate polymers, composed of hydrophobic, charged cationic and polar functional groups and compare it with aggregate morphologies of binary methacrylate polymers, composed only of hydrophobic and charged cationic functional groups. The effect of sequence of the constituent functional groups on aggregate conformation is also studied by considering random and block sequences along the polymer backbone. Our results show that while binary polymers tend to form robust aggregates, replacing some of the hydrophobic groups with overall charge neutral polar groups weakens the aggregate considerably, leading to increased conformational fluctuations and formation of loose-packed, open aggregates, particularly in the case of random ternary polymers. Interaction energy calculations clearly suggest that the role of inclusion of polar groups in ternary polymers is two-fold: (1) to reduce possible strong local concentration of hydrophobic groups and 'smear' the overall hydrophobicity along the polymer backbone to increase the solubility of the polymers (2) to compensate the loss of attractive hydrophobic interactions by forming attractive electrostatic interactions with the charged groups and contribute to aggregation formation, albeit weak. Given that most of the naturally occurring AM peptides have contributions from all the three functional groups, this study elucidates the functionally tuneable role of inclusion of polar groups in the way AM agents interact with each other in solution phase, which can eventually dictate their partitioning behaviour into bacterial and mammalian membranes.
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Affiliation(s)
- Garima Rani
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Kenichi Kuroda
- Department of Biologic and Materials Sciences, School of Dentistry, University of Michigan, Ann Arbor, Michigan 48109, United States of America
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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8
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Shahane G, Ding W, Palaiokostas M, Azevedo HS, Orsi M. Interaction of Antimicrobial Lipopeptides with Bacterial Lipid Bilayers. J Membr Biol 2019; 252:317-329. [PMID: 31098677 PMCID: PMC6790193 DOI: 10.1007/s00232-019-00068-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/03/2019] [Indexed: 02/07/2023]
Abstract
The resistance of pathogens to traditional antibiotics is currently a global issue of enormous concern. As the discovery and development of new antibiotics become increasingly challenging, synthetic antimicrobial lipopeptides (AMLPs) are now receiving renewed attention as a new class of antimicrobial agents. In contrast to traditional antibiotics, AMLPs act by physically disrupting the cell membrane (rather than targeting specific proteins), thus reducing the risk of inducing bacterial resistance. In this study, we use microsecond-timescale atomistic molecular dynamics simulations to quantify the interaction of a short AMLP (C16-KKK) with model bacterial lipid bilayers. In particular, we investigate how fundamental transmembrane properties change in relation to a range of lipopeptide concentrations. A number of structural, mechanical, and dynamical features are found to be significantly altered in a non-linear fashion. At 10 mol% concentration, lipopeptides have a condensing effect on bacterial bilayers, characterized by a decrease in the area per lipid and an increase in the bilayer order. Higher AMLP concentrations of 25 and 40 mol% destabilize the membrane by disrupting the bilayer core structure, inducing membrane thinning and water leakage. Important transmembrane properties such as the lateral pressure and dipole potential profiles are also affected. Potential implications on membrane function and associated proteins are discussed.
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Affiliation(s)
- Ganesh Shahane
- Institute of Bioengineering, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Wei Ding
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Michail Palaiokostas
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Helena S Azevedo
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Mario Orsi
- Department of Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK.
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9
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Shahane G, Ding W, Palaiokostas M, Orsi M. Physical properties of model biological lipid bilayers: insights from all-atom molecular dynamics simulations. J Mol Model 2019; 25:76. [PMID: 30806797 DOI: 10.1007/s00894-019-3964-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/07/2019] [Indexed: 02/04/2023]
Abstract
The physical properties of lipid bilayers are sensitive to the specific type and composition of the lipids that make up the many different types of cell membranes. Studying model bilayers of representative heterogeneous compositions can provide key insights into membrane functionality. In this work, we use atomistic molecular dynamics simulations to characterize key properties in a number of bilayer membranes of varying composition. We first examine basic properties, such as lipid area, volume, and bilayer thickness, of simple, homogeneous bilayers comprising several lipid types, which are prevalent in biological membranes. Such lipids are then used in simulations of heterogeneous systems representative of bacterial, mammalian, and cancer membranes. Our analysis is especially focused on depth-dependent, transmembrane profiles; in particular, we calculate lateral pressure and dipole potential profiles, two fundamental properties which play key roles in a large number of biological functions.
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Affiliation(s)
- Ganesh Shahane
- Institute of Bioengineering, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Wei Ding
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Michail Palaiokostas
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Mario Orsi
- Department of Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK.
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10
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Bejagam KK, An Y, Singh S, Deshmukh SA. Machine-Learning Enabled New Insights into the Coil-to-Globule Transition of Thermosensitive Polymers Using a Coarse-Grained Model. J Phys Chem Lett 2018; 9:6480-6488. [PMID: 30372083 DOI: 10.1021/acs.jpclett.8b02956] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We present a computational framework that integrates coarse-grained (CG) molecular dynamics (MD) simulations and a data-driven machine-learning (ML) method to gain insights into the conformations of polymers in solutions. We employ this framework to study conformational transition of a model thermosensitive polymer, poly( N-isopropylacrylamide) (PNIPAM). Here, we have developed the first of its kind, a temperature-independent CG model of PNIPAM that can accurately predict its experimental lower critical solution temperature (LCST) while retaining the tacticity in the presence of an explicit water model. The CG model was extensively validated by performing CG MD simulations with different initial conformations, varying the radius of gyration of chain, the chain length, and the angle between the adjacent monomers of the initial configuration of PNIPAM (total simulation time = 90 μs). Moreover, for the first time, we utilize the nonmetric multidimensional scaling (NMDS) method, a data-driven ML approach, to gain further insights into the mechanisms and pathways of this coil-to-globule transition by analyzing CG MD simulation trajectories. NMDS analysis provides entirely new insights and shows multiple metastable states of PNIPAM during its coil-to-globule transition above the LCST.
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Affiliation(s)
- Karteek K Bejagam
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Yaxin An
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Samrendra Singh
- CNH Industrial , Burr Ridge , Illinois 60527 , United States
| | - Sanket A Deshmukh
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
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Penetration of antimicrobial peptides in a lung surfactant model. Colloids Surf B Biointerfaces 2018; 167:345-353. [PMID: 29689490 DOI: 10.1016/j.colsurfb.2018.04.030] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 04/12/2018] [Accepted: 04/13/2018] [Indexed: 12/30/2022]
Abstract
Molecular dynamics simulations were successfully performed to understand the absorption mechanism of antimicrobial peptides LL-37, CATH-2, and SMAP-29 in a lung surfactant model. The antimicrobial peptides quickly penetrate in the lung surfactant model in dozens or hundreds nanoseconds, but they electrostatically interact with the lipid polar heads during the simulation time of 2 μs. This electrostatic interaction should be the explanation for the inactivation of the antimicrobial peptides when co-administrated with lung surfactant. As they strongly interact with the lipid polar heads of the lung surfactant, there is no positive charge available on the antimicrobial peptide to attack the negatively charged bacteria membrane. In order to avoid the interaction of peptides with the lipid polar heads, sodium cholate was used to form nanoparticles which act as an absorption enhancer of all antimicrobial peptides used in this investigation. The nanoparticles of 150 molecules of sodium cholate with one peptide were inserted on the top of the lung surfactant model. The nanoparticles penetrated into the lung surfactant model, spreading the sodium cholate molecules around the lipid polar heads. The sodium cholate molecules seem to protect the peptides from the interaction with the lipid polar heads, leaving them free to be delivered to the water phase. The penetration of peptides alone or even the peptide nanoparticles with sodium cholate do not collapse the lung surfactant model, indicating to be a promisor drug delivery system to the lung. The implications of this finding are that antimicrobial peptides may only be co-administered with an absorption enhancer such as sodium cholate into lung surfactant in order to avoid inactivation of their antimicrobial activity.
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12
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Lipkin R, Lazaridis T. Computational studies of peptide-induced membrane pore formation. Philos Trans R Soc Lond B Biol Sci 2018. [PMID: 28630158 DOI: 10.1098/rstb.2016.0219] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A variety of peptides induce pores in biological membranes; the most common ones are naturally produced antimicrobial peptides (AMPs), which are small, usually cationic, and defend diverse organisms against biological threats. Because it is not possible to observe these pores directly on a molecular scale, the structure of AMP-induced pores and the exact sequence of steps leading to their formation remain uncertain. Hence, these questions have been investigated via molecular modelling. In this article, we review computational studies of AMP pore formation using all-atom, coarse-grained, and implicit solvent models; evaluate the results obtained and suggest future research directions to further elucidate the pore formation mechanism of AMPs.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.
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Affiliation(s)
- Richard Lipkin
- Department of Chemistry, City College of New York, 160 Convent Avenue, New York, NY 10031, USA.,Graduate Program in Chemistry, The Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, 160 Convent Avenue, New York, NY 10031, USA
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13
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Greber KE, Ciura K, Belka M, Kawczak P, Nowakowska J, Bączek T, Sawicki W. Characterization of antimicrobial and hemolytic properties of short synthetic cationic lipopeptides based on QSAR/QSTR approach. Amino Acids 2017; 50:479-485. [PMID: 29264738 PMCID: PMC5852172 DOI: 10.1007/s00726-017-2530-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/12/2017] [Indexed: 01/04/2023]
Abstract
In this study, we investigated the influence of molecular descriptors of cationic lipopeptides on their antimicrobial activity and hemolytic properties. The quantitative structure-activity relationship and quantitative structure-property relationship models were constructed. The antimicrobial, hemolytic and retention data were used as dependent variable and structural parameters as the independent ones. The obtained results suggest that the chromatographic indexes can be employed for prediction of antibacterial activity and that lipopeptides present nonspecific interaction between erythrocytes and bacterial membranes.
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Affiliation(s)
- Katarzyna E Greber
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland.
| | - Krzesimir Ciura
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Mariusz Belka
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Piotr Kawczak
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Joanna Nowakowska
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Tomasz Bączek
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Wiesław Sawicki
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
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14
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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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15
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Koh JJ, Lin S, Beuerman RW, Liu S. Recent advances in synthetic lipopeptides as anti-microbial agents: designs and synthetic approaches. Amino Acids 2017; 49:1653-1677. [PMID: 28823054 DOI: 10.1007/s00726-017-2476-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 07/31/2017] [Indexed: 12/31/2022]
Abstract
Infectious diseases impose serious public health burdens and continue to be a global public health crisis. The treatment of infections caused by multidrug-resistant pathogens is challenging because only a few viable therapeutic options are clinically available. The emergence and risk of drug-resistant superbugs and the dearth of new classes of antibiotics have drawn increasing awareness that we may return to the pre-antibiotic era. To date, lipopeptides have been received considerable attention because of the following properties: They exhibit potent antimicrobial activities against a broad spectrum of pathogens, rapid bactericidal activity and have a different antimicrobial action compared with most of the conventional antibiotics used today and very slow development of drug resistance tendency. In general, lipopeptides can be structurally classified into two parts: a hydrophilic peptide moiety and a hydrophobic fatty acyl chain. To date, a significant amount of design and synthesis of lipopeptides have been done to improve the therapeutic potential of lipopeptides. This review will present the current knowledge and the recent research in design and synthesis of new lipopeptides and their derivatives in the last 5 years.
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Affiliation(s)
- Jun-Jie Koh
- Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower Level 6, Singapore, 169856, Singapore
| | - Shuimu Lin
- Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower Level 6, Singapore, 169856, Singapore
- School of Materials Science and Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Roger W Beuerman
- Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower Level 6, Singapore, 169856, Singapore.
- SRP Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, 169857, Singapore.
| | - Shouping Liu
- Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower Level 6, Singapore, 169856, Singapore.
- SRP Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, 169857, Singapore.
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16
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Wenda JM, Juhaniewicz J, Tymecka D, Konarzewska D, Sęk S. Modulation of Activity of Ultrashort Lipopeptides toward Negatively Charged Model Lipid Films. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:4619-4627. [PMID: 28459579 DOI: 10.1021/acs.langmuir.6b04674] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Because of the increasing resistance of pathogens to commonly used antibiotics, there is an urgent need to find alternative antimicrobial compounds with different mechanisms of action. Among them, lipopeptides are recognized as promising candidates. In this work, the Langmuir technique and atomic force microscopy were employed to investigate the interactions of two novel lipopeptides with negatively charged phospholipid membranes, which served as a simplified model of inner membrane of Gram-negative bacteria. Lipid films contained phosphatidylethanolamine and phosphatidylglycerol extracts from E. coli bacteria. Lipopeptides were composed of palmitoyl chain covalently coupled to N-terminus of peptide with Trp-Lys-Leu-Lys amino acid sequence and the conformation of third residue was either d-Leu or l-Leu. It was found that chirality of leucine strongly affects interfacial behavior of these compounds, which was ascribed to the difference in effective size of the peptide portion of the molecules. Although the lipopeptides were the same in terms of amino acid sequence, charge, and identity of lipophilic chain, the experiments revealed that the barrier for their insertion into the lipid membrane is significantly different. Namely, it was lower for lipopeptide containing d-Leu residue. We have also found that insertion of the lipopeptides into the model membranes strongly alters lateral distribution of the membrane components and leads to its substantial fluidization. The dynamics of reorganization was noticeably faster in the presence of lipopeptide with smaller size of peptide moiety, i.e., containing d-Leu. It proves that effective size of the peptide headgroup is an important factor determining lipopeptide activity toward the lipid membranes.
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Affiliation(s)
- Joanna M Wenda
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw , Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Joanna Juhaniewicz
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw , Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Dagmara Tymecka
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw , Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Dorota Konarzewska
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw , Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Sławomir Sęk
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw , Żwirki i Wigury 101, 02-089 Warsaw, Poland
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17
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Lopes D, Jakobtorweihen S, Nunes C, Sarmento B, Reis S. Shedding light on the puzzle of drug-membrane interactions: Experimental techniques and molecular dynamics simulations. Prog Lipid Res 2017; 65:24-44. [DOI: 10.1016/j.plipres.2016.12.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 11/30/2016] [Accepted: 12/03/2016] [Indexed: 12/20/2022]
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18
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Bouvier B. Optimizing the Multivalent Binding of the Bacterial Lectin LecA by Glycopeptide Dendrimers for Therapeutic Purposes. J Chem Inf Model 2016; 56:1193-204. [DOI: 10.1021/acs.jcim.6b00146] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Benjamin Bouvier
- Laboratoire de Glycochimie,
des Antimicrobiens et des Agroressources, CNRS UMR7378/Université de Picardie Jules Verne, 10 rue Baudelocque, 80039 Amiens Cedex, France
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19
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Lin D, Grossfield A. Thermodynamics of Micelle Formation and Membrane Fusion Modulate Antimicrobial Lipopeptide Activity. Biophys J 2016; 109:750-9. [PMID: 26287627 DOI: 10.1016/j.bpj.2015.07.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/04/2015] [Accepted: 07/01/2015] [Indexed: 11/18/2022] Open
Abstract
Antimicrobial lipopeptides (AMLPs) are antimicrobial drug candidates that preferentially target microbial membranes. One class of AMLPs, composed of cationic tetrapeptides attached to an acyl chain, have minimal inhibitory concentrations in the micromolar range against a range of bacteria and fungi. Previously, we used coarse-grained molecular dynamics simulations and free energy methods to study the thermodynamics of their interaction with membranes in their monomeric state. Here, we extended the study to the biologically relevant micellar state, using, to our knowledge, a novel reaction coordinate based on hydrophobic contacts. Using umbrella sampling along this reaction coordinate, we identified the critical transition states when micelles insert into membranes. The results indicate that the binding of these AMLP micelles to membranes is thermodynamically favorable, but in contrast to the monomeric case, there are significant free energy barriers. The height of these free energy barriers depends on the membrane composition, suggesting that the AMLPs' ability to selectively target bacterial membranes may be as much kinetic as thermodynamic. This mechanism highlights the importance of considering oligomeric state in solution as criterion when optimizing peptides or lipopeptides as antibiotic leads.
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Affiliation(s)
- Dejun Lin
- 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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20
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Baul U, Kuroda K, Vemparala S. Interaction of multiple biomimetic antimicrobial polymers with model bacterial membranes. J Chem Phys 2015; 141:084902. [PMID: 25173040 DOI: 10.1063/1.4893440] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using atomistic molecular dynamics simulations, interaction of multiple synthetic random copolymers based on methacrylates on prototypical bacterial membranes is investigated. The simulations show that the cationic polymers form a micellar aggregate in water phase and the aggregate, when interacting with the bacterial membrane, induces clustering of oppositely charged anionic lipid molecules to form clusters and enhances ordering of lipid chains. The model bacterial membrane, consequently, develops lateral inhomogeneity in membrane thickness profile compared to polymer-free system. The individual polymers in the aggregate are released into the bacterial membrane in a phased manner and the simulations suggest that the most probable location of the partitioned polymers is near the 1-palmitoyl-2-oleoyl-phosphatidylglycerol (POPG) clusters. The partitioned polymers preferentially adopt facially amphiphilic conformations at lipid-water interface, despite lacking intrinsic secondary structures such as α-helix or β-sheet found in naturally occurring antimicrobial peptides.
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Affiliation(s)
- Upayan Baul
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
| | - Kenichi Kuroda
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, Ann Arbor, Michigan 48109, USA
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
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21
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Bulacu M, Sevink GJA. Erratum. Computational insight in the role of fusogenic lipopeptides at the onset of liposome fusion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1716-25. [PMID: 26273716 DOI: 10.1016/j.bbamem.2015.03.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We performed an extensive computational study to obtain insight in the molecular mechanisms that take place prior to membrane fusion. We focused on membrane-anchored hybrid macromolecules (lipid–polymer–oligopeptide) that mimic biological SNARE proteins in terms of liposome fusion characteristics [H. Robson Marsden et al., 2009]; efficient micro-second simulation was enabled by combining validated MARTINI force fields for the molecular building blocks in coarse-grained molecular dynamics (CGMD). We find that individual peptide domains in the hybrid macromolecules bind and partially integrate parallel to the membrane surface, in agreement with experimental findings. By varying several experimental design parameters, we observe that peptide domains remain in the solvent phase only in two cases: (1) for solitary lipopeptides (low concentration), below a threshold area per lipid in the membrane, and (2) when the lipopeptide concentration is high enough for the peptide domains to self-assemble into tetrameric homo-complexes. The peptide-membrane binding is not affected by solvent-induced peptide unfolding, which we mimicked by relaxing the usual MARTINI helix constraints. Remarkably, in this case, a reverse transition to a helical secondary structure is observed after binding, highlighting the role of the membrane as a template (partitioning-folding coupling). Our findings undermine the current view of the initial stages towards fusion, in which membranes are thought to be kept in close apposition via dimerization of individual complementary peptides in the solvent phase. Although we did not study actual fusion, our simulations show that the formation of homomers, which is suppressed in experimental peptide pair design and therefore believed to be insignificant for fusion, by peptides anchored to the same membrane does play a key role in this locking mechanism and potentially also in membrane destabilization that precedes fusion.
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22
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Lin D, Grossfield A. Thermodynamics of antimicrobial lipopeptide binding to membranes: origins of affinity and selectivity. Biophys J 2015; 107:1862-1872. [PMID: 25418167 DOI: 10.1016/j.bpj.2014.08.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 08/25/2014] [Accepted: 08/29/2014] [Indexed: 10/24/2022] Open
Abstract
The development of novel antibiotic drugs is one of the most pressing biomedical problems due to the increasing number of antibiotic-resistant pathogens. Antimicrobial peptides and lipopeptides are a promising category of candidates, but the molecular origins of their antimembrane activity is unclear. Here we explore a series of recently developed antimicrobial lipopeptides, using coarse-grained molecular-dynamics simulations and free energy methods to uncover the thermodynamics governing their binding to membranes. Specifically, we quantify C16-KGGK's binding affinity to the two types of membrane by umbrella sampling. We also examined the origin of C16-KGGK's selectivity for bacterial versus mammalian membranes by systematically varying the peptide sequence and salt concentration. Our data showed that the C16 hydrophobic tail is the main contributor to its affinity to lipid membrane, whereas the peptide portion is mainly responsible for its selectivity. Furthermore, the electrostatic interaction between the cationic peptide and anionic bacterial membrane plays a significant role in the selectivity.
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Affiliation(s)
- Dejun Lin
- 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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23
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Berglund NA, Piggot TJ, Jefferies D, Sessions RB, Bond PJ, Khalid S. Interaction of the antimicrobial peptide polymyxin B1 with both membranes of E. coli: a molecular dynamics study. PLoS Comput Biol 2015; 11:e1004180. [PMID: 25885324 PMCID: PMC4401565 DOI: 10.1371/journal.pcbi.1004180] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 02/06/2015] [Indexed: 11/17/2022] Open
Abstract
Antimicrobial peptides are small, cationic proteins that can induce lysis of bacterial cells through interaction with their membranes. Different mechanisms for cell lysis have been proposed, but these models tend to neglect the role of the chemical composition of the membrane, which differs between bacterial species and can be heterogeneous even within a single cell. Moreover, the cell envelope of Gram-negative bacteria such as E. coli contains two membranes with differing compositions. To this end, we report the first molecular dynamics simulation study of the interaction of the antimicrobial peptide, polymyxin B1 with complex models of both the inner and outer membranes of E. coli. The results of >16 microseconds of simulation predict that polymyxin B1 is likely to interact with the membranes via distinct mechanisms. The lipopeptides aggregate in the lipopolysaccharide headgroup region of the outer membrane with limited tendency for insertion within the lipid A tails. In contrast, the lipopeptides readily insert into the inner membrane core, and the concomitant increased hydration may be responsible for bilayer destabilization and antimicrobial function. Given the urgent need to develop novel, potent antibiotics, the results presented here reveal key mechanistic details that may be exploited for future rational drug development.
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Affiliation(s)
- Nils A Berglund
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom; Bioinformatics Institute (A*STAR), Singapore
| | - Thomas J Piggot
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
| | - Damien Jefferies
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
| | | | - Peter J Bond
- Bioinformatics Institute (A*STAR), Singapore; Department of Biological Sciences, National University of Singapore, Singapore
| | - Syma Khalid
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
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24
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Fracchia L, J. Banat J, Cavallo M, Ceresa C, M. Banat I. Potential therapeutic applications of microbial surface-active compounds. AIMS BIOENGINEERING 2015. [DOI: 10.3934/bioeng.2015.3.144] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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25
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Bulacu M, Sevink GJA. Computational insight in the role of fusogenic lipopeptides at the onset of liposome fusion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:848-58. [PMID: 25528473 DOI: 10.1016/j.bbamem.2014.12.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 12/03/2014] [Accepted: 12/09/2014] [Indexed: 10/24/2022]
Abstract
We performed an extensive computational study to obtain insight in the molecular mechanisms that take place prior to membrane fusion. We focused on membrane-anchored hybrid macromolecules (lipid-polymer-oligopeptide) that mimic biological SNARE proteins in terms of liposome fusion characteristics [H. Robson Marsden et al., 2009]; efficient micro-second simulation was enabled by combining validated MARTINI force fields for the molecular building blocks in coarse-grained molecular dynamics (CGMD). We find that individual peptide domains in the hybrid macromolecules bind and partially integrate parallel to the membrane surface, in agreement with experimental findings. By varying several experimental design parameters, we observe that peptide domains remain in the solvent phase only in two cases: (1) for solitary lipopeptides (low concentration), below a threshold area per lipid in the membrane, and (2) when the lipopeptide concentration is high enough for the peptide domains to self-assemble into tetrameric homo-complexes. The peptide-membrane binding is not affected by solvent-induced peptide unfolding, which we mimicked by relaxing the usual MARTINI helix constraints. Remarkably, in this case, a reverse transition to a helical secondary structure is observed after binding, highlighting the role of the membrane as a template (partitioning-folding coupling). Our findings undermine the current view of the initial stages towards fusion, in which membranes are thought to be kept in close apposition via dimerization of individual complementary peptides in the solvent phase. Although we did not study actual fusion, our simulations show that the formation of homomers, which is suppressed in experimental peptide-pair design and therefore believed to be insignificant for fusion, by peptides anchored to the same membrane does play a key role in this locking mechanism and potentially also in membrane destabilization that precede fusion.
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Affiliation(s)
- M Bulacu
- Culgi BV, Galileiweg 8, 2333 BD Leiden, The Netherlands
| | - G J A Sevink
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.
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26
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Romo TD, Leioatts N, Grossfield A. Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations. J Comput Chem 2014; 35:2305-18. [PMID: 25327784 PMCID: PMC4227929 DOI: 10.1002/jcc.23753] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 09/07/2014] [Indexed: 01/13/2023]
Abstract
LOOS (Lightweight Object Oriented Structure-analysis) is a C++ library designed to facilitate making novel tools for analyzing molecular dynamics simulations by abstracting out the repetitive tasks, allowing developers to focus on the scientifically relevant part of the problem. LOOS supports input using the native file formats of most common biomolecular simulation packages, including CHARMM, NAMD, Amber, Tinker, and Gromacs. A dynamic atom selection language based on the C expression syntax is included and is easily accessible to the tool-writer. In addition, LOOS is bundled with over 140 prebuilt tools, including suites of tools for analyzing simulation convergence, three-dimensional histograms, and elastic network models. Through modern C++ design, LOOS is both simple to develop with (requiring knowledge of only four core classes and a few utility functions) and is easily extensible. A python interface to the core classes is also provided, further facilitating tool development.
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Affiliation(s)
- Tod D Romo
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York, 14642
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27
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Sharma D, Mandal SM, Manhas RK. Purification and characterization of a novel lipopeptide from Streptomyces amritsarensis sp. nov. active against methicillin-resistant Staphylococcus aureus. AMB Express 2014; 4:50. [PMID: 25006539 PMCID: PMC4077001 DOI: 10.1186/s13568-014-0050-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/27/2014] [Indexed: 11/28/2022] Open
Abstract
Nowadays antimicrobial lipopeptides are being widely exploited for developing potential therapeutic agents for treating bacterial infections. In the present study, we have purified and characterized an antimicrobial lipopeptide produced by Streptomyces amritsarensis sp. nov. (= MTCC 11845(T) = JCM 19660(T)). The lipopeptide was purified using silica gel chromatography, size exclusion chromatography and reverse phase- HPLC. The MS/MS analysis of the lipopeptide revealed that it has amino acid sequence as Ala-Thr-Gly-Ser-His-Gln and a long chain fatty acid tail with six times repeated the molecular mass of 161 Da which is corresponding to -C12H19. Based on the molecular mass (878.5 Da) and amino acid composition, the lipopeptide was identified as a novel lipopeptide. The MIC values of purified lipopeptide against Bacillus subtilis (MTCC 619), Staphylococcus epidermidis (MTCC 435), Mycobacterium smegmatis (MTCC 6) and clinical strain, Methicillin Resistant Staphylococcus aureus (MRSA) were found to be 10, 15, 25 and 45 μg/ml, respectively. It was completely stable at 70°C for 1 h and retained 81.8% activity after autoclaving (121°C for 15 min). It did not show any change in its activity profile between pH 5.0 - 9.0 and is stable to trypsin, proteinase K and lipase enzymes. It was found to be non-mutagenic against Salmonella typhimurium (TA98) and did not show cytotoxicity when checked against Chinese hamster ovary (CHO) cell line. In addition to antibacterial activity it also exhibits biosurfactant activity.
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Affiliation(s)
- Deepika Sharma
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Santi M Mandal
- Central Research Facility, Indian Institute of Technology, Kharagpur 721302, West Bengal, India
| | - Rajesh Kumari Manhas
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
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28
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Sikorska E, Dawgul M, Greber K, Iłowska E, Pogorzelska A, Kamysz W. Self-assembly and interactions of short antimicrobial cationic lipopeptides with membrane lipids: ITC, FTIR and molecular dynamics studies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2625-34. [PMID: 24978107 DOI: 10.1016/j.bbamem.2014.06.016] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 05/13/2014] [Accepted: 06/23/2014] [Indexed: 11/28/2022]
Abstract
In this work, the self-organization and the behavior of the surfactant-like peptides in the presence of biological membrane models were studied. The studies were focused on synthetic palmitic acid-containing lipopeptides, C16-KK-NH2 (I), C16-KGK-NH2 (II) and C16-KKKK-NH2 (III). The self-assembly was explored by molecular dynamics simulations using a coarse-grained force field. The critical micellar concentration was estimated by the surface tension measurements. The thermodynamics of the peptides binding to the anionic and zwitterionic lipids were established using isothermal titration calorimetry (ITC). The influence of the peptides on the lipid acyl chain ordering was determined using FTIR spectroscopy. The compounds studied show surface-active properties with a distinct CMC over the millimolar range. An increase in the steric and electrostatic repulsion between polar head groups shifts the CMC toward higher values and reduces the aggregation number. An analysis of the peptide-membrane binding revealed a unique interplay between the initial electrostatic and the subsequent hydrophobic interactions enabling the lipopeptides to interact with the lipid bilayer. In the case of C16-KKKK-NH2 (III), compensation of the electrostatic and hydrophobic interactions upon binding to the anionic membrane has been suggested and consequently no overall binding effects were noticed in ITC thermograms and FTIR spectra.
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Affiliation(s)
- Emilia Sikorska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Małgorzata Dawgul
- Faculty of Pharmacy with Subfaculty of Laboratory Medicine, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland
| | - Katarzyna Greber
- Faculty of Pharmacy with Subfaculty of Laboratory Medicine, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland
| | - Emilia Iłowska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Aneta Pogorzelska
- Faculty of Pharmacy with Subfaculty of Laboratory Medicine, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland
| | - Wojciech Kamysz
- Faculty of Pharmacy with Subfaculty of Laboratory Medicine, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland
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29
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Horn JN, Cravens A, Grossfield A. Interactions between fengycin and model bilayers quantified by coarse-grained molecular dynamics. Biophys J 2014; 105:1612-23. [PMID: 24094402 DOI: 10.1016/j.bpj.2013.08.034] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/20/2013] [Accepted: 08/22/2013] [Indexed: 11/28/2022] Open
Abstract
Bacteria, particularly of the genus Bacillus, produce a wide variety of antifungal compounds. They act by affecting the lipid bilayers of fungal membranes, causing curvature-induced strain and eventual permeabilization. One class of these, known as fengycins, has been commercialized for treating agricultural infections and shows some promise as a possible antifungal pharmaceutical. Understanding the mechanism by which fengycins damage lipid bilayers could prove useful to the future development of related antifungal treatments. In this work, we present multi-microsecond-long simulations of fengycin interacting with different lipid bilayer systems. We see fengycin aggregation and uncover a clear aggregation pattern that is partially influenced by bilayer composition. We also quantify some local bilayer perturbations caused by fengycin binding, including curvature of the lipid bilayer and local electrostatic-driven reorganization.
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Affiliation(s)
- Joshua N Horn
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York
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30
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Loison C, Nasir MN, Benichou E, Besson F, Brevet PF. Multi-scale modeling of mycosubtilin lipopeptides at the air/water interface: structure and optical second harmonic generation. Phys Chem Chem Phys 2014; 16:2136-48. [DOI: 10.1039/c3cp53101e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Bacteriocin AS-48 binding to model membranes and pore formation as revealed by coarse-grained simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2524-31. [DOI: 10.1016/j.bbamem.2013.05.036] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Revised: 05/24/2013] [Accepted: 05/31/2013] [Indexed: 02/05/2023]
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32
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Horn JN, Romo TD, Grossfield A. Simulating the mechanism of antimicrobial lipopeptides with all-atom molecular dynamics. Biochemistry 2013; 52:5604-10. [PMID: 23875688 DOI: 10.1021/bi400773q] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The emergence of antibiotic resistant pathogens is one of the major medical concerns of the 21st century, prompting renewed interest in the development of novel antimicrobial compounds. Here we use microsecond-scale all-atom molecular dynamics simulations to characterize the structure, dynamics, and membrane-binding mechanism of a synthetic antimicrobial lipopeptide, C16-KGGK. Our simulations suggest that these lipopeptides prefer to aggregate in solution and alter the intrinsic order of the lipid bilayer upon binding. From these results and previous coarse-grained simulations, we have developed a simple model for the binding and insertion process for these lipopeptides.
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Affiliation(s)
- Joshua N Horn
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
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33
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Mandal SM, Barbosa AEAD, Franco OL. Lipopeptides in microbial infection control: scope and reality for industry. Biotechnol Adv 2013; 31:338-45. [PMID: 23318669 DOI: 10.1016/j.biotechadv.2013.01.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 01/04/2013] [Accepted: 01/04/2013] [Indexed: 01/12/2023]
Abstract
Lipopeptides are compounds that are formed by cyclic or short linear peptides linked with a lipid tail or other lipophilic molecules. Recently, several lipopeptides were characterized, showing surfactant, antimicrobial and cytotoxic activities. The properties of lipopeptides may lead to applications in diverse industrial fields including the pharmaceutical industry as conventional antibiotics; the cosmetic industry for dermatological product development due to surfactant and anti-wrinkle properties; in food production acting as emulsifiers in various foodstuffs; and also in the field of biotechnology as biosurfactants. Some lipopeptides have reached a commercial antibiotic status, such as daptomycin, caspofungin, micafungin, and anidulafungin. This will be the focus of this review. Moreover, the review presented here will focus on the biotechnological utilization of lipopeptides in different fields as well as the functional-structure relation, connecting recent aspects of synthesis and structure diversity.
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Affiliation(s)
- Santi M Mandal
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur 721302, W B, India
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34
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Baindara P, Mandal SM, Chawla N, Singh PK, Pinnaka AK, Korpole S. Characterization of two antimicrobial peptides produced by a halotolerant Bacillus subtilis strain SK.DU.4 isolated from a rhizosphere soil sample. AMB Express 2013; 3:2. [PMID: 23289832 PMCID: PMC3549917 DOI: 10.1186/2191-0855-3-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Accepted: 01/02/2013] [Indexed: 11/10/2022] Open
Abstract
A bacterial strain producing two antimicrobial peptides was isolated from a rhizosphere soil sample and identified as Bacillus subtilis based on both phenotypic and 16S rRNA gene sequence phylogenetic analysis. It grew optimally up to 14% NaCl and produced antimicrobial peptide within 24 h of growth. The peptides were purified using a combination of chemical extraction and chromatographic techniques. The MALDI-TOF analysis of HPLC purified fractions revealed that the strain SK.DU.4 secreted a bacteriocin-like peptide with molecular mass of 5323.9 Da and a surface-active lipopeptide (m/z 1056 Da). The peptide mass fingerprinting of low-molecular-weight bacteriocin exhibited significant similarity with stretches of secreted lipoprotein of Methylomicrobium album BG8 and displayed 70% sequence coverage. MALDI MS/MS analysis elucidated the lipopeptide as a cyclic lipopeptide with a β-hydroxy fatty acid linked to Ser of a peptide with seven α-amino acids (Asp-Tyr-Asn-Gln-Pro-Asn-Ser) and assigned it to iturin-like group of antimicrobial biosurfactants. However, it differed in amino acid composition with other members of the iturin family. Both peptides were active against Gram-positive bacteria, suggesting that they had an additive effect.
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Affiliation(s)
- Piyush Baindara
- MTCC and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Santi M Mandal
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Niharika Chawla
- MTCC and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Pradip Kumar Singh
- MTCC and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Anil Kumar Pinnaka
- MTCC and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Suresh Korpole
- MTCC and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
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35
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36
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de Jong DH, Singh G, Bennett WFD, Arnarez C, Wassenaar TA, Schäfer LV, Periole X, Tieleman DP, Marrink SJ. Improved Parameters for the Martini Coarse-Grained Protein Force Field. J Chem Theory Comput 2012; 9:687-97. [DOI: 10.1021/ct300646g] [Citation(s) in RCA: 922] [Impact Index Per Article: 76.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Djurre H. de Jong
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials,
University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Gurpreet Singh
- Department of Biological Sciences
and Institute for Biocomplexity and Informatics, University of Calgary,
2500 University Dr. NW, Calgary, AB, Canada, T2N 1N4
| | - W. F. Drew Bennett
- Department of Biological Sciences
and Institute for Biocomplexity and Informatics, University of Calgary,
2500 University Dr. NW, Calgary, AB, Canada, T2N 1N4
| | - Clement Arnarez
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials,
University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Tsjerk A. Wassenaar
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials,
University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Lars V. Schäfer
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials,
University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Xavier Periole
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials,
University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - D. Peter Tieleman
- Department of Biological Sciences
and Institute for Biocomplexity and Informatics, University of Calgary,
2500 University Dr. NW, Calgary, AB, Canada, T2N 1N4
| | - 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
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