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Blanco-González A, Wurl A, Mendes Ferreira T, Piñeiro Á, Garcia-Fandino R. Simulating Bacterial Membrane Models at the Atomistic Level: A Force Field Comparison. J Chem Theory Comput 2024. [PMID: 39226695 DOI: 10.1021/acs.jctc.4c00204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Molecular dynamics (MD) simulations are currently an indispensable tool to understand both the dynamic and nanoscale organization of cell membrane models. A large number of quantitative parameters can be extracted from these simulations, but their reliability is determined by the quality of the employed force field and the simulation parameters. Much of the work on parametrizing and optimizing force fields for biomembrane modeling has been focused on homogeneous bilayers with a single phospholipid type. However, these may not perform effectively or could even be unsuitable for lipid mixtures commonly employed in membrane models. This work aims to fill this gap by comparing MD simulation results of several bacterial membrane models using different force fields and simulation parameters, namely, CHARMM36, Slipids, and GROMOS-CKP. Furthermore, the hydrogen isotope exchange (HIE) method, combined with GROMOS-CKP (GROMOS-H2Q), was also tested to check for the impact of this acceleration strategy on the performance of the force field. A common set of simulation parameters was employed for all of the force fields in addition to those corresponding to the original parametrization of each of them. Furthermore, new experimental order parameter values determined from NMR of several lipid mixtures are also reported to compare them with those determined from MD simulations. Our results reveal that most of the calculated physical properties of bacterial membrane models from MD simulations are substantially force field and lipid composition dependent. Some lipid mixtures exhibit nearly ideal behaviors, while the interaction of different lipid types in other mixtures is highly synergistic. None of the employed force fields seem to be clearly superior to the other three, each having its own strengths and weaknesses. Slipids are notably effective at replicating the order parameters for all acyl chains, including those in lipid mixtures, but they offer the least accurate results for headgroup parameters. Conversely, CHARMM provides almost perfect estimates for the order parameters of the headgroups but tends to overestimate those of the lipid tails. The GROMOS parametrizations deliver reasonable order parameters for entire lipid molecules, including multicomponent bilayers, although they do not reach the accuracy of Slipids for tails or CHARMM for headgroups. Importantly, GROMOS-H2Q stands out for its computational efficiency, being at least 3 times faster than GROMOS, which is already faster than both CHARMM and Slipids. In turn, GROMOS-H2Q yields much higher compressibilities compared to all other parametrizations.
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Affiliation(s)
- Alexandre Blanco-González
- Facultad de Física, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
- Singular Research Centre in Chemical Biology and Molecular Materials, (CIQUS), Organic Chemistry Department, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
- MD.USE Innovations S.L, Edificio Emprendia, 15782 Santiago de Compostela, Spain
| | - Anika Wurl
- Institute of Physics, Faculty of Natural Sciences II, Betty-Heimann-Str. 7, 06120 Halle/Saale, Germany
| | - Tiago Mendes Ferreira
- Institute of Physics, Faculty of Natural Sciences II, Betty-Heimann-Str. 7, 06120 Halle/Saale, Germany
| | - Ángel Piñeiro
- Facultad de Física, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
| | - Rebeca Garcia-Fandino
- Singular Research Centre in Chemical Biology and Molecular Materials, (CIQUS), Organic Chemistry Department, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
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2
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Shobhna, Dutta A, Kumari P, Kashyap HK. Stability of Cytoplasmic Membrane of Escherichia coli Bacteria in Aqueous and Ethanolic Environment. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:2893-2906. [PMID: 38311936 DOI: 10.1021/acs.langmuir.3c02780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
The mechanism of action of any antibacterial agent or disinfectant depends largely on their interaction with the bacterial membrane. Herein, we use the SPICA (surface property fitting coarse graining) force-field and develop a coarse-grained (CG) model for the structure of the cytoplasmic membrane of Escherichia coli (E. coli) and its interaction with water and ethanol. We elucidate the impact of different concentrations of ethanol on the cytoplasmic membrane bilayers and vesicles of E. coli using the CG molecular dynamics (CG MD) simulations. Our modeling approach first focuses on the parametrization of the required force-field for POPG lipid and its interaction with water, ethanol, and POPE lipid. Subsequently, the structural stability of the E. coli bacterial membrane in the presence of high and low concentrations of ethanol is delineated. Both flat bilayers as well as vesicles of E. coli membrane were considered for the CG MD. Our results reveal that, at low ethanol concentrations (<30 mol %), the size of the E. coli vesicles increases with discernible deformations in their shapes. Because of ethanol-induced interdigitation, thinning of the E. coli vesicular membrane is also observed. However, at higher ethanol concentrations (>30 mol %), the integrity of the vesicles is lost because of deteriorating invasion of ethanol molecules into the vesicle bilayer and significant weakening of lipid-lipid interactions. At higher ethanol concentrations (40 and 70 mol %), both the multivesicle and single-vesicle bacterial membranes exhibit a similar rupturing pattern wherein the extraction of lipids from the membrane and formation of aggregates of the component lipids are observed. These aggregates consist of polar head groups of 3-5 POPE/POPG lipids with intertwined nonpolar tails.
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Affiliation(s)
- Shobhna
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Ayishwarya Dutta
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Pratibha Kumari
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Hemant K Kashyap
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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3
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Dorgan B, Liu Y, Wang S, Aduse-Opoku J, Whittaker SBM, Roberts MAJ, Lorenz CD, Curtis MA, Garnett JA. Structural Model of a Porphyromonas gingivalis type IX Secretion System Shuttle Complex. J Mol Biol 2022; 434:167871. [PMID: 36404438 DOI: 10.1016/j.jmb.2022.167871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 10/14/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
Porphyromonas gingivalis is a gram-negative oral anaerobic pathogen and is one of the key causative agents of periodontitis. P. gingivalis utilises a range of virulence factors, including the cysteine protease RgpB, to drive pathogenesis and these are exported and attached to the cell surface via the type IX secretion system (T9SS). All cargo proteins possess a conserved C-terminal signal domain (CTD) which is recognised by the T9SS, and the outer membrane β-barrel protein PorV (PG0027/LptO) can interact with cargo proteins as they are exported to the bacterial surface. Using a combination of solution nuclear magnetic resonance (NMR) spectroscopy, biochemical analyses, machine-learning-based modelling and molecular dynamics (MD) simulations, we present a structural model of a PorV:RgpB-CTD complex from P. gingivalis. This is the first structural insight into CTD recognition by the T9SS and shows how the conserved motifs in the CTD are the primary sites that mediate binding. In PorV, interactions with extracellular surface loops are important for binding the CTD, and together these appear to cradle and lock RgpB-CTD in place. This work provides insight into cargo recognition by PorV but may also have important implications for understanding other aspects of type-IX dependent secretion.
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Affiliation(s)
- Ben Dorgan
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK; School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Yichao Liu
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Sunjun Wang
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Joseph Aduse-Opoku
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Sara B-M Whittaker
- Institute of Cancer & Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Mark A J Roberts
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK
| | - Christian D Lorenz
- Biological Physics & Soft Matter Research Group, Department of Physics, King's College London, London, UK
| | - Michael A Curtis
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK.
| | - James A Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK.
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4
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Grünewald F, Punt MH, Jefferys EE, Vainikka PA, König M, Virtanen V, Meyer TA, Pezeshkian W, Gormley AJ, Karonen M, Sansom MSP, Souza PCT, Marrink SJ. Martini 3 Coarse-Grained Force Field for Carbohydrates. J Chem Theory Comput 2022; 18:7555-7569. [PMID: 36342474 DOI: 10.1021/acs.jctc.2c00757] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Martini 3 force field is a full reparametrization of the Martini coarse-grained model for biomolecular simulations. Due to the improved interaction balance, it allows for a more accurate description of condensed phase systems. In the present work, we develop a consistent strategy to parametrize carbohydrate molecules accurately within the framework of Martini 3. In particular, we develop a canonical mapping scheme which decomposes arbitrarily large carbohydrates into a limited number of fragments. Bead types for these fragments have been assigned by matching physicochemical properties of mono- and disaccharides. In addition, guidelines for assigning bonds, angles, and dihedrals were developed. These guidelines enable a more accurate description of carbohydrate conformations than in the Martini 2 force field. We show that models obtained with this approach are able to accurately reproduce osmotic pressures of carbohydrate water solutions. Furthermore, we provide evidence that the model differentiates correctly the solubility of the polyglucoses dextran (water-soluble) and cellulose (water insoluble but soluble in ionic liquids). Finally, we demonstrate that the new building blocks can be applied to glycolipids. We show they are able to reproduce membrane properties and induce binding of peripheral membrane proteins. These test cases demonstrate the validity and transferability of our approach.
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Affiliation(s)
- Fabian Grünewald
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Mats H Punt
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Elizabeth E Jefferys
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Petteri A Vainikka
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Melanie König
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Valtteri Virtanen
- Natural Chemistry Research Group, Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Travis A Meyer
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Weria Pezeshkian
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands.,The Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Copenhagen 2100, Denmark
| | - Adam J Gormley
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Maarit Karonen
- Natural Chemistry Research Group, Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS and University of Lyon, Lyon 69367, France
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
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5
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Qi Y, Chen Y, Yan X, Liu W, Ma L, Liu Y, Ma Q, Liu S. Co-Exposure of Ambient Particulate Matter and Airborne Transmission Pathogens: The Impairment of the Upper Respiratory Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15892-15901. [PMID: 36240448 PMCID: PMC9670849 DOI: 10.1021/acs.est.2c03856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 10/04/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Recent evidence has pinpointed the positive relevance between air particulate matter (PM) pollution and epidemic spread. However, there are still significant knowledge gaps in understanding the transmission and infection of pathogens loaded on PMs, for example, the interactions between pathogens and pre-existing atmospheric PM and the health effects of co-exposure on the inhalation systems. Here, we unraveled the interactions between fine particulate matter (FPM) and Pseudomonas aeruginosa (P. aeruginosa) and evaluated the infection and detrimental effects of co-exposure on the upper respiratory systems in both in vitro and in vivo models. We uncovered the higher accessibility and invasive ability of pathogens to epithelial cells after loading on FPMs, compared with the single exposure. Furthermore, we designed a novel laboratory exposure model to simulate a real co-exposure scenario. Intriguingly, the co-exposure induced more serious functional damage and longer inflammatory reactions to the upper respiratory tract, including the nasal cavity and trachea. Collectively, our results provide a new point of view on the transmission and infection of pathogens loaded on FPMs and uncover the in vivo systematic impairments of the inhalation tract under co-exposure through a novel laboratory exposure model. Hence, this study sheds light on further investigations of the detrimental effects of air pollution and epidemic spread.
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Affiliation(s)
- Yu Qi
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China
- College
of Resources and Environment, University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Yucai Chen
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China
- College
of Resources and Environment, University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Xu Yan
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China
- College
of Resources and Environment, University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Liu
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China
- College
of Resources and Environment, University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Ma
- Aerosol
and Haze Laboratory, Advanced Innovation Center for Soft Matter Science
and Engineering, Beijing University of Chemical
Technology, Beijing 100029, China
| | - Yongchun Liu
- Aerosol
and Haze Laboratory, Advanced Innovation Center for Soft Matter Science
and Engineering, Beijing University of Chemical
Technology, Beijing 100029, China
| | - Qingxin Ma
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China
- College
of Resources and Environment, University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Sijin Liu
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China
- College
of Resources and Environment, University
of Chinese Academy of Sciences, Beijing 100049, China
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6
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Srivastava D, Patra N. Self-Uptake Mechanism of Polymyxin-Based Lipopeptide against Gram-Negative Bacterial Membrane: Role of the First Adsorbed Lipopeptide. J Phys Chem B 2022; 126:8222-8232. [PMID: 36126341 DOI: 10.1021/acs.jpcb.2c03827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Research in the continuously increasing threat of polymyxin-resistant multidrug-resistant Pseudomonas aeruginosa, which causes severe infection in immunocompromised patients, has resulted in the development of several polymyxin-derived cyclic lipopeptides containing l-α-γ- diamino butyric acid-like FADDI-019 (F19). In this work, F19's insertion into a minimal model of the asymmetric outer membrane of the bacterium, which contained only penta-acylated lipid A (LipA) and lacked keto-d-octulosonic acid and O-antigens, in the top leaflet and phospholipids in the bottom leaflet, was studied. F19 exhibited all of the hallmarks of the self-uptake mechanism into the asymmetric bilayer. While a single monomer of the lipopeptide did not get partitioned into the inside of the bilayer, it competitively displaced Ca2+ from the membrane surface, observed as a decrease in Ca2+ coordination number with phosphate groups (1.89 vs 1.718), resulting in membrane destabilization. This resulted in an increment of the average defect size and the probability of interplay between lipid tails and hydrophobic residues of another F19. When more than one monomer was present in the system, the first monomer remained docked on the surface, while other monomers intercalated into the bilayer interior with their hydrophobic moieties "sleeved" by lipid acyl chains. The free energy barrier for partial insertion of the lipopeptide into a bilayer in the presence of surface-docked second F19 was recorded at ∼1.3 kcal/mol using two-dimensional (2D) well-tempered metadynamics, making it a low barrier process at 300 K. This study is an attempt to demonstrate the self-uptake mechanism of F19 during intercalation process into the bilayer interior, which may help in the design of better alternates for polymyxins to work against polymyxin resistance.
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Affiliation(s)
- Diship Srivastava
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
| | - Niladri Patra
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
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7
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Maleš M, Zoranić L. Simulation Study of the Effect of Antimicrobial Peptide Associations on the Mechanism of Action with Bacterial and Eukaryotic Membranes. MEMBRANES 2022; 12:891. [PMID: 36135911 PMCID: PMC9502835 DOI: 10.3390/membranes12090891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Antimicrobial peptides (AMPs) can be directed to specific membranes based on differences in lipid composition. In this study, we performed atomistic and coarse-grained simulations of different numbers of the designed AMP adepantin-1 with a eukaryotic membrane, cytoplasmic Gram-positive and Gram-negative membranes, and an outer Gram-negative membrane. At the core of adepantin-1's behavior is its amphipathic α-helical structure, which was implemented in its design. The amphipathic structure promotes rapid self-association of peptide in water or upon binding to bacterial membranes. Aggregates initially make contact with the membrane via positively charged residues, but with insertion, the hydrophobic residues are exposed to the membrane's hydrophobic core. This adaptation alters the aggregate's stability, causing the peptides to diffuse in the polar region of the membrane, mostly remaining as a single peptide or pairing up to form an antiparallel dimer. Thus, the aggregate's proposed role is to aid in positioning the peptide into a favorable conformation for insertion. Simulations revealed the molecular basics of adepantin-1 binding to various membranes, and highlighted peptide aggregation as an important factor. These findings contribute to the development of novel anti-infective agents to combat the rapidly growing problem of bacterial resistance to antibiotics.
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Affiliation(s)
- Matko Maleš
- Faculty of Maritime Studies, University of Split, 21000 Split, Croatia
| | - Larisa Zoranić
- Department of Physics, Faculty of Science, University of Split, 21000 Split, Croatia
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8
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Montero Vega S, Booth V, Rowley CN. Interaction between Antimicrobial Peptide Magainin 2 and Nonlipid Components in the Bacterial Outer Envelope. J Phys Chem B 2022; 126:5473-5480. [PMID: 35829704 DOI: 10.1021/acs.jpcb.2c02768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Antimicrobial peptides (AMPs) offer advantages over conventional antibiotics; for example, bacteria develop more resistance to small-molecule antibiotics than to AMPs. The interaction of the AMPs with the lipopolysaccharide (LPS) layer of the Gram-negative bacteria cell envelope is not well understood. A MARTINI model was constructed of a Gram-negative bacterial outer membrane interacting with the AMP Magainin 2. In a 20 μs molecular dynamics (MD) simulation, the AMP diffused to the LPS layer of the cell envelope and remained there, suggesting interactions between the Magainin 2 and the LPS layer, causing the AMP to concentrate at that position. The free energy profile for the insertion of the Magainin 2 into the membrane was also calculated using umbrella sampling, which showed that the AMP positioned such that the cationic side chains of the AMP coordinated to the negatively charged phosphate groups of the LPS layer. These simulations indicate that the AMP Magainin 2 partition into the LPS layer of a bacterial membrane.
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Affiliation(s)
- Sheyla Montero Vega
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Valerie Booth
- Department of Biochemistry, Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador A1C 5S7, Canada
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9
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González-Fernández C, Bringas E, Oostenbrink C, Ortiz I. In silico investigation and surmounting of Lipopolysaccharide barrier in Gram-Negative Bacteria: How far has molecular dynamics Come? Comput Struct Biotechnol J 2022; 20:5886-5901. [PMID: 36382192 PMCID: PMC9636410 DOI: 10.1016/j.csbj.2022.10.039] [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: 08/26/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 11/29/2022] Open
Abstract
Lipopolysaccharide (LPS), a main component of the outer membrane of Gram-negative bacteria, has crucial implications on both antibiotic resistance and the overstimulation of the host innate immune system. Fighting against these global concerns calls for the molecular understanding of the barrier function and immunostimulatory ability of LPS. Molecular dynamics (MD) simulations have become an invaluable tool for uncovering important findings in LPS research. While the reach of MD simulations for investigating the immunostimulatory ability of LPS has been already outlined, little attention has been paid to the role of MD simulations for exploring its barrier function and synthesis. Herein, we give an overview about the impact of MD simulations on gaining insight into the shield role and synthesis pathway of LPS, which have attracted considerable attention to discover molecules able to surmount antibiotic resistance, either circumventing LPS defenses or disrupting its synthesis. We specifically focus on the enhanced sampling and free energy calculation methods that have been combined with MD simulations to address such research. We also highlight the use of special-purpose MD supercomputers, the importance of appropriate LPS and ions parameterization to obtain reliable results, and the complementary views that MD and wet-lab experiments provide. Thereby, this work, which covers the last five years of research, apart from outlining the phenomena and strategies that are being explored, evidences the valuable insights that are gained by MD, which may be useful to advance antibiotic design, and what the prospects of this in silico method could be in LPS research.
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Affiliation(s)
- Cristina González-Fernández
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
| | - Eugenio Bringas
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, BOKU – University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Inmaculada Ortiz
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
- Corresponding author.
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10
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Oyeka EE, Babahan I, Eboma B, Ifeanyieze KJ, Okpareke OC, Coban EP, Özmen A, Coban B, Aksel M, Özdemir N, Groutso T, Ayogu JI, Yildiz U, Dinçer Bilgin M, Halil Biyik H, Schrage BR, Ziegler CJ, Asegbeloyin JN. Biologically active acylthioureas and their Ni(II) and Cu(II) Complexes: Structural, spectroscopic, anti-proliferative, nucleolytic and antimicrobial studies. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2021.120590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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11
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González-Fernández C, Basauri A, Fallanza M, Bringas E, Oostenbrink C, Ortiz I. Fighting Against Bacterial Lipopolysaccharide-Caused Infections through Molecular Dynamics Simulations: A Review. J Chem Inf Model 2021; 61:4839-4851. [PMID: 34559524 PMCID: PMC8549069 DOI: 10.1021/acs.jcim.1c00613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Lipopolysaccharide
(LPS) is the primary component of the outer
leaflet of Gram-negative bacterial outer membranes. LPS elicits an
overwhelming immune response during infection, which can lead to life-threatening
sepsis or septic shock for which no suitable treatment is available
so far. As a result of the worldwide expanding multidrug-resistant
bacteria, the occurrence and frequency of sepsis are expected to increase;
thus, there is an urge to develop novel strategies for treating bacterial
infections. In this regard, gaining an in-depth understanding about
the ability of LPS to both stimulate the host immune system and interact
with several molecules is crucial for fighting against LPS-caused
infections and allowing for the rational design of novel antisepsis
drugs, vaccines and LPS sequestration and detection methods. Molecular
dynamics (MD) simulations, which are understood as being a computational
microscope, have proven to be of significant value to understand LPS-related
phenomena, driving and optimizing experimental research studies. In
this work, a comprehensive review on the methods that can be combined
with MD simulations, recently applied in LPS research, is provided.
We focus especially on both enhanced sampling methods, which enable
the exploration of more complex systems and access to larger time
scales, and free energy calculation approaches. Thereby, apart from
outlining several strategies for surmounting LPS-caused infections,
this work reports the current state-of-the-art of the methods applied
with MD simulations for moving a step forward in the development of
such strategies.
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Affiliation(s)
- Cristina González-Fernández
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
| | - Arantza Basauri
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
| | - Marcos Fallanza
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
| | - Eugenio Bringas
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Inmaculada Ortiz
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
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Rybenkov VV, Zgurskaya HI, Ganguly C, Leus IV, Zhang Z, Moniruzzaman M. The Whole Is Bigger than the Sum of Its Parts: Drug Transport in the Context of Two Membranes with Active Efflux. Chem Rev 2021; 121:5597-5631. [PMID: 33596653 PMCID: PMC8369882 DOI: 10.1021/acs.chemrev.0c01137] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cell envelope plays a dual role in the life of bacteria by simultaneously protecting it from a hostile environment and facilitating access to beneficial molecules. At the heart of this ability lie the restrictive properties of the cellular membrane augmented by efflux transporters, which preclude intracellular penetration of most molecules except with the help of specialized uptake mediators. Recently, kinetic properties of the cell envelope came into focus driven on one hand by the urgent need in new antibiotics and, on the other hand, by experimental and theoretical advances in studies of transmembrane transport. A notable result from these studies is the development of a kinetic formalism that integrates the Michaelis-Menten behavior of individual transporters with transmembrane diffusion and offers a quantitative basis for the analysis of intracellular penetration of bioactive compounds. This review surveys key experimental and computational approaches to the investigation of transport by individual translocators and in whole cells, summarizes key findings from these studies and outlines implications for antibiotic discovery. Special emphasis is placed on Gram-negative bacteria, whose envelope contains two separate membranes. This feature sets these organisms apart from Gram-positive bacteria and eukaryotic cells by providing them with full benefits of the synergy between slow transmembrane diffusion and active efflux.
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Affiliation(s)
- Valentin V Rybenkov
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Chhandosee Ganguly
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Inga V Leus
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Zhen Zhang
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Mohammad Moniruzzaman
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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13
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Paternò GM, Moscardi L, Donini S, Ross AM, Pietralunga SM, Dalla Vedova N, Normani S, Kriegel I, Lanzani G, Scotognella F. Integration of bio-responsive silver in 1D photonic crystals: towards the colorimetric detection of bacteria. Faraday Discuss 2020; 223:125-135. [PMID: 32720674 DOI: 10.1039/d0fd00026d] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The colour purity and versatility of fabrication of one-dimensional photonic crystals (1D PhCs) make them ideal candidates for colorimetric sensing of a variety of analytes. For instance, the detection of bacterial contaminants in food via colorimetric sensors can be highly appealing, as most of the existing detection techniques are in general time-consuming and the read-out requires specialised personnel. Here, we present a colorimetric sensor based on hybrid plasmonic/photonic 1D crystals. We demonstrate that the modification of the silver plasmon resonance brought about by the effective silver/bacterium interaction can be translated into the visible spectral region, producing a change in the structural colour. In addition, we observe a superior colorimetric sensitivity against the Gram negative Escherichia coli compared to the Gram positive Micrococcus luteus, a result that we attribute to the more efficient electrostatic interaction and cellular adhesion between the silver surface and the Gram-negative bacteria outer membrane. This approach demonstrates that in principle an easy colorimetric detection of bacterial contaminants can be achieved through the use of bio-responsive plasmonic materials, such as silver, whose selective electrostatic interaction with bacterial cell wall is well-known and occurs without the need of chemical functionalisation.
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Affiliation(s)
- Giuseppe M Paternò
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia (IIT), Via Pascoli 10, Milano, 20133, Italy.
| | - Liliana Moscardi
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia (IIT), Via Pascoli 10, Milano, 20133, Italy. and Physics Department, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milano, Italy
| | - Stefano Donini
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia (IIT), Via Pascoli 10, Milano, 20133, Italy.
| | - Aaron M Ross
- Physics Department, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milano, Italy
| | - Silvia M Pietralunga
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia (IIT), Via Pascoli 10, Milano, 20133, Italy. and Institute for Photonics and Nanotechnologies (IFN), Consiglio Nazionale delle Ricerche (CNR), Piazza L. da Vinci 32, 20133 Milano, Italy
| | - Nicholas Dalla Vedova
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia (IIT), Via Pascoli 10, Milano, 20133, Italy.
| | - Simone Normani
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia (IIT), Via Pascoli 10, Milano, 20133, Italy.
| | - Ilka Kriegel
- Department of Nanochemistry, Istituto Italiano di Tecnologia (IIT), via Morego, 30, 16163 Genova, Italy
| | - Guglielmo Lanzani
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia (IIT), Via Pascoli 10, Milano, 20133, Italy. and Physics Department, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milano, Italy
| | - Francesco Scotognella
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia (IIT), Via Pascoli 10, Milano, 20133, Italy. and Physics Department, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milano, Italy
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14
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Harnentis H, Marlida Y, Nur YS, Wizna W, Santi MA, Septiani N, Adzitey F, Huda N. Novel probiotic lactic acid bacteria isolated from indigenous fermented foods from West Sumatera, Indonesia. Vet World 2020; 13:1922-1927. [PMID: 33132606 PMCID: PMC7566266 DOI: 10.14202/vetworld.2020.1922-1927] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/28/2020] [Indexed: 01/16/2023] Open
Abstract
Background and Aim: Probiotics play an important role in maintaining a healthy gut and consequently promote good health. This study aimed to find novel probiotic lactic acid bacteria (LAB) from indigenous fermented foods of West Sumatera, Indonesia. Materials and Methods: This study utilized 10 LAB previously isolated from fermented buffalo milk (dadih), fermented fish (budu), and fermented cassava (tape) which have the ability to produce gamma-aminobutyric acid. The study commenced with the screening of LAB for certain properties, such as resistance to acid and bile salts, adhesion to mucosal surface, and antagonism against enteric pathogens (Escherichia coli, Salmonella Enteritidis, and Staphylococcus aureus). The promising isolates were identified through biochemical and gram staining methods. Results: All isolates in this study were potential novel probiotics. They survived at a pH level of 2.5 for 3 h (55.27-98.18%) and 6 h (50.98-84.91%). Survival in bile at a concentration of 0.3% was 39.90-58.61% and the survival rate was 28.38-52.11% at a concentration of 0.5%. The inhibitory diameter ranged from 8.75 to 11.54 mm for E. coli, 7.02 to 13.42 mm for S. aureus, and 12.49 to 19.00 mm for S. Enteritidis. All the isolates (84.5-92%) exhibited the ability to adhere to mucosal surfaces. This study revealed that all the isolates were potential probiotics but N16 proved to be superior because it was viable at a pH level of 2 (84.91%) and it had a good survival rate in bile salts assay (55.07%). This isolate was identified as Lactobacillus spp., Gram-positive bacilli bacteria, and tested negative in both the catalase and oxidase tests. Conclusion: All the isolates in this study may be used as probiotics, with isolate N16 (Lactobacillus spp.) as the most promising novel probiotic for poultry applications based on its ability to inhibit pathogenic bacteria.
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Affiliation(s)
- Harnentis Harnentis
- Department of Animal Nutrition and Feed Technology, Faculty of Animal Science, Andalas University, West Sumatera, Indonesia
| | - Yetti Marlida
- Department of Animal Nutrition and Feed Technology, Faculty of Animal Science, Andalas University, West Sumatera, Indonesia
| | - Yuliaty Shafan Nur
- Department of Animal Nutrition and Feed Technology, Faculty of Animal Science, Andalas University, West Sumatera, Indonesia
| | - Wizna Wizna
- Department of Animal Nutrition and Feed Technology, Faculty of Animal Science, Andalas University, West Sumatera, Indonesia
| | - Melia Afnida Santi
- Department of Animal Nutrition, Faculty Animal Husbandry, Universitas Muhammadiyah Tapanuli Selatan, North Sumatera, Indonesia
| | - Nadia Septiani
- Department of Animal Nutrition and Feed Technology, Faculty of Animal Science, Andalas University, West Sumatera, Indonesia
| | - Frederick Adzitey
- Department of Veterinary Science, Faculty of Agriculture, University for Development Studies, Box TL 1882, Tamale, Ghana
| | - Nurul Huda
- Department of Food Science and Nutrition, Faculty Food Science and Nutrition, Universiti Malaysia Sabah, 88400, Kota Kinabalu, Sabah, Malaysia.,Department of Food Technology, Faculty of Agriculture, Universitas Sultan Ageng Tirtayasa, Banten 42124, Indonesia
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15
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Claro B, González-Freire E, Calvelo M, Bessa LJ, Goormaghtigh E, Amorín M, Granja JR, Garcia-Fandiño R, Bastos M. Membrane targeting antimicrobial cyclic peptide nanotubes - an experimental and computational study. Colloids Surf B Biointerfaces 2020; 196:111349. [PMID: 32992285 DOI: 10.1016/j.colsurfb.2020.111349] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 02/07/2023]
Abstract
The search of new antibiotics, particularly with new mechanisms of action, is nowadays a very important public health issue, due to the worldwide increase of resistant pathogens. Within this effort, much research has been done on antimicrobial peptides, because having the membrane as a target, they represent a new antibiotic paradigm. Among these, cyclic peptides (CPs) made of sequences of D- and L-amino acids have emerged as a new class of potential antimicrobial peptides, due to their expected higher resistance to protease degradation. These CPs are planar structures that can form Self-assembled Cyclic Peptide Nanotubes (SCPNs), in particular in the presence of lipid membranes. Aiming at understanding their mechanism of action, we used biophysical experimental techniques (DSC and ATR-FTIR) together with Coarse-grained molecular dynamics (CG-MD) simulations, to characterize the interaction of these CPs with model membranes of different electrostatic charges' contents. DSC results revealed that the CPs show a strong interaction with negatively charged membranes, with differences in the strength of interactions depending on peptide and on membrane charge content, at odds with no or mild interactions with zwitterionic membranes. ATR-FTIR suggested that the peptides self-assemble at the membrane surface, adopting mainly a β-structure. The experiments with polarized light showed that in most cases they lie parallel to the membrane surface, but other forms and orientations are also apparent, depending on peptide structure and lipid:peptide ratio. The nanotube formation and orientation, as well as the dependence on membrane charge were also confirmed by the CG-MD simulations. These provide detail on the position and interactions, in agreement with the experimental results. Based on the findings reported here, we could proceed to the design and synthesis of a second-generation CPs, based on CP2 (soluble peptide), with increased activity and reduced toxicity.
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Affiliation(s)
- Bárbara Claro
- CIQUP, Centro de Investigação em Química, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Eva González-Freire
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Martin Calvelo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Lucinda J Bessa
- LAQV/Requimte, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Erik Goormaghtigh
- Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, ULB, Brussels, Belgium
| | - Manuel Amorín
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Juan R Granja
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Rebeca Garcia-Fandiño
- CIQUP, Centro de Investigação em Química, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal; Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Margarida Bastos
- CIQUP, Centro de Investigação em Química, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
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16
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Sowlati-Hashjin S, Carbone P, Karttunen M. Insights into the Polyhexamethylene Biguanide (PHMB) Mechanism of Action on Bacterial Membrane and DNA: A Molecular Dynamics Study. J Phys Chem B 2020; 124:4487-4497. [DOI: 10.1021/acs.jpcb.0c02609] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Shahin Sowlati-Hashjin
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
- The Centre of Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Paola Carbone
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Mikko Karttunen
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
- The Centre of Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
- Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
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17
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Rice A, Rooney MT, Greenwood AI, Cotten ML, Wereszczynski J. Lipopolysaccharide Simulations Are Sensitive to Phosphate Charge and Ion Parameterization. J Chem Theory Comput 2020; 16:1806-1815. [PMID: 32023054 DOI: 10.1021/acs.jctc.9b00868] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The high proportion of lipopolysaccharide (LPS) molecules in the outer membrane of Gram-negative bacteria makes it a highly effective barrier to small molecules, antibiotic drugs, and other antimicrobial agents. Given this vital role in protecting bacteria from potentially hostile environments, simulations of LPS bilayers and outer membrane systems represent a critical tool for understanding the mechanisms of bacterial resistance and the development of new antibiotic compounds that circumvent these defenses. The basis of these simulations is parameterizations of LPS, which have been developed for all major molecular dynamics force fields. However, these parameterizations differ in both the protonation state of LPS and how LPS membranes behave in the presence of various ion species. To address these discrepancies and understand the effects of phosphate charge on bilayer properties, simulations were performed for multiple distinct LPS chemotypes with different ion parameterizations in both protonated or deprotonated lipid A states. These simulations show that bilayer properties, such as the area per lipid and inter-lipid hydrogen bonding, are highly influenced by the choice of phosphate group charges, cation type, and ion parameterization, with protonated LPS and monovalent cations with modified nonbonded parameters providing the best match to the experiments. Additionally, alchemical free energy simulations were performed to determine theoretical pKa values for LPS and subsequently validated by 31P solid-state nuclear magnetic resonance experiments. Results from these complementary computational and experimental studies demonstrate that the protonated state dominates at physiological pH, contrary to the deprotonated form modeled by many LPS force fields. Overall, these results highlight the sensitivity of LPS simulations to phosphate charge and ion parameters while offering recommendations for how existing models should be updated for consistency between force fields as well as to best match experiments.
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Affiliation(s)
- Amy Rice
- Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Mary T Rooney
- Department of Applied Science, College of William and Mary, Williamsburg, Virginia 23185, United States
| | - Alexander I Greenwood
- Department of Applied Science, College of William and Mary, Williamsburg, Virginia 23185, United States.,Department of Physics, College of William and Mary, Williamsburg, Virginia 23185, United States
| | - Myriam L Cotten
- Department of Applied Science, College of William and Mary, Williamsburg, Virginia 23185, United States
| | - Jeff Wereszczynski
- Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois 60616, United States
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18
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Clifton LA, Paracini N, Hughes AV, Lakey JH, Steinke NJ, Cooper JFK, Gavutis M, Skoda MWA. Self-Assembled Fluid Phase Floating Membranes with Tunable Water Interlayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:13735-13744. [PMID: 31553881 DOI: 10.1021/acs.langmuir.9b02350] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We present a reliable method for the fabrication of fluid phase, unsaturated lipid bilayers by self-assembly onto charged Self-Assembled Monolayer (SAM) surfaces with tunable membrane to surface aqueous interlayers. Initially, the formation of water interlayers between membranes and charged surfaces was characterized using a comparative series of bilayers deposited onto charged, self-assembled monolayers by sequential layer deposition. Using neutron reflectometry, a bilayer to surface water interlayer of ∼8 Å was found between the zwitterionic phospholipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) membrane and an anionic carboxyl terminated grafted SAM with the formation of this layer attributed to bilayer repulsion by hydration water on the SAM surface. Furthermore, we found we could significantly reduce the technical complexity of sample fabrication through self-assembly of planar membranes onto the SAM coated surfaces. Vesicle fusion onto carboxyl-terminated monolayers yielded high coverage (>95%) bilayers of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) which floated on a 7-11 Å solution interlayer between the membrane and the surface. The surface to membrane distance was then tuned via the addition of 200 mM NaCl to the bulk solution immersing a POPC floating membrane, which caused the water interlayer to swell reversibly to ∼33 Å. This study reveals that biomimetic membrane models can be readily self-assembled from solution onto functionalized surfaces without the use of polymer supports or tethers. Once assembled, surface to membrane distance can be tailored to the experimental requirements using physiological concentrations of electrolytes. These planar bilayers only very weakly interact with the substrate and are ideally suited for use as biomimetic models for accurate in vitro biochemical and biophysical studies, as well as for technological applications, such as biosensors.
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Affiliation(s)
- Luke A Clifton
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council , Rutherford Appleton Laboratory, Harwell Science and Innovation Campus , Didcot , Oxfordshire OX11 OQX , U.K
| | - Nicoló Paracini
- Institute for Cell and Molecular Biosciences , Newcastle University , Framlington Place , Newcastle upon Tyne , NE2 4HH , United Kingdom
| | - Arwel V Hughes
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council , Rutherford Appleton Laboratory, Harwell Science and Innovation Campus , Didcot , Oxfordshire OX11 OQX , U.K
| | - Jeremy H Lakey
- Institute for Cell and Molecular Biosciences , Newcastle University , Framlington Place , Newcastle upon Tyne , NE2 4HH , United Kingdom
| | - Nina-Juliane Steinke
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council , Rutherford Appleton Laboratory, Harwell Science and Innovation Campus , Didcot , Oxfordshire OX11 OQX , U.K
| | - Joshaniel F K Cooper
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council , Rutherford Appleton Laboratory, Harwell Science and Innovation Campus , Didcot , Oxfordshire OX11 OQX , U.K
| | - Martynas Gavutis
- Department of Nanoengineering , Center for Physical Sciences and Technology , Savanoriu ave 231 , LT-02300 Vilnius , Lithuania
| | - Maximilian W A Skoda
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council , Rutherford Appleton Laboratory, Harwell Science and Innovation Campus , Didcot , Oxfordshire OX11 OQX , U.K
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19
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Paternò GM, Moscardi L, Donini S, Ariodanti D, Kriegel I, Zani M, Parisini E, Scotognella F, Lanzani G. Hybrid One-Dimensional Plasmonic-Photonic Crystals for Optical Detection of Bacterial Contaminants. J Phys Chem Lett 2019; 10:4980-4986. [PMID: 31407906 DOI: 10.1021/acs.jpclett.9b01612] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Photonic crystal-based biosensors hold great promise as low-cost devices for real-time monitoring of a variety of biotargets, for example, bacterial contaminants in food. Here, we report the proof-of-concept for a new colorimetric sensor of bacterial contamination, which is based on a novel hybrid plasmonic-photonic device. Our system consists of a layer of silver, a plasmonic metal exhibiting a well-known bioactivity, on top of a one-dimensional photonic crystal. We attribute the bioresponsivity to the formation of polarization charges at the Ag/bacterium interface within a sort of "bio-doping" mechanism. Interestingly, this triggers a blue shift in the photonic response. As an example, we assessed the validity of our approach by detecting one of the most hazardous contaminants, Escherichia coli. This work demonstrates that our device can be a low-cost and portable platform for the detection of common bacterial contaminants.
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Affiliation(s)
- Giuseppe Maria Paternò
- Center for Nano Science and Technology@PoliMi, Istituto Italiano di Tecnologia, Via Giovanni Pascoli, 70/3, 20133 Milano, Italy
| | - Liliana Moscardi
- Center for Nano Science and Technology@PoliMi, Istituto Italiano di Tecnologia, Via Giovanni Pascoli, 70/3, 20133 Milano, Italy
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Stefano Donini
- Center for Nano Science and Technology@PoliMi, Istituto Italiano di Tecnologia, Via Giovanni Pascoli, 70/3, 20133 Milano, Italy
| | - Davide Ariodanti
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "Giulio Natta", Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Ilka Kriegel
- Department of Nanochemistry, Istituto Italiano di Tecnologia (IIT), via Morego, 30, 16163 Genova, Italy
| | - Maurizio Zani
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Emilio Parisini
- Center for Nano Science and Technology@PoliMi, Istituto Italiano di Tecnologia, Via Giovanni Pascoli, 70/3, 20133 Milano, Italy
| | - Francesco Scotognella
- Center for Nano Science and Technology@PoliMi, Istituto Italiano di Tecnologia, Via Giovanni Pascoli, 70/3, 20133 Milano, Italy
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Guglielmo Lanzani
- Center for Nano Science and Technology@PoliMi, Istituto Italiano di Tecnologia, Via Giovanni Pascoli, 70/3, 20133 Milano, Italy
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
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20
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21
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Holdbrook DA, Huber RG, Marzinek JK, Stubbusch A, Schmidtchen A, Bond PJ. Multiscale modeling of innate immune receptors: Endotoxin recognition and regulation by host defense peptides. Pharmacol Res 2019; 147:104372. [PMID: 31351116 DOI: 10.1016/j.phrs.2019.104372] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 07/23/2019] [Accepted: 07/23/2019] [Indexed: 01/16/2023]
Abstract
The innate immune system provides a first line of defense against foreign microorganisms, and is typified by the Toll-like receptor (TLR) family. TLR4 is of particular interest, since over-stimulation of its pathway by excess lipopolysaccharide (LPS) molecules from the outer membranes of Gram-negative bacteria can result in sepsis, which causes millions of deaths each year. In this review, we outline our use of molecular simulation approaches to gain a better understanding of the determinants of LPS recognition, towards the search for novel immunotherapeutics. We first describe how atomic-resolution simulations have enabled us to elucidate the regulatory conformational changes in TLR4 associated with different LPS analogues, and hence a means to rationalize experimental structure-activity data. Furthermore, multiscale modelling strategies have provided a detailed description of the thermodynamics and intermediate structures associated with the entire TLR4 relay - which consists of a number of transient receptor/coreceptor complexes - allowing us trace the pathway of LPS transfer from bacterial membranes to the terminal receptor complex at the plasma membrane surface. Finally, we describe our efforts to leverage these computational models, in order to elucidate previously undisclosed anti-inflammatory mechanisms of endogenous host-defense peptides found in wounds. Collectively, this work represents a promising avenue for the development of novel anti-septic treatments, inspired by nature's innate defense strategies.
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Affiliation(s)
- Daniel A Holdbrook
- Bioinformatics Institute, A⁎STAR (Agency for Science, Technology and Research), Singapore
| | - Roland G Huber
- Bioinformatics Institute, A⁎STAR (Agency for Science, Technology and Research), Singapore
| | - Jan K Marzinek
- Bioinformatics Institute, A⁎STAR (Agency for Science, Technology and Research), Singapore
| | - Astrid Stubbusch
- Bioinformatics Institute, A⁎STAR (Agency for Science, Technology and Research), Singapore
| | - Artur Schmidtchen
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, Sweden; Copenhagen Wound Healing Center, Bispebjerg Hospital, Department of Biomedical Sciences, University of Copenhagen, Denmark; Dermatology, Skane University Hospital, Sweden
| | - Peter J Bond
- Bioinformatics Institute, A⁎STAR (Agency for Science, Technology and Research), Singapore; Department of Biological Sciences, National University of Singapore, Singapore.
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22
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Maia P, Pérez-Rodríguez G, Pérez-Pérez M, Fdez-Riverola F, Lourenço A, Azevedo NF. Application of agent-based modelling to assess single-molecule transport across the cell envelope of E. coli. Comput Biol Med 2019; 107:218-226. [DOI: 10.1016/j.compbiomed.2019.02.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 01/16/2023]
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23
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Shearer J, Jefferies D, Khalid S. Outer Membrane Proteins OmpA, FhuA, OmpF, EstA, BtuB, and OmpX Have Unique Lipopolysaccharide Fingerprints. J Chem Theory Comput 2019; 15:2608-2619. [PMID: 30848905 DOI: 10.1021/acs.jctc.8b01059] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The outer membrane of Gram-negative bacteria has a highly complex asymmetrical architecture, containing a mixture of phospholipids in the inner leaflet and almost exclusively lipopolysaccharide (LPS) molecules in the outer leaflet. In E. coli, the outer membrane contains a wide range of proteins with a β barrel architecture, that vary in size from the smallest having eight strands to larger barrels composed of 22 strands. Here we report coarse-grained molecular dynamics simulations of six proteins from the E. coli outer membrane OmpA, OmpX, BtuB, FhuA, OmpF, and EstA in a range of membrane environments, which are representative of the in vivo conditions for different strains of E. coli. We show that each protein has a unique pattern of interaction with the surrounding membrane, which is influenced by the composition of the protein, the level of LPS in the outer leaflet, and the differing mobilities of the lipids in the two leaflets of the membrane. Overall we present analyses from over 200 μs of simulation for each protein.
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Affiliation(s)
- Jonathan Shearer
- School of Chemistry , University of Southampton, Highfield , Southampton , SO17 1BJ United Kingdom
| | - Damien Jefferies
- School of Chemistry , University of Southampton, Highfield , Southampton , SO17 1BJ United Kingdom
| | - Syma Khalid
- School of Chemistry , University of Southampton, Highfield , Southampton , SO17 1BJ United Kingdom
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24
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Baltoumas FA, Hamodrakas SJ, Iconomidou VA. The gram‐negative outer membrane modeler: Automated building of lipopolysaccharide‐rich bacterial outer membranes in four force fields. J Comput Chem 2019; 40:1727-1734. [DOI: 10.1002/jcc.25823] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/18/2019] [Accepted: 03/03/2019] [Indexed: 01/11/2023]
Affiliation(s)
- Fotis A. Baltoumas
- Section of Cell Biology and Biophysics, Department of Biology, School of SciencesNational and Kapodistrian University of Athens Panepistimiopolis, 15701, Athens Greece
| | - Stavros J. Hamodrakas
- Section of Cell Biology and Biophysics, Department of Biology, School of SciencesNational and Kapodistrian University of Athens Panepistimiopolis, 15701, Athens Greece
| | - Vassiliki A. Iconomidou
- Section of Cell Biology and Biophysics, Department of Biology, School of SciencesNational and Kapodistrian University of Athens Panepistimiopolis, 15701, Athens Greece
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25
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Hughes AV, Patel DS, Widmalm G, Klauda JB, Clifton LA, Im W. Physical Properties of Bacterial Outer Membrane Models: Neutron Reflectometry & Molecular Simulation. Biophys J 2019; 116:1095-1104. [PMID: 30850116 DOI: 10.1016/j.bpj.2019.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 01/25/2019] [Accepted: 02/05/2019] [Indexed: 12/13/2022] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria is an asymmetric bilayer having phospholipids in the inner leaflet and lipopolysaccharides in the outer leaflet. This unique asymmetry and the complex carbohydrates in lipopolysaccharides make it a daunting task to study the asymmetrical OM structure and dynamics, its interactions with OM proteins, and its roles in translocation of substrates, including antibiotics. In this study, we combine neutron reflectometry and molecular simulation to explore the physical properties of OM mimetics. There is excellent agreement between experiment and simulation, allowing experimental testing of the conclusions from simulations studies and also atomistic interpretation of the behavior of experimental model systems, such as the degree of lipid asymmetry, the lipid component (tail, head, and sugar) profiles along the bilayer normal, and lateral packing (i.e., average surface area per lipid). Therefore, the combination of both approaches provides a powerful new means to explore the biological and biophysical behavior of the bacterial OM.
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Affiliation(s)
- Arwel V Hughes
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Oxford Campus, Didcot, Oxfordshire, United Kingdom.
| | - Dhilon S Patel
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, Pennsylvania
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockhozlm, Sweden
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, Biophysics Program, University of Maryland, College Park, Maryland
| | - Luke A Clifton
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Oxford Campus, Didcot, Oxfordshire, United Kingdom
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, Pennsylvania.
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26
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Yadav K, Kumar S, Mishra D, Asad M, Mitra M, Yavvari PS, Gupta S, Vedantham M, Ranga P, Komalla V, Pal S, Sharma P, Kapil A, Singh A, Singh N, Srivastava A, Thukral L, Bajaj A. Deciphering the Role of Intramolecular Networking in Cholic Acid–Peptide Conjugates on the Lipopolysaccharide Surface in Combating Gram-Negative Bacterial Infections. J Med Chem 2019; 62:1875-1886. [DOI: 10.1021/acs.jmedchem.8b01357] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Kavita Yadav
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
- Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Sandeep Kumar
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
- Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Deepakkumar Mishra
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
| | - Mohammad Asad
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
| | - Madhurima Mitra
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
| | - Prabhu S. Yavvari
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal 462030, Madhya Pradesh, India
| | - Siddhi Gupta
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
| | - Madhukar Vedantham
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
| | - Pavit Ranga
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
| | - Varsha Komalla
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
| | - Sanjay Pal
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
- Kalinga Institute of Industrial Technology, Bhubaneswar 751024, Odisha, India
| | - Priyanka Sharma
- Department of Microbiology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Archana Singh
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
| | - Nirpendra Singh
- Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
| | - Aasheesh Srivastava
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal 462030, Madhya Pradesh, India
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
| | - Avinash Bajaj
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
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27
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Golla VK, Sans-Serramitjana E, Pothula KR, Benier L, Bafna JA, Winterhalter M, Kleinekathöfer U. Fosfomycin Permeation through the Outer Membrane Porin OmpF. Biophys J 2019; 116:258-269. [PMID: 30616836 PMCID: PMC6350074 DOI: 10.1016/j.bpj.2018.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/21/2018] [Accepted: 12/03/2018] [Indexed: 01/14/2023] Open
Abstract
Fosfomycin is a frequently prescribed drug in the treatment of acute urinary tract infections. It enters the bacterial cytoplasm and inhibits the biosynthesis of peptidoglycans by targeting the MurA enzyme. Despite extensive pharmacological studies and clinical use, the permeability of fosfomycin across the bacterial outer membrane is largely unexplored. Here, we investigate the fosfomycin permeability across the outer membrane of Gram-negative bacteria by electrophysiology experiments as well as by all-atom molecular dynamics simulations including free-energy and applied-field techniques. Notably, in an electrophysiological zero-current assay as well as in the molecular simulations, we found that fosfomycin can rapidly permeate the abundant Escherichia coli porin OmpF. Furthermore, two triple mutants in the constriction region of the porin have been investigated. The permeation rates through these mutants are slightly lower than that of the wild type but fosfomycin can still permeate. Altogether, this work unravels molecular details of fosfomycin permeation through the outer membrane porin OmpF of E. coli and moreover provides hints for understanding the translocation of phosphonic acid antibiotics through other outer membrane pores.
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Affiliation(s)
- Vinaya Kumar Golla
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen, Germany
| | | | | | - Lorraine Benier
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Jayesh Arun Bafna
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen, Germany.
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28
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Ulmschneider JP, Ulmschneider MB. Molecular Dynamics Simulations Are Redefining Our View of Peptides Interacting with Biological Membranes. Acc Chem Res 2018; 51:1106-1116. [PMID: 29667836 DOI: 10.1021/acs.accounts.7b00613] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Ever since the first molecular mechanics computer simulations of biological molecules became possible, there has been the dream to study all complex biological phenomena in silico, simply bypassing the enormous experimental challenges and their associated costs. For this, two inherent requirements need to be met: First, the time scales achievable in simulations must reach up to the millisecond range and even longer. Second, the computational model must accurately reproduce what is measured experimentally. Despite some recent successes, the general consensus in the field to date has been that neither of these conditions have yet been met and that the dream will be realized, if at all, only in the distant future. In this Account, we show that this view is wrong; instead, we are actually in the middle of the in silico molecular dynamics (MD) revolution, which is reshaping how we think about protein function. The example explored in this Account is a recent advance in the field of membrane-active peptides (MAPs). MD simulations have succeeded in accurately capturing the process of peptide binding, folding, and partitioning into lipid bilayers as well as revealing how channels form spontaneously from polypeptide fragments and conduct ionic and other cargo across membranes, all at atomic resolution. These game-changing advances have been made possible by a combination of steadily advancing computational power, more efficient algorithms and techniques, clever accelerated sampling schemes, and thorough experimental verifications. The great advantage of MD is the spatial and temporal resolution, directly providing a molecular movie of a protein undergoing folding and cycling through a functional process. This is especially important for proteins with transitory functional states, such as pore-forming MAPs. Recent successes are demonstrated here for the large class of antimicrobial peptides (AMPs). These short peptides are an essential part of the nonadaptive immune system for many organisms, ubiquitous in nature, and of particular interest to the pharmaceutical industry in the age of rising bacterial resistance to conventional antibiotic treatments. Unlike integral membrane proteins, AMPs are sufficiently small to allow converged sampling with the unbiased high-temperature sampling methodology outlined here and are relatively easy to handle experimentally. At the same time, AMPs exhibit a wealth of complex and poorly understood interactions with lipid bilayers, which allow not only tuning and validation of the simulation methodology but also advancement of our knowledge of protein-lipid interactions at a fundamental level. Space constraints limit our discussion to AMPs, but the MD methodologies outlined here can be applied to all phenomena involving peptides in membranes, including cell-penetrating peptides, signaling peptides, viral channel forming peptides, and fusion peptides, as well as ab initio membrane protein folding and assembly. For these systems, the promise of MD simulations to predict the structure of channels and to provide complete-atomic-detail trajectories of the mechanistic processes underlying their biological functions appears to rapidly become a reality. The current challenge is to design joint experimental and computational benchmarks to verify and tune MD force fields. With this, MD will finally fulfill its promise to become an inexpensive, powerful, and easy-to-use tool providing atomic-detail insights to researchers as part of their investigations into membrane biophysics and beyond.
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Affiliation(s)
- Jakob P. Ulmschneider
- Institute of Natural Sciences and School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
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