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For: Boags A, Hsu PC, Samsudin F, Bond PJ, Khalid S. Progress in Molecular Dynamics Simulations of Gram-Negative Bacterial Cell Envelopes. J Phys Chem Lett 2017;8:2513-2518. [PMID: 28467715 DOI: 10.1021/acs.jpclett.7b00473] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Number Cited by Other Article(s)
1
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]
2
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]
3
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]
4
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]
5
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]
6
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]
7
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]
8
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]
9
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
10
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]
11
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]
12
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]
13
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]
14
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
15
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]
16
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]
17
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]
18
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]
19
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]
20
Multiscale models of infection. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2019. [DOI: 10.1016/j.cobme.2019.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
21
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]
22
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]
23
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]
24
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]
25
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
26
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]
27
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
28
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]
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