Fluorescence spectroscopy and molecular dynamics simulations in studies on the mechanism of membrane destabilization by antimicrobial peptides

2011 ◽  
Vol 68 (13) ◽  
pp. 2281-2301 ◽  
Author(s):  
Gianfranco Bocchinfuso ◽  
Sara Bobone ◽  
Claudia Mazzuca ◽  
Antonio Palleschi ◽  
Lorenzo Stella
Keyword(s):  
Molecular Dynamics ◽  
Fluorescence Spectroscopy ◽  
Antimicrobial Peptides ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations ◽  
Membrane Destabilization

scholarly journals Different mechanisms of action of antimicrobial peptides: insights from fluorescence spectroscopy experiments and molecular dynamics simulations

2009 ◽  
Vol 15 (9) ◽  
pp. 550-558 ◽  
Author(s):  
Gianfranco Bocchinfuso ◽  
Antonio Palleschi ◽  
Barbara Orioni ◽  
Giacinto Grande ◽  
Fernando Formaggio ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Fluorescence Spectroscopy ◽  
Antimicrobial Peptides ◽  
Molecular Dynamics Simulations ◽  
Mechanisms Of Action ◽  
Dynamics Simulations

Strategies for modulating the luminescence properties of pyronin Y dye–clay films: an experimental and theoretical study

2016 ◽  
Vol 18 (12) ◽  
pp. 8730-8738 ◽  
Author(s):  
Nerea Epelde-Elezcano ◽  
Virginia Martínez-Martínez ◽  
Eduardo Duque-Redondo ◽  
Inés Temiño ◽  
Hegoi Manzano ◽  
...  
Keyword(s):  
Thin Films ◽  
Molecular Dynamics ◽  
Fluorescence Spectroscopy ◽  
Molecular Dynamics Simulations ◽  
Electronic Absorption ◽  
Theoretical Study ◽  
Aggregation Process ◽  
Absorption And Fluorescence Spectroscopy ◽  
Smectite Clays ◽  
Dynamics Simulations

The aggregation process of pyronin Y (PY) dye into thin films of different smectite clays, LAPONITE® and saponite, is deeply studied by means of electronic absorption and fluorescence spectroscopy and by molecular dynamics simulations.

scholarly journals Probing the self-assembly dynamics and internal structure of amphiphilic hyaluronic acid conjugates by fluorescence spectroscopy and molecular dynamics simulations

Soft Matter ◽  
2018 ◽  
Vol 14 (23) ◽  
pp. 4762-4771 ◽  
Author(s):  
Denis Svechkarev ◽  
Alexander Kyrychenko ◽  
William M. Payne ◽  
Aaron M. Mohs
Keyword(s):  
Molecular Dynamics ◽  
Hyaluronic Acid ◽  
Fluorescence Spectroscopy ◽  
Molecular Dynamics Simulations ◽  
Internal Structure ◽  
Self Assembly ◽  
The Self ◽  
Dynamics Simulations

Side substituents on the hyaluronic acid backbone determine the morphology and hydration of the HA-derived nanoparticles hydrophobic domains.

Synergistic effects of magainin 2 and PGLa on their heterodimer formation, aggregation, and insertion into the bilayer

RSC Advances ◽  
2015 ◽  
Vol 5 (3) ◽  
pp. 2047-2055 ◽  
Author(s):  
Eol Han ◽  
Hwankyu Lee
Keyword(s):  
Molecular Dynamics ◽  
Antimicrobial Peptides ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Synergistic Effects ◽  
Coarse Grained ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

We performed coarse-grained molecular dynamics simulations of antimicrobial peptides PGLa and magainin 2 in lipid bilayers.

scholarly journals Structural characterization of the antimicrobial peptides myxinidin and WMR in bacterial membrane mimetic micelles and bicelles

2021 ◽  
Author(s):  
Yevhen K. Cherniavskyi ◽  
Rosario Oliva ◽  
Marco Stellato ◽  
Pompea Del Vecchio ◽  
Stefania Galdiero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Antimicrobial Peptides ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Structural Characterization ◽  
Bacterial Membrane ◽  
Membrane Composition ◽  
Membrane Mimetic ◽  
Dynamics Simulations

Antimicrobial peptides are a promising class of alternative antibiotics that interact selectively with negatively charged lipid bilayers. This paper presents the structural characterization of the antimicrobial peptides myxinidin and WMR associated with bacterial membrane mimetic micelles and bicelles by NMR, CD spectroscopy, and Molecular Dynamics simulations. Both peptides adopt a different conformation in the lipidic environment than in aqueous solution. The location of peptides in micelles and bicelles has been studied by paramagnetic relaxation enhancement experiments with paramagnetic tagged 5- and 16-doxyl stearic acid (5-/16-SASL). Multi-microsecond long molecular dynamics simulations of multiple copies of the peptides were used to gain an atomic level of detail on membrane-peptide and peptide-peptide interactions. Our results highlight an essential role of the negatively charged membrane mimetic in the structural stability of both myxinidin and WMR. The peptides localize predominantly in the membrane's headgroup region and have a noticeable membrane thinning effect on the overall bilayer structure. Myxinidin and WMR show different tendency to self-aggregate, which is also influenced by the membrane composition (DOPE/DOPG versus DOPE/DOPG/CL) and can be related to the previously observed difference in the ability of the peptides to disrupt different types of model membranes.

scholarly journals Quantitative sampling of conformational heterogeneity of a DNA hairpin using molecular dynamics simulations and ultrafast fluorescence spectroscopy

2016 ◽  
Vol 44 (7) ◽  
pp. 3408-3419 ◽  
Author(s):  
Karine Voltz ◽  
Jérémie Léonard ◽  
Patricia Tourón Touceda ◽  
Jamie Conyard ◽  
Ziyad Chaker ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Fluorescence Spectroscopy ◽  
Molecular Dynamics Simulations ◽  
Conformational Heterogeneity ◽  
Dna Hairpin ◽  
Quantitative Sampling ◽  
Dynamics Simulations
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