Lipid a from lipopolysaccharide recognition: Structure, dynamics and cooperativity by molecular dynamics simulations

2013 ◽  
Vol 81 (4) ◽  
pp. 658-674 ◽  
Author(s):  
Jose Antonio Garate ◽  
Chris Oostenbrink
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid A ◽  
Structure Dynamics ◽  
Dynamics Simulations

Protic ammonium carboxylate ionic liquids: insight into structure, dynamics and thermophysical properties by alkyl group functionalization

2017 ◽  
Vol 19 (16) ◽  
pp. 10358-10370 ◽  
Author(s):  
Th. Dhileep N. Reddy ◽  
Bhabani S. Mallik
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquids ◽  
Molecular Dynamics Simulations ◽  
Thermophysical Properties ◽  
Alkyl Group ◽  
Structure Dynamics ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations ◽  
Insight Into

This study is aimed at characterising the structure, dynamics and thermophysical properties of five alkylammonium carboxylate ionic liquids (ILs) from classical molecular dynamics simulations.

scholarly journals Properties of Lipid a Bilayers Analyzed by Molecular Dynamics Simulations

2011 ◽  
Vol 100 (3) ◽  
pp. 321a
Author(s):  
Danielle Stuhlsatz ◽  
Richard Venable ◽  
Wonpil Im
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid A ◽  
Dynamics Simulations

Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations

Biopolymers ◽  
2006 ◽  
Vol 82 (5) ◽  
pp. 504-520 ◽  
Author(s):  
Kamila Réblová ◽  
Filip Lankas̆ ◽  
Filip Rázga ◽  
Maryna V. Krasovska ◽  
Jaroslav Koc̆a ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
16S Rrna ◽  
Molecular Dynamics Simulations ◽  
Structure Dynamics ◽  
Dynamics Simulations

Interaction of fullerene chains and a lipid membrane via computer simulations

RSC Advances ◽  
2014 ◽  
Vol 4 (57) ◽  
pp. 30215-30220 ◽  
Author(s):  
Wen-de Tian ◽  
Kang Chen ◽  
Yu-qiang Ma
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Computer Simulations ◽  
Membrane Structure ◽  
Lipid Membrane ◽  
Coarse Grained ◽  
Structure Dynamics ◽  
Dynamics Simulations ◽  
Fullerene Polymers ◽  
Coarse Grained Molecular Dynamics

Coarse-grained molecular dynamics simulations were employed to study the fullerene polymers with various functionalization degrees interacting with the DPPC membrane. Structure, dynamics, and thermodynamics of systems were analyzed.

Deconstructing the behavior of donor–acceptor copolymers in solution & the melt: the case of PTB7

2019 ◽  
Vol 21 (15) ◽  
pp. 7802-7813 ◽  
Author(s):  
Sean M. Ryno ◽  
Chad Risko
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Condensed Phase ◽  
Structure Dynamics ◽  
Donor Acceptor ◽  
Dynamics Simulations

Molecular dynamics simulations of the donor–acceptor copolymer PTB7 at near experimental scale reveal structure–dynamics correlations in the condensed phase.

scholarly journals Molecular dynamics simulations informed by membrane lipidomics reveal the structure–interaction relationship of polymyxins with the lipid A-based outer membrane of Acinetobacter baumannii

2020 ◽  
Vol 75 (12) ◽  
pp. 3534-3543 ◽  
Author(s):  
Xukai Jiang ◽  
Kai Yang ◽  
Bing Yuan ◽  
Meiling Han ◽  
Yan Zhu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Acinetobacter Baumannii ◽  
Outer Membrane ◽  
Electrostatic Interactions ◽  
Lipid A ◽  
Gram Negative ◽  
Structure Interaction ◽  
Dynamics Simulations ◽  
Interaction Relationship

Abstract Background MDR bacteria represent an urgent threat to human health globally. Polymyxins are a last-line therapy against life-threatening Gram-negative ‘superbugs’, including Acinetobacter baumannii. Polymyxins exert antimicrobial activity primarily via permeabilizing the bacterial outer membrane (OM); however, the mechanism of interaction between polymyxins and the OM remains unclear at the atomic level. Methods We constructed a lipid A-based OM model of A. baumannii using quantitative membrane lipidomics data and employed all-atom molecular dynamics simulations with umbrella sampling techniques to elucidate the structure–interaction relationship and thermodynamics governing the penetration of polymyxins [B1 and E1 (i.e. colistin A) representing the two clinically used polymyxins] into the OM. Results Polymyxin B1 and colistin A bound to the A. baumannii OM by the initial electrostatic interactions between the Dab residues of polymyxins and the phosphates of lipid A, competitively displacing the cations from the headgroup region of the OM. Both polymyxin B1 and colistin A formed a unique folded conformation upon approaching the hydrophobic centre of the OM, consistent with previous experimental observations. Polymyxin penetration induced reorientation of the headgroups of the OM lipids near the penetration site and caused local membrane disorganization, thereby significantly increasing membrane permeability and promoting the subsequent penetration of polymyxin molecules into the OM and periplasmic space. Conclusions The thermodynamics governing the penetration of polymyxins through the outer leaflet of the A. baumannii OM were examined and novel structure–interaction relationship information was obtained at the atomic and membrane level. Our findings will facilitate the discovery of novel polymyxins against MDR Gram-negative pathogens.

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