scholarly journals Ion Selectivity of α-Hemolysin with β-Cyclodextrin Adapter. II. Multi-Ion Effects Studied with Grand Canonical Monte Carlo/Brownian Dynamics Simulations

2010 ◽  
Vol 114 (8) ◽  
pp. 2901-2909 ◽  
Author(s):  
Bernhard Egwolf ◽  
Yun Luo ◽  
D. Eric Walters ◽  
Benoît Roux
Keyword(s):  
Monte Carlo ◽  
Brownian Dynamics ◽  
Ion Selectivity ◽  
Grand Canonical Monte Carlo ◽  
Ion Effects ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations ◽  
Grand Canonical

scholarly journals Dynamic Interaction of Norfloxacin to Magnesium Monitored by Bacterial Outer Membrane Nanopores

2020 ◽  
Author(s):  
Jiajun Wang ◽  
Jigneshkumar Dahyabhai Prajapati ◽  
Ulrich Kleinekathöfer ◽  
Mathias Winterhalter
Keyword(s):  
Outer Membrane ◽  
Lipid Bilayers ◽  
Brownian Dynamics ◽  
Single Channel ◽  
Ion Selectivity ◽  
Computational Modelling ◽  
Free Energy Calculations ◽  
Divalent Ions ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations

The effect of divalent ions on the permeability of norfloxacin across the major outer membrane channels from <i>E. coli</i> (OmpF, OmpC) and <i>E. aerogenes</i> (Omp35, Omp36) has been investigated at the single channel level. To understand the rate limiting steps in permeation, we reconstituted single porin into planar lipid bilayers and analyzed the ion current fluctuations caused in the presence of norfloxacin. To obtain an atomistic view, we complemented the experiments with millisecond-long free energy calculations based on temperature-accelerated Brownian dynamics simulations to identify the most probable permeation pathways of the antibiotics through the respective pore. Both, experimental analysis and computational modelling, suggest that norfloxacin is able to permeate through the larger porins, i.e., OmpF, OmpC, and Omp35, whereas it only binds to the slightly narrower porin Omp36. Moreover, divalent ions can bind to negatively charged residues inside the porin, reversing the ion selectivity of the pore. In addition, the divalent ions can chelate with the fluoroquinolones and alter their physicochemical properties. The results suggest that the conjugation must break with either one of them when the antibiotics molecules bypass the lumen of the porin, with the conjugation to the antibiotic being more stable than that to the pore. In general, the permeation or binding process of fluoroquinolone in porins occurs irrespective of the presence of divalent ions, but the presences of divalent ions can vary the kinetics significantly.

BROMOCEA Code: An Improved Grand Canonical Monte Carlo/Brownian Dynamics Algorithm Including Explicit Atoms

2016 ◽  
Vol 12 (5) ◽  
pp. 2401-2417 ◽  
Author(s):  
Carlos J. F. Solano ◽  
Karunakar R. Pothula ◽  
Jigneshkumar D. Prajapati ◽  
Pablo M. De Biase ◽  
Sergei Yu. Noskov ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Brownian Dynamics ◽  
Grand Canonical Monte Carlo ◽  
Grand Canonical
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