Potential of mean force for insertion of antimicrobial peptide melittin into a pore in mixed DOPC/DOPG lipid bilayer by molecular dynamics simulation

2017 ◽  
Vol 146 (15) ◽  
pp. 155101 ◽  
Author(s):  
Yuan Lyu ◽  
Ning Xiang ◽  
Xiao Zhu ◽  
Ganesan Narsimhan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Antimicrobial Peptide ◽  
Lipid Bilayer ◽  
Potential Of Mean Force ◽  
Dynamics Simulation

A multi-scale molecular dynamics simulation of PMAL facilitated delivery of siRNA

RSC Advances ◽  
2015 ◽  
Vol 5 (83) ◽  
pp. 68227-68233 ◽  
Author(s):  
Jipeng Li ◽  
Yiyun Ouyang ◽  
Xian Kong ◽  
Jingying Zhu ◽  
Diannan Lu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Lipid Bilayer ◽  
Dynamics Simulation ◽  
Lipid Bilayer Membranes ◽  
Bilayer Membranes ◽  
Multi Scale

PMAL as a novel carrier for the delivery of siRNA into lipid bilayer membranes.

scholarly journals Molecular Dynamics Simulation of Transmembrane Transport of Chloride Ions in Mutants of Channelrhodopsin

Biomolecules ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 852
Author(s):  
Wenying Zhang ◽  
Ting Yang ◽  
Shuangyan Zhou ◽  
Jie Cheng ◽  
Shuai Yuan ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Ion Channel ◽  
Ion Selectivity ◽  
Potential Of Mean Force ◽  
Chloride Ions ◽  
Dynamics Simulation ◽  
Mutant Proteins ◽  
Transmembrane Channel ◽  
Anion Conduction

Channelrhodopsins (ChRs) are light-gated transmembrane cation channels which are widely used for optogenetic technology. Replacing glutamate located at the central gate of the ion channel with positively charged amino acid residues will reverse ion selectivity and allow anion conduction. The structures and properties of the ion channel, the transport of chloride, and potential of mean force (PMF) of the chimera protein (C1C2) and its mutants, EK-TC, ER-TC and iChloC, were investigated by molecular dynamics simulation. The results show that the five-fold mutation in E122Q-E129R-E140S-D195N-T198C (iChloC) increases the flexibility of the transmembrane channel protein better than the double mutations in EK-TC and ER-TC, and results in an expanded ion channel pore size and decreased steric resistance. The iChloC mutant was also found to have a higher affinity for chloride ions and, based on surface electrostatic potential analysis, provides a favorable electrostatic environment for anion conduction. The PMF free energy curves revealed that high affinity Cl− binding sites are generated near the central gate of the three mutant proteins. The energy barriers for the EK-TC and ER-TC were found to be much higher than that of iChloC. The results suggest that the transmembrane ion channel of iChloC protein is better at facilitating the capture and transport of chloride ions.

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