DNA Transfection Efficiency of Antimicrobial Peptide as Revealed by Molecular Dynamics Simulation

2013 ◽  
Vol 1569 ◽  
pp. 109-114
Author(s):  
Namsrai Javkhlantugs ◽  
Janlav Munkhtsetseg ◽  
Chimed Ganzorig ◽  
Kazuyoshi Ueda
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Transfection Efficiency ◽  
Dynamics Simulation ◽  
Amino Acid Residues ◽  
Dna Transfection ◽  
Amphipathic Peptide ◽  
Endosomal Membrane ◽  
N Terminus ◽  
Dna Complex

ABSTRACTThe peptide-DNA complex was investigated by using molecular dynamics simulation to analyze the transfection efficiency of cationic amphipathic peptide. Previously, the cationic peptide, LFampinB, with positively charged amino acid residues of Lysines was used to investigate the orientation and interaction energies for entering the cell though disruption of the endosomal membrane. The same interactions were obtained for N-terminus of the LFampinB peptide with membrane and with plasmid DNA. The N-terminus of LFampinB can bind at minor groove of DNA to make complexation of the peptide with DNA.

scholarly journals Binding interactions of epididymal protease inhibitor and semenogelin-1: a homology modeling, docking and molecular dynamics simulation study

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7329 ◽  
Author(s):  
Changyu Shan ◽  
Hongwei Li ◽  
Yuping Zhang ◽  
Yuyan Li ◽  
Yingchun Chen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Homology Modeling ◽  
Protease Inhibitor ◽  
Hormonal Contraceptive ◽  
Dynamics Simulation ◽  
Binding Interaction ◽  
Binding Interactions ◽  
C Terminus ◽  
N Terminus

Epididymal protease inhibitor (EPPIN) that is located on the sperm surface and specific to the male reproductive system is a non-hormonal contraceptive target, since the binding of EPPIN with the seminal plasma protein semenogelin-1 (SEMG1) causes a loss of sperm function. Here, we investigated the binding interactions between EPPIN and SEMG1 by homology modeling, docking and molecular dynamics simulation. Since no crystal structure was reported for EPPIN, its 3D structure was constructed by homology modeling and refined by dynamics simulation, illustrating the C-terminus domain of EPPIN could bind with its N-terminus domain through the residues 30–32 and 113–116. The binding interaction of SEMG110-8 peptide and EPPIN was investigated by Z-DOCK and dynamics simulation. After evaluating the models according to the calculated binding free energies, we demonstrated that C-terminus domain of EPPIN was important for the binding of SEMG1 via residues Tyr107, Gly112, Asn116, Gln118 and Asn122, while residue Arg32 in N-terminus domain also had contribution for their binding interaction. Additionally, the binding pocket of EPPIN was defined according to these key residues and verified by molecular docking with reported inhibitor EP055, suggesting that the pocket formed by Arg32, Asn114, Asn116, Phe117 and Asn122 could be important for the design of new ligands. This study might be helpful for the understanding of biological function of EPPIN and would encourage the discovery of non-hormonal contraceptive leads/drugs in the future.

scholarly journals Molecular Insights Into the Gating Kinetics of the Cardiac hERG Channel, Illuminated by Structure and Molecular Dynamics

2021 ◽  
Vol 12 ◽  
Author(s):  
Zheng Zequn ◽  
Lian Jiangfang
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Herg Channel ◽  
Single Amino Acid ◽  
Delayed Rectifier ◽  
Amino Acid Residues ◽  
Structural Domains ◽  
Gating Kinetics

The rapidly activating delayed rectifier K+ current generated by the cardiac hERG potassium channel encoded by KCNH2 is the most important reserve current for cardiac repolarization. The unique inward rectification characteristics of the hERG channel depend on the gating regulation, which involves crucial structural domains and key single amino acid residues in the full-length hERG channel. Identifying critical molecules involved in the regulation of gating kinetics for the hERG channel requires high-resolution structures and molecular dynamics simulation models. Based on the latest progress in hERG structure and molecular dynamics simulation research, summarizing the molecules involved in the changes in the channel state helps to elucidate the unique gating characteristics of the channel and the reason for its high affinity to cardiotoxic drugs. In this review, we aim to summarize the significant advances in understanding the voltage gating regulation of the hERG channel based on its structure obtained from cryo-electron microscopy and computer simulations, which reveal the critical roles of several specific structural domains and amino acid residues.

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