scholarly journals Unravelling the mechanism of glucose binding in a protein-based fluorescence probe: molecular dynamics simulation with a tailor-made charge model

2022 ◽  
Author(s):  
Ziwei Pang ◽  
Monja Sokolov ◽  
Tomáš Kubař ◽  
Marcus Elstner
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Medical Devices ◽  
Potential Application ◽  
Fluorescence Probe ◽  
Binding Protein ◽  
Glucose Sensors ◽  
Dynamics Simulation ◽  
Glucose Binding ◽  
Charge Model

Fluorophores linked to the glucose/galactose-binding protein (GGBP) are a promising class of glucose sensors with potential application in medical devices for diabetes patients. Several different fluorophores at different positions in...

Molecular Dynamics Simulation of Gas Transport in Polyisoprene Matrix

2013 ◽  
Vol 844 ◽  
pp. 209-213
Author(s):  
Natthida Rakkapao
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Model ◽  
Material Properties ◽  
Diffusion Coefficients ◽  
Potential Application ◽  
Md Simulation ◽  
Gas Transport ◽  
Dynamics Simulation ◽  
Membrane Properties

Molecular Dynamics (MD) simulation was employed to study the diffusivity of biogas in a PI matrix with the aim to verify simulations as a useful tool to predict PI membrane properties for biogas treatment. The simulation model of PI numerical was reliable and accurate in predicting both the material properties and the diffusivity of gases in PI matrix. The diffusion coefficients (D) of the major components in biogas, namely CH4, CO2, H2O, O2, and N2, were computed by simulating trajectories of each gas in PI matrix at 300 K. The simulations gave DCO2 that was 6 times larger than DCH4, and this agrees well with permeabilities reported in the literature. This suggests that PI membranes could be used to treat biogas by separating CO2 and CH4. However, the diffusivities of N2, H2O, and CH4 are closely similar, so PI membranes are not capable of separating these. The potential application of PI membrane to CO2/CH4 separation seems worth further exploration.

An electrostatic energy-based charge model for molecular dynamics simulation

2021 ◽  
Vol 154 (13) ◽  
pp. 134107
Author(s):  
Xianwei Wang ◽  
Jinhua Yan ◽  
Hang Zhang ◽  
Zhousu Xu ◽  
John Z. H. Zhang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Electrostatic Energy ◽  
Charge Model

scholarly journals A novel GATA-binding protein 4 gene variation associated with familial atrial septal defect

2018 ◽  
Author(s):  
Yongchao Yang ◽  
Yu Xia ◽  
Yueheng Wu ◽  
Shufang Huang ◽  
Yun Teng ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Atrial Septal Defect ◽  
Septal Defect ◽  
Binding Protein ◽  
Dynamics Simulation ◽  
Luciferase Reporter ◽  
Chromosomal Microarray ◽  
Incomplete Penetrance ◽  
Gene Assay

AbstractAtrial septal defect (ASD) is the most common congenital heart defect. Part of ASD exhibits familial predisposition, but the genetic mechanism remains largely unknown. In the current study, we use multiple methods to identify and confirm the gene associated with a familial ASD. Chromosomal microarray analyses, whole exome sequencing, Sanger sequencing, multiple bioinformatics programs, in silico protein structure modeling and molecular dynamics simulation were performed to predict the pathogenic of the variant gene. Dual-Luciferase reporter gene assay was performed to evaluate the influence of downstream target gene of the target variation. A novel, heterozygous, missense variant GATA-binding protein 4 (GATA4):c.958C>T, p.R320W was identified. An autosomal dominant inheritance pattern with incomplete penetrance was observed in the family. Multiple prediction indicate the variant in GATA4 to be deleterious. Molecular dynamics simulation further revealed that the variation of p.R320W could prevent the zinc finger of GATA4 from interacting with the DNA. Dual-Luciferase reporter assay demonstrated a significant decrease in transcriptional activity (0.90±0.099 vs 1.50±0.079, p = 0.001) of the variant GATA4 compared with the wild type. We believe the novel variation of GATA4 (c.958C>T, p.R320W) with a pattern of incomplete inheritance that may be highly associated with this familial ASD. The finding enriched our knowledge of variations that may associated with ASD.

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