scholarly journals 3P119 Analysis for the effect of choline ions on the stability of DNA base pairs using molecular dynamics simulation(05A. Nucleic acid: Structure & Property,Poster)

2013 ◽  
Vol 53 (supplement1-2) ◽  
pp. S231
Author(s):  
Miki Nakano ◽  
Hisae Tateishi-Karimata ◽  
Naoki Sugimoto
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Structure Property ◽  
Nucleic Acid Structure ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Base Pairs ◽  
The Stability ◽  
Acid Structure

Can modified DNA base pairs with chalcogen bonding expand the genetic alphabet? A combined quantum chemical and molecular dynamics simulation study

2020 ◽  
Vol 22 (41) ◽  
pp. 23754-23765
Author(s):  
Karan Deep Sharma ◽  
Preetleen Kathuria ◽  
Stacey D. Wetmore ◽  
Purshotam Sharma
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Hydrogen Bonds ◽  
Quantum Chemical ◽  
Computational Study ◽  
Dynamics Simulation ◽  
Base Pairs ◽  
Dna Base ◽  
Modified Dna ◽  
Dna Base Pairs

A comprehesive computational study is presented with the goal to design and analyze model chalcogen-bonded modified nucleobase pairs that replace one or two Watson–Crick hydrogen bonds of the canonical A:T or G:C pair with chalcogen bond(s).

scholarly journals Hydrogen Bond Stability of Quinazoline Derivatives Compounds in Complex against EGFR using Molecular Dynamics Simulation

2019 ◽  
Vol 19 (2) ◽  
pp. 461
Author(s):  
Herlina Rasyid ◽  
Bambang Purwono ◽  
Thomas S Hofer ◽  
Harno Dwi Pranowo
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Binding Free Energy ◽  
Dynamics Simulation ◽  
Inhibition Mechanism ◽  
Energy Calculation ◽  
Protein Receptor ◽  
The Stability

Lung cancer was a second common cancer case due to the high cigarette smoking activity both in men and women. One of protein receptor which plays an important role in the growth of the tumor is Epidermal Growth Factor Receptor (EGFR). EGFR protein is the most frequent protein mutation in cancer and promising target to inhibit the cancer growth. In this work, the stability of the hydrogen bond as the main interaction in the inhibition mechanism of cancer will be evaluated using molecular dynamics simulation. There were two compounds (A1 and A2) as new potential inhibitors that were complexed against the EGFR protein. The dynamic properties of each complexed were compared with respect to erlotinib against EGFR. The result revealed that both compounds had an interaction in the main catalytic area of protein receptor which is at methionine residue. Inhibitor A1 showed additional interactions during simulation time but the interactions tend to be weak. Inhibitor A2 displayed a more stable interaction. Following dynamics simulation, binding free energy calculation was performed by two scoring techniques MM/GB(PB)SA method and gave a good correlation with the stability of the complex. Furthermore, potential inhibitor A2 had a lower binding free energy as a direct consequence of the stability of hydrogen bond interaction.

Sign in / Sign up

Export Citation Format

Share Document