How a crosslinker agent interacts with the β-glucosidase enzyme surface in an aqueous solution: Insight from quantum mechanics calculations and molecular dynamics simulations

2021 ◽  
Vol 203 ◽  
pp. 111761
Author(s):  
Samira Hozhabr Araghi ◽  
Amalraj John ◽  
Mohammad Sadegh Sadeghi Googheri
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Quantum Mechanics ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations

scholarly journals Trimethylamine-N-oxide: its hydration structure, surface activity, and biological function, viewed by vibrational spectroscopy and molecular dynamics simulations

2017 ◽  
Vol 19 (10) ◽  
pp. 6909-6920 ◽  
Author(s):  
Tatsuhiko Ohto ◽  
Johannes Hunger ◽  
Ellen H. G. Backus ◽  
Wataru Mizukami ◽  
Mischa Bonn ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulations ◽  
Surface Activity ◽  
Vibrational Spectroscopy ◽  
Biological Function ◽  
Molecular Simulations ◽  
Structure Surface ◽  
Dynamics Simulations ◽  
Hydrophilicity And Hydrophobicity

Vibrational spectroscopy and molecular simulations revealed the hydrophilicity and hydrophobicity of TMAO in aqueous solution.

UNDERSTANDING DIFFERENT LCST LEVELS OF POLY(N-ALKYLACRYLAMIDE)S BY MOLECULAR DYNAMICS SIMULATIONS AND QUANTUM MECHANICS CALCULATIONS

2011 ◽  
Vol 10 (03) ◽  
pp. 359-370 ◽  
Author(s):  
JUAN PANG ◽  
HU YANG ◽  
JING MA ◽  
RONGSHI CHENG
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Aqueous Solutions ◽  
Molecular Dynamics Simulations ◽  
Steric Effect ◽  
Conformational Transition ◽  
Methyl Group ◽  
Branched Chain ◽  
Dynamics Simulations ◽  
Different Levels

Poly(N-alkylacrylamide) is a group of thermo-sensitive polymers that include poly (N-isopropylacrylamide), poly(N-n-propylacrylamide), poly(N-isopropylmethacryl-amide), and so on. The polymers exhibit different levels of lower critical solution temperatures (LCST) in aqueous solutions. In this article, their monomers and oligomers with 10 repeating units are selected, respectively, to demonstrate the cause of different LCST levels of the polymers in aqueous solutions using molecular dynamics simulations and quantum mechanics calculations. The monomers have functional groups of different steric volume that greatly affect the conformational transition of chains and LCST levels of the polymers. A branched chain of N-propyl group in N-isopropylacrylamide and an additional methyl group at α-carbon in N-isopropylmethacrylamide both increase the steric effect, making it more difficult for monomers to draw closer and resulting in higher LCST levels of the polymers. In addition, the simulated results from their corresponding oligomers exhibit the similar trend to those from the monomers.

scholarly journals Molecular-Dynamics Simulations of C- and N-Terminal Peptide Derivatives of GCN4-p1 in Aqueous Solution

2005 ◽  
Vol 2 (8) ◽  
pp. 1086-1104 ◽  
Author(s):  
John H. Missimer ◽  
Michel O. Steinmetz ◽  
Wolfgang Jahnke ◽  
Fritz K. Winkler ◽  
Wilfred F. van Gunsteren ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulations ◽  
Peptide Derivatives ◽  
C And N ◽  
Dynamics Simulations ◽  
Derivatives Of
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