Molecular mechanism of interactions between inhibitory tripeptide GEF and angiotensin-converting enzyme in aqueous solutions by molecular dynamic simulations

2018 ◽  
Vol 249 ◽  
pp. 389-396 ◽  
Author(s):  
Chunyan Qi ◽  
Rong Zhang ◽  
Fuzhi Liu ◽  
Tong Zheng ◽  
Wenjuan Wu
Keyword(s):  
Angiotensin Converting Enzyme ◽  
Aqueous Solutions ◽  
Molecular Dynamic ◽  
Molecular Mechanism ◽  
Molecular Dynamic Simulations ◽  
Converting Enzyme ◽  
Dynamic Simulations

Investigations of clustering of ions and diffusivity in concentrated aqueous solutions of lithium chloride by molecular dynamic simulations

RSC Advances ◽  
2015 ◽  
Vol 5 (20) ◽  
pp. 15328-15337 ◽  
Author(s):  
Meena B. Singh ◽  
Vishwanath H. Dalvi ◽  
Vilas G. Gaikar
Keyword(s):  
Diffusion Coefficient ◽  
Aqueous Solutions ◽  
Molecular Dynamic ◽  
Lithium Chloride ◽  
Molecular Dynamic Simulations ◽  
Coordination Structure ◽  
Dynamic Simulations ◽  
Concentrated Aqueous Solutions

The diffusion coefficient of Li+ ions decreases with increase in LiCl concentration which depends on the size of coordination structure of ions formed in solutions.

Molecular-Dynamic Simulations on Aqueous Solutions Confined Between Uniformly Charged Hydrophobic Plates

2009 ◽  
Author(s):  
Hoang Hai ◽  
Sangmo Kang ◽  
Yong Kweon Suh
Keyword(s):  
Aqueous Solutions ◽  
Molecular Dynamic ◽  
Numerical Study ◽  
Dynamic Properties ◽  
Water Molecules ◽  
Molecular Dynamic Simulations ◽  
Ewald Summation ◽  
Dynamic Simulations ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation

In this paper, we present the numerical study on the properties of aqueous solution confined between uniformly charged hydrophobic plates using the molecular-dynamic simulations. Two kinds of aqueous solutions used in our study are aqueous sodium and aqueous chloride. The SPC/E model and combination of quaternion coordinates with Euler angles are used to model the water molecules and constraint the structure of water molecules, respectively. The hydrophobic plates are separated by 2.6 nm and the space contains 680 water molecules and 20 ions. The charge density on each surface of the plate is the same with each other and satisfies the charge-neutralization criterion over the whole domain. We employed the modified Ewald summation for the uniformly charged surface PPPM method (particle-particle-particle-mesh) to compute the long-range interactions. The static and dynamic properties of solvent and ions are computed. We also compare our results with those provided by solving the Poisson-Boltzmann equation.

Studies on the bioactivities and molecular mechanism of antioxidant peptides by 3D-QSAR, in vitro evaluation and molecular dynamic simulations

2020 ◽  
Vol 11 (4) ◽  
pp. 3043-3052 ◽  
Author(s):  
Wenli Yan ◽  
Guimei Lin ◽  
Rong Zhang ◽  
Zhen Liang ◽  
Wenjuan Wu
Keyword(s):  
Molecular Dynamic ◽  
Molecular Mechanism ◽  
3D Qsar ◽  
Md Simulations ◽  
Molecular Dynamic Simulations ◽  
Antioxidant Peptides ◽  
Dynamic Simulations ◽  
In Vitro Evaluation

The bioactivities and molecular mechanism of two novel antioxidant peptides were investigated by 3D-QSAR, in vitro evaluation and MD simulations.

scholarly journals Hydration of C-H groups in natural dithymidine nucleotide and its methylphosphonate analogues.

1998 ◽  
Vol 45 (4) ◽  
pp. 977-985 ◽  
Author(s):  
K Kulińska ◽  
T Kuliński ◽  
J Stawiński
Keyword(s):  
Aqueous Solutions ◽  
Molecular Dynamic ◽  
Specific Interaction ◽  
Methyl Groups ◽  
Water Molecules ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Better Than

In this paper we report our preliminary studies on the hydration pattern of selected C-H groups in natural thymidyl(3'-5)thymidine and its Rp and Sp-methylphosphonate analogues using Molecular Dynamic simulations in aqueous solutions. The methyl groups attached to the phosphorus center (P-Me) in methylphosphonate analogues are hydrated by water molecules as efficiently as the hydrophilic P=O group in the natural dithymidine nucleotide and better than the neutral P=O functions in these compounds, although the nature of the hydration is different. The C5-Me centers of the 3'-yl units seem to be better hydrated in the methylphosphonate analogues than in the natural dithymidine phosphate and than other centers of the thymine bases in methylphosphonate analogues. Due to chirality of the phosphorus center, the C5-Me group of the 5'-yl unit in the Sp diastereomer coordinates more water than that in the Rp diastereomer. The C6-H group in the 5'-yl unit of the Sp diastereomer exhibits a specific interaction with water.

Sign in / Sign up

Export Citation Format

Share Document