Conformational Studies of the Emp-AKH Peptide Using Molecular and Langevin Dynamics Methods

1998 ◽  
Vol 53 (9-10) ◽  
pp. 857-862 ◽  
Author(s):  
Igor Zbigniew Zubrzycki
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Hydrogen Bonds ◽  
Minimum Energy ◽  
Langevin Dynamics ◽  
Dynamics Simulation ◽  
Vacuum Model ◽  
Conformational Studies ◽  
Backbone Structure ◽  
Langevin Dynamics Simulation

The secondary structure of the member of the AKH/RPCH family has been studied by Molecular Dynamics and Langevin Dynamics methods. Molecular dynamics simulation were performed in vacuum, model aqueous solution and simulated membrane. Langevin dynamics simulation was performed using the friction factor γ equal to 2 ps-1. Molecular dynamics as well as Langevin Dynamics simulation were conducted at 300 K. All minimum energy conformers have similar backbone structure characterised by the turn consisted out of 3 amino acids, Thr, Pro and Asn7. Structures obtained from Molecular Dynamics simulation are characterised by the lack of hydrogen bonds whereas the structure obtained form Langevin Dynamics simulation is stabilised by the web of hydrogen bonds.

Molecular dynamics simulation insight into the temperature dependence and healing mechanism of an intrinsic self-healing polyurethane elastomer

2020 ◽  
Vol 22 (31) ◽  
pp. 17620-17631
Author(s):  
Xianling Chen ◽  
Jing Zhu ◽  
Yanlong Luo ◽  
Jun Chen ◽  
Xiaofeng Ma ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Hydrogen Bonds ◽  
Molecular Diffusion ◽  
Healing Process ◽  
The Self ◽  
Dynamics Simulation ◽  
Polyurethane Elastomer ◽  
Self Healing ◽  
Insight Into

The changes in the type and number of hydrogen bonds as well as the microscopic behavior of molecular diffusion in the self-healing process of polyurethane are revealed.

scholarly journals Solvent Effects on Catechol Crystal Habits and Aspect Ratios: A Combination of Experiments and Molecular Dynamics Simulation Study

Crystals ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 316 ◽  
Author(s):  
Dan Zhu ◽  
Shihao Zhang ◽  
Pingping Cui ◽  
Chang Wang ◽  
Jiayu Dai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Hydrogen Bonds ◽  
Solvent Effects ◽  
Dynamics Simulation ◽  
Crystal Habit ◽  
Aspect Ratios ◽  
Solvent Environment ◽  
Solvent Adsorption ◽  
Attachment Energy

This work could help to better understand the solvent effects on crystal habits and aspect ratio changes at the molecular level, which provide some guidance for solvent selection in industrial crystallization processes. With the catechol crystal habits acquired using both experimental and simulation methods in isopropanol, methyl acetate and ethyl acetate, solvent effects on crystal morphology were explored based on the modified attachment energy model. Firstly, morphologically dominant crystal faces were obtained with the predicted crystal habit in vacuum. Then, modified attachment energies were calculated by the molecular dynamics simulation to modify the crystal shapes in a real solvent environment, and the simulation results were in agreement with the experimental ones. Meanwhile, the surface properties such as roughness and the diffusion coefficient were introduced to analyze the solvent adsorption behaviors and the radial distribution function curves were generated to distinguish diverse types of interactions like hydrogen bonds and van der Waals forces. Results show that the catechol crystal habits were affected by the combination of the attachment energy, surface structures and molecular interaction types. Moreover, the changing aspect ratios of catechol crystals are closely related to the existence of hydrogen bonds which contribute to growth inhibition on specific faces.

The influence of a type III antifreeze protein and its mutants on methane hydrate adsorption–inhibition: a molecular dynamics simulation study

2019 ◽  
Vol 21 (39) ◽  
pp. 21836-21846 ◽  
Author(s):  
Mitra Maddah ◽  
Mina Maddah ◽  
Kiana Peyvandi
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Dynamics Simulation ◽  
Hydrogen Bonds ◽  
Simulation Study ◽  
Methane Hydrate ◽  
Hydrophobic Interactions ◽  
Dynamics Simulation ◽  
Antifreeze Activity ◽  
Adsorption Inhibition

Antifreeze proteins inhibit hydrate growth by hydrophobic interactions in cooperation with hydrogen bonds. Mutation of three polar amino acids (Asn14, Thr18, and Gln44) elucidates the molecular mechanism of AFP III antifreeze activity.

MOLECULAR DYNAMICS SIMULATION OF ADSORPTION OF ANILINE BY α-ZIRCONIUM PHOSPHATE

2010 ◽  
Vol 09 (05) ◽  
pp. 861-873 ◽  
Author(s):  
RUO-YU CHEN ◽  
JING ZHONG ◽  
CHI-RUEI GU ◽  
CHENG-LUNG CHEN
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Zirconium Phosphate ◽  
Minimum Energy ◽  
Power Spectra ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Molar Ratios ◽  
Diffraction Patterns ◽  
Structure Properties

Molecular dynamics simulation and minimization process were carried out to study the structure properties of α-zirconium phosphate (α- ZrP ) loaded with aniline molecules. Two minimum-energy configurations of α- ZrP with interlayer distances 14.14 and 19.0 Å were found for the systems of molar ratios of aniline to ZrP = 1:1 and 2:1. The structure properties of aniline and α- ZrP and also the interaction between aniline and α- ZrP were analyzed. The phase behavior was analyzed by calculated diffraction patterns, power spectra, and various distribution functions.

scholarly journals Molecular Dynamics Simulation of VEGFR2 with Sorafenib and Other Urea-Substituted Aryloxy Compounds

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Fancui Meng
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Molecular Dynamics Simulation ◽  
Hydrogen Bonds ◽  
Md Simulation ◽  
Binding Mode ◽  
Dynamics Simulation ◽  
Dynamics Simulations ◽  
Simulation Time ◽  
Dynamics Method

The binding mode of sorafenib with VEGFR2 was studied using molecular docking and molecular dynamics method. The docking results show that sorafenib forms hydrogen bonds with Asp1046, Cys919, and Glu885 of VEGFR2 receptor. Molecular dynamics simulation suggests that the hydrogen bond involving Asp1046 is the most stable one, and it is almost preserved during all the MD simulation time. The hydrogen bond formed with Cys919 occurs frequently after 6 ns, while the bifurcated hydrogen bonds involving Glu885 occurs occasionally. Meantime, molecular dynamics simulations of VEGFR2 with 11 other urea-substituted aryloxy compounds have also been performed, and the results indicate that a potent VEGFR2 inhibitor should have lower interaction energy with VEGFR2 and create at least 2 hydrogen bonds with VEGFR2.

Structure and hydrogen bonds of γS-crystallin and γS-G18V studied by molecular dynamics simulation

2017 ◽  
Author(s):  
A. Ozawa ◽  
H. Yamada ◽  
S. Mori ◽  
Y. Noguchi ◽  
T. Miyakawa ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Hydrogen Bonds ◽  
Dynamics Simulation

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).

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