scholarly journals Rational design of a three-heptad coiled-coil protein and comparison by molecular dynamics simulation with the GCN4 coiled coil: Presence of interior three-center hydrogen bonds

1994 ◽  
Vol 3 (2) ◽  
pp. 345-355 ◽  
Author(s):  
James E. Rozzelle ◽  
Alexander Tropsha ◽  
Bruce W. Erickson
RSC Advances ◽  
2015 ◽  
Vol 5 (93) ◽  
pp. 76642-76650 ◽  
Author(s):  
Kiana Gholamjani Moghaddam ◽  
Seyed Majid Hashemianzadeh

Our study provides insight into the effect of different substituents on the G-quadruplex–ligand interactions which helps us rational ligand design.


2020 ◽  
Vol 22 (31) ◽  
pp. 17620-17631
Author(s):  
Xianling Chen ◽  
Jing Zhu ◽  
Yanlong Luo ◽  
Jun Chen ◽  
Xiaofeng Ma ◽  
...  

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.


Crystals ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 316 ◽  
Author(s):  
Dan Zhu ◽  
Shihao Zhang ◽  
Pingping Cui ◽  
Chang Wang ◽  
Jiayu Dai ◽  
...  

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.


2019 ◽  
Vol 21 (39) ◽  
pp. 21836-21846 ◽  
Author(s):  
Mitra Maddah ◽  
Mina Maddah ◽  
Kiana Peyvandi

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.


2019 ◽  
Vol 131 (23) ◽  
pp. 7784-7789 ◽  
Author(s):  
Xiaohuan Sun ◽  
Laura Riccardi ◽  
Federico De Biasi ◽  
Federico Rastrelli ◽  
Marco De Vivo ◽  
...  

2019 ◽  
Vol 58 (23) ◽  
pp. 7702-7707 ◽  
Author(s):  
Xiaohuan Sun ◽  
Laura Riccardi ◽  
Federico De Biasi ◽  
Federico Rastrelli ◽  
Marco De Vivo ◽  
...  

1998 ◽  
Vol 53 (9-10) ◽  
pp. 857-862 ◽  
Author(s):  
Igor Zbigniew Zubrzycki

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.


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