Characteristics of hydration water around hen egg lysozyme as the protein model in aqueous solution. FTIR spectroscopy and molecular dynamics simulation

2012 ◽  
Vol 14 (45) ◽  
pp. 15765 ◽  
Author(s):  
Aneta Panuszko ◽  
Marek Wojciechowski ◽  
Piotr Bruździak ◽  
Paulina W. Rakowska ◽  
Janusz Stangret
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulation ◽  
Ftir Spectroscopy ◽  
Dynamics Simulation ◽  
Hydration Water ◽  
Protein Model ◽  
Hen Egg ◽  
Hen Egg Lysozyme

Improved Sampling Strategies for Protein Model Refinement based on Molecular Dynamics Simulation

2020 ◽  
Author(s):  
Lim Heo ◽  
Collin Arbour ◽  
Michael Feig
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Structure Prediction ◽  
Protein Structures ◽  
Conformational Space ◽  
Dynamics Simulation ◽  
Model Refinement ◽  
Protein Model ◽  
Lower Accuracy ◽  
Simulation Based

Protein structures provide valuable information for understanding biological processes. Protein structures can be determined by experimental methods such as X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, or cryogenic electron microscopy. As an alternative, in silico methods can be used to predict protein structures. Those methods utilize protein structure databases for structure prediction via template-based modeling or for training machine-learning models to generate predictions. Structure prediction for proteins distant from proteins with known structures often results in lower accuracy with respect to the true physiological structures. Physics-based protein model refinement methods can be applied to improve model accuracy in the predicted models. Refinement methods rely on conformational sampling around the predicted structures, and if structures closer to the native states are sampled, improvements in the model quality become possible. Molecular dynamics simulations have been especially successful for improving model qualities but although consistent refinement can be achieved, the improvements in model qualities are still moderate. To extend the refinement performance of a simulation-based protocol, we explored new schemes that focus on an optimized use of biasing functions and the application of increased simulation temperatures. In addition, we tested the use of alternative initial models so that the simulations can explore conformational space more broadly. Based on the insight of this analysis we are proposing a new refinement protocol that significantly outperformed previous state-of-the-art molecular dynamics simulation-based protocols in the benchmark tests described here. <br>

Molecular dynamics simulation of homogeneous nucleation of supersaturated potassium chloride (KCl) in aqueous solutions

CrystEngComm ◽  
2019 ◽  
Vol 21 (48) ◽  
pp. 7507-7518 ◽  
Author(s):  
Soroush Ahmadi ◽  
Yuanyi Wu ◽  
Sohrab Rohani
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulation ◽  
Aqueous Solutions ◽  
Potassium Chloride ◽  
Homogeneous Nucleation ◽  
Md Simulation ◽  
Crystal Nucleation ◽  
Dynamics Simulation

Molecular dynamics (MD) simulation is used to investigate the mechanism of crystal nucleation of potassium chloride (KCl) in a supersaturated aqueous solution at 293 K and 1 atm.

Molecular dynamics simulation in aqueous solution of N -methylazetidinone as a model of β -lactam antibiotics

1999 ◽  
Vol 101 (5) ◽  
pp. 336-342 ◽  
Author(s):  
Jesús Pitarch ◽  
Juan-Luis Pascual-Ahuir ◽  
Estanislao Silla ◽  
Iñaki Tuñón ◽  
Manuel F. Ruiz-López ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation
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