scholarly journals Molecular Dynamics Simulation and Kinetic Study of Fluoride Binding to V21C/V66C Myoglobin with a Cytoglobin-like Disulfide Bond

2020 ◽  
Vol 21 (7) ◽  
pp. 2512
Author(s):  
Lu-Lu Yin ◽  
Jia-Kun Xu ◽  
Xiao-Juan Wang ◽  
Shu-Qin Gao ◽  
Ying-Wu Lin
Keyword(s):  
Molecular Dynamics ◽  
Disulfide Bond ◽  
Rational Design ◽  
Double Mutant ◽  
Md Simulation ◽  
Experimental Studies ◽  
Heme Iron ◽  
Dynamics Simulation ◽  
Fluoride Ion ◽  
Artificial Proteins

Protein design is able to create artificial proteins with advanced functions, and computer simulation plays a key role in guiding the rational design. In the absence of structural evidence for cytoglobin (Cgb) with an intramolecular disulfide bond, we recently designed a de novo disulfide bond in myoglobin (Mb) based on structural alignment (i.e., V21C/V66C Mb double mutant). To provide deep insight into the regulation role of the Cys21-Cys66 disulfide bond, we herein perform molecular dynamics (MD) simulation of the fluoride–protein complex by using a fluoride ion as a probe, which reveals detailed interactions of the fluoride ion in the heme distal pocket, involving both the distal His64 and water molecules. Moreover, we determined the kinetic parameters of fluoride binding to the double mutant. The results agree with the MD simulation and show that the formation of the Cys21-Cys66 disulfide bond facilitates both fluoride binding to and dissociating from the heme iron. Therefore, the combination of theoretical and experimental studies provides valuable information for understanding the structure and function of heme proteins, as regulated by a disulfide bond. This study is thus able to guide the rational design of artificial proteins with tunable functions in the future.

Rational Design and Engineering of a Mutant Variant of Urate Oxidase as a Therapeutic Enzyme: A Molecular Dynamics Simulation Approach

2017 ◽  
Vol 13 (1) ◽  
pp. 30-38
Author(s):  
Sajjad Ahrari ◽  
Fatemeh Dabbagh ◽  
Sobhan Ahrari ◽  
Younes Ghasemi ◽  
Navid Mogharrab ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Rational Design ◽  
Dynamics Simulation ◽  
Urate Oxidase ◽  
Simulation Approach ◽  
Mutant Variant

scholarly journals Molecular dynamics simulation of sI methane hydrate under compression and tension

2020 ◽  
Vol 18 (1) ◽  
pp. 69-76
Author(s):  
Qiang Wang ◽  
Qizhong Tang ◽  
Sen Tian
Keyword(s):  
Molecular Dynamics ◽  
Methane Hydrate ◽  
Fracture Process ◽  
Md Simulation ◽  
Maximum Stress ◽  
Dynamics Simulation ◽  
Tensile Fracture ◽  
Maximum Compressive Stress ◽  
Motion State ◽  
Stress States

AbstractMolecular dynamics (MD) analysis of methane hydrate is important for the application of methane hydrate technology. This study investigated the microstructure changes of sI methane hydrate and the laws of stress–strain evolution under the condition of compression and tension by using MD simulation. This study further explored the mechanical property and stability of sI methane hydrate under different stress states. Results showed that tensile and compressive failures produced an obvious size effect under a certain condition. At low temperature and high pressure, most of the clathrate hydrate maintained a stable structure in the tensile fracture process, during which only a small amount of unstable methane broke the structure, thereby, presenting a free-motion state. The methane hydrate cracked when the system reached the maximum stress in the loading process, in which the maximum compressive stress is larger than the tensile stress under the same experimental condition. This study provides a basis for understanding the microscopic stress characteristics of methane hydrate.

Molecular Dynamics Simulation of AFM-Based Nanomachining Processes

2011 ◽  
Author(s):  
Rapeepan Promyoo ◽  
Hazim El-Mounayri ◽  
Kody Varahramyan ◽  
Ashlie Martini
Keyword(s):  
Molecular Dynamics ◽  
Friction Coefficient ◽  
Md Simulation ◽  
Computational Models ◽  
Dynamics Simulation ◽  
Radius Of Curvature ◽  
Force Microscopy ◽  
Indentation Force ◽  
Atomic Force ◽  
Development And Validation

Recently, atomic force microscopy (AFM) has been widely used for nanomachining and fabrication of micro/ nanodevices. This paper describes the development and validation of computational models for AFM-based nanomachining (nanoindentation and nanoscratching). The Molecular Dynamics (MD) technique is used to model and simulate mechanical indentation and scratching at the nanoscale in the case of gold and silicon. The simulation allows for the prediction of indentation forces and the friction force at the interface between an indenter and a substrate. The effects of tip curvature and speed on indentation force and friction coefficient are investigated. The material deformation and indentation geometry are extracted based on the final locations of atoms, which are displaced by the rigid tool. In addition to modeling, an AFM was used to conduct actual indentation at the nanoscale, and provide measurements to validate the predictions from the MD simulation. The AFM provides resolution on nanometer (lateral) and angstrom (vertical) scales. A three-sided pyramid indenter (with a radius of curvature ∼ 50 nm) is raster scanned on top of the surface and in contact with it. It can be observed from the MD simulation results that the indentation force increases as the depth of indentation increases, but decreases as the scratching speed increases. On the other hand, the friction coefficient is found to be independent of scratching speed.

The effect of amino substituents on the interactions of quinazolone derivatives with c-KIT G-quadruplex: insight from molecular dynamics simulation study for rational design of ligands

RSC Advances ◽  
2015 ◽  
Vol 5 (93) ◽  
pp. 76642-76650 ◽  
Author(s):  
Kiana Gholamjani Moghaddam ◽  
Seyed Majid Hashemianzadeh
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Rational Design ◽  
Ligand Design ◽  
Dynamics Simulation ◽  
Rational Ligand Design ◽  
G Quadruplex ◽  
Ligand Interactions ◽  
Insight Into

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

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.

scholarly journals Material Analysis and Molecular Dynamics Simulation for Cavitation Erosion and Corrosion Suppression in Water Hydraulic Valves

Materials ◽  
2020 ◽  
Vol 13 (2) ◽  
pp. 453 ◽  
Author(s):  
Masoud Kamoleka Mlela ◽  
He Xu ◽  
Feng Sun ◽  
Haihang Wang ◽  
Gabriel Donald Madenge
Keyword(s):  
Molecular Dynamics ◽  
Md Simulation ◽  
Essential Role ◽  
Corrosion Inhibitors ◽  
Cavitation Erosion ◽  
Dynamics Simulation ◽  
Preference Ranking ◽  
Water Hydraulics ◽  
The Impact ◽  
Hydraulic Valves

In the milestone of straggling to make water hydraulics more advantageous, the choice of coating polymer for water hydraulics valves plays an essential role in alleviating the impact of cavitation erosion and corrosion, and this is a critical task for designers. Fulfilling the appropriate selection, we conflicted properties that are vital for erosion and corrosion inhibitors, as well as the tribology in the sense of coefficient of friction. This article aimed to choose the best alternative polymer for coating on the selected substrate, that is, Cr2O3, Al2O3, Ti2O3. By applying PROMETHEE (Preference Ranking Organization Method for Enrichment Evaluations), the best polymer obtained with an analyzed performance attribute is Polytetrafluoroethylene (PTFE) that comes up with higher outranking (0.5932052). A Molecular Dynamics (MD) simulation was conducted to identify the stronger bonding with the regards of the better cleave plane between Polytetrafluoroethylene (PTFE) and the selected substrate. Polytetrafluoroethylene (PTFE)/Al2O3 cleaved in (010) plane was observed to be the strongest bond in terms of binding energy (3188 kJ/mol) suitable for further studies.

scholarly journals Preparation and Molecular Dynamics Simulation of RDX/MUF Nanocomposite Energetic Microspheres with Reduced Sensitivity

Processes ◽  
2019 ◽  
Vol 7 (10) ◽  
pp. 692
Author(s):  
Jia ◽  
Hu ◽  
Xu ◽  
Liu ◽  
Ma ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Binding Energy ◽  
Emulsion Polymerization ◽  
Md Simulation ◽  
Urea Formaldehyde ◽  
Urea Formaldehyde Resin ◽  
Experimental Results ◽  
Dynamics Simulation ◽  
Formaldehyde Resin ◽  
Process Conditions

In order to improve the general problem of irregular coating morphology and low mechanical strength of the coating layer in existing coating desensitization technology, nano-cyclotrimethylene trinitramine/melamine-urea-formaldehyde (RDX/MUF) composite energetic microspheres were prepared by an improved emulsion polymerization, taking the MUF as the binder and RDX as the main explosive. In order to judge whether RDX/MUF possessed good stability, the combination of differential scanning calorimetry (DSC) and molecular dynamics (MD) simulation was used to determine the level of binding binding energy between urea-formaldehyde resin binder (UF) and RDX. In addition, to investigate the optimal reaction temperature for the preparation of MUF/RDX, the binding energy between UF and RDX at different temperatures was simulated. And then the morphology and thermal properties of the as-prepared composite energetic microspheres were analyzed by scanning electron microscopy (SEM) and DSC, the impact sensitivity and friction sensitivity of the resultant samples were tested as well. Moreover, RDX/MUF with the same MUF content was prepared by physical mixing for comparative analysis. MD simulation demonstrated that UF and RDX possessed good binding ability at 298 K. The DSC method indicatec that UF and RDX had good compatibility, and the comprehensive performance of RDX after coating was not significantly deteriorated; The optimal binding temperature between UF and RDX was 60~70 °C which is consistent with the experimental results. The experimental results showed that the optimum process conditions for the preparation of RDX/MUF could be listed as follows: the temperature for preparing RDX/MUF composite energetic microspheres by the improved emulsion polymerization was 70 °C the optimal pH value of the urea-formaldehyde resin prepolymer solution was 3, and the optimal melamine-urea molar ratio was 0.4.

scholarly journals Molecular Dynamics Simulation reveals the mechanism by which the Influenza Cap-dependent Endonuclease acquires resistance against Baloxavir marboxil

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ryunosuke Yoshino ◽  
Nobuaki Yasuo ◽  
Masakazu Sekijima
Keyword(s):  
Molecular Dynamics ◽  
Aromatic Ring ◽  
Influenza A ◽  
Md Simulation ◽  
Binding Free Energy ◽  
Complex Structure ◽  
Antiviral Drug ◽  
Rna Replication ◽  
Dynamics Simulation ◽  
Dependent Endonuclease

AbstractBaloxavir marboxil (BXM), an antiviral drug for influenza virus, inhibits RNA replication by binding to RNA replication cap-dependent endonuclease (CEN) of influenza A and B viruses. Although this drug was only approved by the FDA in October 2018, drug resistant viruses have already been detected from clinical trials owing to an I38 mutation of CEN. To investigate the reduction of drug sensitivity by the I38 mutant variants, we performed a molecular dynamics (MD) simulation on the CEN-BXM complex structure to analyze variations in the mode of interaction. Our simulation results suggest that the side chain methyl group of I38 in CEN engages in a CH-pi interaction with the aromatic ring of BXM. This interaction is abolished in various I38 mutant variants. Moreover, MD simulation on various mutation models and binding free energy prediction by MM/GBSA method suggest that the I38 mutation precludes any interaction with the aromatic ring of BXA and thereby reduces BXA sensitivity.

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