Effects of Normal and Aberrant Glycosylation on the Stability of α1-Anti Trypsin Through Molecular Dynamic Simulation

2021 ◽  
Vol 15 (10) ◽  
pp. 3066-3069
Author(s):  
Mujeeb Alam Khan ◽  
Ehtesham . ◽  
Muhammad Shoaib ◽  
Roshan Ali ◽  
Muhammad Idrees
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Dynamics Simulation ◽  
Mean Square ◽  
Glycated Protein ◽  
Alpha 1 Antitrypsin ◽  
The Stability

The Alpha-1 antitrypsin belonging to serpin family is a protease inhibitor, the level of which rises by a factor of ten during inflammation Purpose: To investigate the stability of normal and aberrantly glycosylated α1-antitrypsin through molecular dynamics simulation Study Design: Experimental study Methodology: Current project was conducted in the department of Biochemistry at Institute of Basic Medical Sciences Khyber Medical University, Peshawar. A1AT FASTA sequence was retrieved from UniProt database (UniProt ID: P01009). Post-Translational Modifications (PTM) regions were identified from the same database. GLYCONNECT database was used to understand N-linked glycation with the asparagine residues found at position 70, 107, and 271 amino acid residue regions Statistical analysis: Different bioinformatics analyses such that Root Mean Square Deviation, Radius of gyration, Root Mean Square fluctuation, Hydrogen-bonding, Secondary Structure Determination, and Principal Component Analysis were executed for 100 ns molecular dynamics simulation run Results: RMSd, RMSf, and Rgyr significantly differ between the native type and cancer isoform. More H-bonding and strong protein stability and folding were seen in the native type. PCA analysis further confirms native type compact motion in the parallel direction during MD simulation Conclusion: It was concluded that glycated protein appears to have high structural stability than its aberrant glycated protein. However, it will be utilized for the prompt production of the anti-cancer drugs to effectively treating cancer disease Key Words: Alpha-1 Antitrypsin, Aberrant Glycosylation and Molecular Dynamic Simulation.

scholarly journals Surfactants Enhanced Heavy Oil–Solid Separation from Carbonate Asphalt Rocks-Experiment and Molecular Dynamic Simulation

Nanomaterials ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1835
Author(s):  
Jinjian Hou ◽  
Jinze Du ◽  
Hong Sui ◽  
Lingyu Sun
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Energy Balance ◽  
Aromatic Hydrocarbon ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Saturated Hydrocarbon ◽  
Dynamics Simulation ◽  
Simulation Results

In this study, surfactants were used to enhance heavy oil–solid separation, and a detailed mechanism was explored by SARA (saturates, aromatics, resins, asphaltenes) analysis, element analysis, AFM measurement, and molecular dynamic simulation. Surfactants could effectively decrease oil/solid interaction force and then oil–solid separation would be enhanced. The oil–solid interactive force was in relation to surfactants concentration, pH value, asphaltene content, and salinity. The molecular dynamics simulation results show that the dissociation of saturated hydrocarbon, aromatic hydrocarbon, resin, and asphaltene (SARA) on carbonate minerals is gradually weakened for all surfactants. In the process of molecular dynamics simulation of surfactant stripping SARA, firstly, the surfactant molecules adsorb on the surface of SARA molecules. After that, the surfactant peels SARA molecules off the surface of calcite under the influence of molecular thermal motion. In this process, surfactant molecules will not be directly adsorbed on the surface of trace minerals. The results of energy/temperature balance indicated that saturates, aromatics and resins could remain stable when the molecular dynamics simulation time reached 2000 ps with the phenomenon that saturates, aromatics could liberate from minerals totally within 2000 ps. The molecular dynamics simulation of asphaltenes will not liberate from calcite surface within 6000 ps, meanwhile, they could not reach the energy balance/energy balance within 6000 ps. The functional groups of surfactant molecules would have interactions with the SARA functional group, resulting in different dissociation effects of SARA. The results of molecular dynamics simulation are consistent with the experiment results. The separation effect of saturated hydrocarbon, aromatic hydrocarbon, resin, and asphaltene in five kinds of surfactants were different. The molecular dynamic simulation results were in accordance with the SARA analysis.

Docking and Molecular Dynamic Simulation of Temozolomide with Carbonic Anhydrase XIII

2020 ◽  
Vol 5 (4) ◽  
pp. 332-339
Author(s):  
R. Meenashi ◽  
K. Selvaraju ◽  
P. Jayalakshmi ◽  
P.V. Nidhin ◽  
A. David Stephen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Carbonic Anhydrase ◽  
Dynamic Simulation ◽  
Alkylating Agent ◽  
Docking Studies ◽  
Dynamics Simulation ◽  
Cancer Treatments ◽  
The Stability ◽  
Protein Environment

The effect of inhibition of temozolomide, an alkylating agent widely used in cancer treatments, with carbonic anhydrase XIII protein was investigated using docking studies. The stability of temozolomide in the protein environment was assessed and analyzed by molecular dynamics simulation. The topological and charge density variations of temozolomide were studied in detail to perceive the primary insight of the pharmaceutical actions.

scholarly journals Effects of the Temperature and the pH on the Main Protease of SARS-CoV-2: A Molecular Dynamics Simulation Study

2021 ◽  
Vol 12 (6) ◽  
pp. 7239-7248
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Root Mean Square ◽  
Dynamics Simulation ◽  
Effect Of Temperature ◽  
Water Molecules ◽  
Mean Square ◽  
Main Protease ◽  
Decreasing Ph ◽  
Increasing Temperature

The novel coronavirus, recognized as COVID-19, is the cause of an infection outbreak in December 2019. The effect of temperature and pH changes on the main protease of SARS-CoV-2 were investigated using all-atom molecular dynamics simulation. The obtained results from the root mean square deviation (RMSD) and root mean square fluctuations (RMSF) analyses showed that at a constant temperature of 25℃ and pH=5, the conformational change of the main protease is more significant than that of pH=6 and 7. Also, by increasing temperature from 25℃ to 55℃ at constant pH=7, a remarkable change in protein structure was observed. The radial probability of water molecules around the main protease was decreased by increasing temperature and decreasing pH. The weakening of the binding energy between the main protease and water molecules due to the increasing temperature and decreasing pH has reduced the number of hydrogen bonds between the main protease and water molecules. Finding conditions that alter the conformation of the main protease could be fundamental because this change could affect the virus’s functionality and its ability to impose illness.

Study on Nanolithography Process of Polycrystalline Copper Using Molecular Dynamic Simulation

2007 ◽  
Vol 340-341 ◽  
pp. 961-966
Author(s):  
Chan Il Kim ◽  
Young Suk Kim ◽  
Sang Il Hyun ◽  
Seung Han Yang ◽  
Jun Young Park ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Grain Boundary ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Diamond Like Carbon ◽  
Polycrystalline Copper ◽  
Berkovich Indenter ◽  
Contact Surfaces ◽  
Dynamics Simulations

Molecular dynamics simulations are performed to verify the effect of grain boundary on nanolithography process. The model with about two hundred thousand copper (Cu) atoms is composed of two different crystal orientations of which contact surfaces are (101) and (001) planes. The grain boundary is located on the center of model and has 45 degreeangle in xz-plane. The tool is made of diamond-like-carbon with the shape of Berkovich indenter. As the tool is indented and plowed on the surface, dislocations are generated. Moreover, during the plowing process, the steps as well as the typical pile-ups are formed in front of the tool. These defects propagate into the surface of the substrate. As the tool approaches to the grain boundary, the defects are seen to be accumulated near the grain boundary. The shape of the grain boundary is also significantly deformed after the tool passes it. We observed the forces exerted on the tool by the contact with substrate, so that the friction coefficients can be obtained to address the effect of the grain boundary on the friction characteristics.

scholarly journals Molecular Dynamics Simulation of Barnase: Contribution of Noncovalent Intramolecular Interaction to Thermostability

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
Zhiguo Chen ◽  
Yi Fu ◽  
Wenbo Xu ◽  
Ming Li
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Molecular Dynamics Simulation ◽  
Root Mean Square ◽  
Clinical Medicine ◽  
Intramolecular Interaction ◽  
Salt Bridge ◽  
Dynamics Simulation ◽  
Mean Square ◽  
Thermal Stability Of

Bacillus amyloliquefaciensribonuclease Barnase (RNase Ba) is a 12 kD (kilodalton) small extracellular ribonuclease. It has broad application prospects in agriculture, clinical medicine, pharmaceutical, and so forth. In this work, the thermal stability of Barnase has been studied using molecular dynamics simulation at different temperatures. The present study focuses on the contribution of noncovalent intramolecular interaction to protein stability and how they affect the thermal stability of the enzyme. Profiles of root mean square deviation and root mean square fluctuation identify thermostable and thermosensitive regions of Barnase. Analyses of trajectories in terms of secondary structure content, intramolecular hydrogen bonds and salt bridge interactions indicate distinct differences in different temperature simulations. In the simulations, Four three-member salt bridge networks (Asp8-Arg110-Asp12, Arg83-Asp75-Arg87, Lys66-Asp93-Arg69, and Asp54-Lys27-Glu73) have been identified as critical salt bridges for thermostability which are maintained stably at higher temperature enhancing stability of three hydrophobic cores. The study may help enlighten our knowledge of protein structural properties, noncovalent interactions which can stabilize secondary peptide structures or promote folding, and also help understand their actions better. Such an understanding is required for designing efficient enzymes with characteristics for particular applications at desired working temperatures.

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