E-ISSN 2582-5178
 

Research Article 


Homology Modeling, Molecular dynamics simulation and docking studies of XerD in Mycobacterium tuberculosis

Budhayash Gautam, Hari Om Sharn and Satendra Singh.

Abstract
Mycobacterium tuberculosis (MTB) is a pathogenic, acid fast bacterium of family Mycobacteriacea. It is the most
common causative agent of various cases of tuberculosis (TB). Tyrosine recombinase (abbreviated as Tyr or Y) or 4-
hydroxyphenylalanine is one of the 22 amino acids that are used by cells to synthesize proteins. Homology modeling
was performed by SWISS-MODEL, HHPred, ModWeb and Protein structure prediction server respectively. And 3D
structures of modelled structures were visualized using the Rasmol tool. The structure were evaluated by Structure
Analysis and Verification Servers (SAVES), uses PROCHECK, WHAT_IF, ERRAT, VERIFY 3D, and PROVE.
The best model of Tyrosine recombinase was predicted by Protein structure prediction server. The energy
minimization of the modelled structure of Tyrosine recombinase was done to improve the quality of the model using
SPDBV tool and further evaluated by SAVES. The molecular dynamic simulation (MDS) study with GROMACS
program used to check the stability of predicted 3D structure of Tyrosine recombinase. After doing molecular
dynamic simulation it was found that the modelled structure was stable by graph. For avoiding unnecessary
distribution of the protein, parameters set as 100 pico second time scale and 50000 steps. MDS results have shown
the considerable stability to the modelled structure of Tyrosine recombinase. Docking of 3D structure was carried out
by Patch dock.reaction) or DNA sequencing. The purity of DNA constitutes an essential step before applying
molecular techniques. Although there exist a variety of protocols (1,2,3) but the current protocol is a modification of
existing phenol chloroform method to gives surety of a ratio of A260/A280 more than 1.9 compared to earlier
protocols.

Key words: DNA, Isolation, Tissue, OD, Purity


 
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Pubmed Style

Gautam B, Singh HOSaS. Homology Modeling, Molecular dynamics simulation and docking studies of XerD in Mycobacterium tuberculosis. IJLSAS. 2019; 1(1): 11-18.


Web Style

Gautam B, Singh HOSaS. Homology Modeling, Molecular dynamics simulation and docking studies of XerD in Mycobacterium tuberculosis. https://www.ijlsas.com/?mno=302644882 [Access: January 14, 2023].


AMA (American Medical Association) Style

Gautam B, Singh HOSaS. Homology Modeling, Molecular dynamics simulation and docking studies of XerD in Mycobacterium tuberculosis. IJLSAS. 2019; 1(1): 11-18.



Vancouver/ICMJE Style

Gautam B, Singh HOSaS. Homology Modeling, Molecular dynamics simulation and docking studies of XerD in Mycobacterium tuberculosis. IJLSAS. (2019), [cited January 14, 2023]; 1(1): 11-18.



Harvard Style

Gautam, B. & Singh, H. O. S. a. S. (2019) Homology Modeling, Molecular dynamics simulation and docking studies of XerD in Mycobacterium tuberculosis. IJLSAS, 1 (1), 11-18.



Turabian Style

Gautam, Budhayash, and Hari Om Sharn and Satendra Singh. 2019. Homology Modeling, Molecular dynamics simulation and docking studies of XerD in Mycobacterium tuberculosis. International Journal Of Life Sciences and Applied Sciences, 1 (1), 11-18.



Chicago Style

Gautam, Budhayash, and Hari Om Sharn and Satendra Singh. "Homology Modeling, Molecular dynamics simulation and docking studies of XerD in Mycobacterium tuberculosis." International Journal Of Life Sciences and Applied Sciences 1 (2019), 11-18.



MLA (The Modern Language Association) Style

Gautam, Budhayash, and Hari Om Sharn and Satendra Singh. "Homology Modeling, Molecular dynamics simulation and docking studies of XerD in Mycobacterium tuberculosis." International Journal Of Life Sciences and Applied Sciences 1.1 (2019), 11-18. Print.



APA (American Psychological Association) Style

Gautam, B. & Singh, H. O. S. a. S. (2019) Homology Modeling, Molecular dynamics simulation and docking studies of XerD in Mycobacterium tuberculosis. International Journal Of Life Sciences and Applied Sciences, 1 (1), 11-18.





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