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

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. make italicmake italic