HOMOLOGY MODELLING AND EVALUATION OF ENTEROCOCCUS GELATINASE (COCCOLYSIN)

Anna Kurian, Muhsina Mahamood, Sweety S Kollannur and Leyon Varghese*

A better understanding of three dimensional structures of proteins is necessary to elucidate their biochemical function and is very crucial in several fields such as drug discovery. Homology modelling is a reliable in silico approach for predicting three dimensional structures of proteins based on sequence similarity. Here we present a newly predicted 3D model for exometalloprotease gelatinase (cocccolyin) of Enterococcus faecalis keeping the Gentlyase protein of Paenibacillus polymyxa as template. The quality parameters and 2D structure analysis of the predicted model was validated using Swiss-Model and Procheck servers and was found to be acceptable. Gromacs steepest descent algorithm was used to do the potential energy minimisation of the predicted model. We obtained a QMEAN score of -1.9, GMQE score of 0.32. The Z score valueof our predicted model lies between 0 and 1. The results showed that the newly predicted model is more reliable and close to native conditions. Molecular docking studies were then performed using the predicted models to confirm its integrity to use for further application.