Homology modeling and molecular dynamics simulation of a novel beta-galactosidase antarctic psychrophilic bacterium planococcus antarcticus dsm 14505

• Main Authors: Omar, Mohd. Shahir Shamsir, Ibrahim, Ammar, Mohd. Noor, Mohd. Redhuan, Mahmoud, Azzam Aladdin, Ramli, Muhammad Faidhi, Bouna, Ahmed
• Format: Article
• Published: 2015
• Subjects: Q Science (General)
• Online Access: http://eprints.utm.my/id/eprint/60263/

ß-galactosidase is an enzyme that catalyzes both hydrolytic cleavage of ß (1–4) linkage of lactose to glucose and galactose and transglycosylation reactions. The present study aims to model and validate the 3D structure of a novel cold-active ß-galactosidase from Planococcus antarcticus 14505. The 3D structure was predicted by itasser software. Model validation was performed using PROCHECK to generate the Ramachandran plot, which indicated that 86.6% of residues is in favorable regions that indicate the model is acceptable. Molecular dynamics simulation of the model protein was performed in water for 10 nanoseconds in which 31 Na+ was added to neutralize the negative charge and achieve energy minimization. The energy value and RMSD fluctuation of carbon alpha backbone of the model were computed and confirmed the stability of the model protein.