earticle

영어

Many marine bacteria have been found to produce a large amount of alginate lyases and many genes encoding alginate lyases from marine bacteria have been cloned and sequenced. Alginate lyase mutants with high activity against alginate are highly desired for use in the food, pharmaceutical, and medical industries. Hence, we have amplified the alyVI gene from the marine bacterium Vibrio sp. QY101 using plasmid pGEX-4T-1 for mutagenesis. We have also performed a computational study of alginate binding with wild-type and mutants of alyVI. Our goal is to increase the catalytic efficiency of alyVI toward alginate by site-directed mutagenesis based on computational technology. The combined molecular docking, molecular dynamics simulations, binding free energy calculations, and binding energy decompositions provide valuable insights into the detailed binding of Aliginate Lyase AlyVI with its substrate. Subsequently the computational simulations followed by site directed mutagenesis and AlyVI activity assays, have led to a detailed understanding of Aliginate Lyase AlyVI interacting with its substrate. Results obtained from the binding energy decomposition reveal the contribution of each residue at the protein-ligand interaction interface to the binding affinity. The data from wet experimental tests are consistent with the computational predictions.