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In Silico Modification of Thermostable Lipase From Geobacillus sp. Strain T1

M.B.A. Rahman, C.K. Khan, M. Basri, A.B. Salleh and R.N.Z.A. Rahman
Universiti Putra Malaysia, MY

Keywords:
thermostable, lipase, modified protein, molecular docking

Abstract:
Protein cavities provide binding sites for biomolecular interaction with chemical ligands and metals. Interaction specificities and physical properties characterization of protein cavities as binding sites is the initial platform to design a semisynthetic metalloenzyme for the usage as industrial biocatalyst. Lab grown thermostable lipase from Geobacillus sp. Strain T1 was selected as the backbone for the modification with putative chemical ligands using latest molecular modeling tools like AutoDock 3.05, DS Modeling 1.1 and Insight II softwares. A set of 65 pockets were detected, however only nine pockets showed the most favorable binding sites for protein-ligand interaction. SER113, ASP317 and HIS358 are the catalytic triads for thermostable lipase and located in pocket 57 and 59, respectively. Out of ten chemical ligands (based on bidentate and multi-functional groups) screened from the PDB (Protein Database Bank), phenylalanine generated the lowest final docked energy of -6.71 Kcal/mol at pocket 62. Mean while 1,3-propandiol generated lowest final docked energy of -4.69 Kcal/mol at pocket 60.

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