INTERACTION STUDY OF HALOACID DEHALOGENASE FROM BACILLUS CEREUS INDB1 ON VARIATION OF 2-(MONO-, DI-, TRI-)-HALOACETIC ACID SUBSTRATES

• Main Author: Nurulita Aridayani, Elsa
• Format: Final Project
• Language: Indonesia
• Subjects: Kimia
• Online Access: https://digilib.itb.ac.id/gdl/view/57296
• Institution: Institut Teknologi Bandung

Organohalides are organic compounds that contain at least one covalent bond between carbon and halides. Organohalides are known as pollutants because they are toxic and difficult to be degraded. Some bacteria are known to produce haloacid dehalogenase, an enzyme that catalyzes the breakdown of carbon and halides on haloacid substrates. Based on the stereoselectivity and the mechanism of dehalogenation, these enzymes are classified into 2 different groups, namely GroupI and GroupII. The gene encoding the haloacid dehalogenase from Bacillus cereus IndB1, named as bcfd1, has been successfully cloned, sequenced, and expressed in E. coli BL21 (DE3). In this research, a computational approach was conducted to study the effect of haloacid substrate with various halide substituents (F, Cl, Br, I) and halide number (mono, di, tri) on its interaction with Bcfd1 through molecular docking. The first step is to determine the best tertiary structure model and classify the Bcfd1 type. Modeling using threading (I-Tasser), fragment assembly (trRosetta from Yang Lab and Baker Lab), and ab initio (Raptor-X, C-QUARK, and Robetta) provides six Bcfd1 tertiary structure models. Stereochemistry and geometry evaluation using Mol Probity resulted two best models. Evaluation for type determination performed by sequence identities, comparison of secondary structure, secondary structure analysis, superimpose analysis (similarity, RMSD, and % identity structure), and active site analysis indicated that Bcfd1 is more similar to HAD Group II. The best model of Bcfd1 was obtained by the trRosetta from Baker Lab. Molecular docking showed that hydrogen interactions occured at Met1 and Asp2 residues, while hydrophobic interactions occured with Ser34, Gly35, and Lys204. Variation of halogen atoms in the substrates, monohaloacetic acid, dihaloacetic acid, and trihaloacetic acid, did not show significant interaction differences, except for iodo atoms which showed different orientations. Variations of halogen atom number resulted in significant interaction changes, particularly in trihaloacetic acid (except for trichloroacetate), where hydrogen interactions between Asp2 and C-carbonyl were replaced by Gly35. From the docking scores and substrate interactions analysis with Bcfd1, it could be ascertained that all 12 substrates can finely bind on Bcfd1 binding site, but proves by wet experiments are still needed to ensure that dehalogenation were occured on all of these substrates.