Scholarlink

<p>Haloacetic acids (HAAs) are prevalent contaminants commonly detected in drinking water and aquatic environments as byproducts of water treatment using halogen-based disinfectants. Important HAA group, called HAA5, comprises five halogenated acids, monochloroacetic acid (MCA), monobromoacetic acid (MBA), dichloroacetic acid (DCA), dibromoacetic acid (DBA), and trichloroacetic acid (TCA). These compounds could be detoxified by removing the halogen atoms, catalyzed by haloacid dehalogenase. <i>Pseudomonas aeruginosa</i> ITB1 is known to produce haloacid dehalogenase (Paed-d). This study investigates the molecular interactions between the nucleophilic residues Asp7 and Asp181 of Paed-d and the HAA5 substrates through molecular docking and molecular dynamics simulation. All HAA5 ligands exhibited negative docking energies, indicating favorable binding, with TCA showing the strongest affinity. MCA and MBA preferentially bind to Asp7, whereas DCA, DBA, and TCA favor interactions with Asp181. Molecular dynamics simulation confirmed the stability of all HAA5 ligands within the Paed-d active site, with low root mean square deviation (RMSD). Root means square fluctuation (RMSF) analysis indicated that both Asp7 and Asp181 residues maintain structural stability during ligand binding. Distance analyses showed that MCA and MBA maintain close distance to Asp7, whereas DCA, DBA, and TCA remain close to Asp181. Binding free energy calculations using molecular mechanics generalized Born surface area (MMGBSA) revealed negative values for all ligands, with TCA exhibiting the lowest energy. These findings provide detailed insights into the substrate specificity and binding mechanisms of Paed-d, informing future enzyme engineering efforts for enhanced bioremediation of halogenated contaminants. </p> Graphical Abstract <p></p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

Molecular Docking and Molecular Dynamic Simulations to Study the Interaction of HAA5 with Haloacid Dehalogenase from Pseudomonas Aeruginosa ITB1

  • 期刊论文

  • 发表日期：

    2026年4月18日

查看全文
  • Wa Ode Sri Rizki,
  • Dio Jordy,
  • Intan Khoerunnisa,
  • Aprijal Ghiyas Setiawan,
  • Rizarullah Rizarullah,
  • Joko Pebrianto Trinugroho,
  • Enny Ratnaningsih

摘要

Haloacetic acids (HAAs) are prevalent contaminants commonly detected in drinking water and aquatic environments as byproducts of water treatment using halogen-based disinfectants. Important HAA group, called HAA5, comprises five halogenated acids, monochloroacetic acid (MCA), monobromoacetic acid (MBA), dichloroacetic acid (DCA), dibromoacetic acid (DBA), and trichloroacetic acid (TCA). These compounds could be detoxified by removing the halogen atoms, catalyzed by haloacid dehalogenase. Pseudomonas aeruginosa ITB1 is known to produce haloacid dehalogenase (Paed-d). This study investigates the molecular interactions between the nucleophilic residues Asp7 and Asp181 of Paed-d and the HAA5 substrates through molecular docking and molecular dynamics simulation. All HAA5 ligands exhibited negative docking energies, indicating favorable binding, with TCA showing the strongest affinity. MCA and MBA preferentially bind to Asp7, whereas DCA, DBA, and TCA favor interactions with Asp181. Molecular dynamics simulation confirmed the stability of all HAA5 ligands within the Paed-d active site, with low root mean square deviation (RMSD). Root means square fluctuation (RMSF) analysis indicated that both Asp7 and Asp181 residues maintain structural stability during ligand binding. Distance analyses showed that MCA and MBA maintain close distance to Asp7, whereas DCA, DBA, and TCA remain close to Asp181. Binding free energy calculations using molecular mechanics generalized Born surface area (MMGBSA) revealed negative values for all ligands, with TCA exhibiting the lowest energy. These findings provide detailed insights into the substrate specificity and binding mechanisms of Paed-d, informing future enzyme engineering efforts for enhanced bioremediation of halogenated contaminants.

Graphical Abstract