همایش ملی بیوانفورماتیک ایران

صفحه اصلی / 4th international edition and 13th Iranian Conference on Bioinformatics

Bioinformatics analysis of the binding of various ligands to the acylhemoserine lactonase derived from Bacillus.

نویسندگان :

Nasim Forghani¹ Matia sadat Borhani² Zoheir Heshmatipour³ Mahmoud Salehi⁴ Mohadeseh Piri⁵

1- دانشگاه گنبد کاووس 2- دانشگاه گنبد کاووس 3- دانشگاه آزاد اسلامی واحد تنکابن 4- دانشگاه گنبد کاووس 5- دانشگاه مازندران

کلمات کلیدی :

Bacillus،aiiA gene،molecular docking،homology modeling

چکیده :

Quorum sensing is a fundamental communication system in bacteria, regulating key processes including biofilm formation, virulence factor production, and antibiotic resistance (Paluch and Rewak, 2020). This study aimed to investigate the genetic diversity of the aiiA gene in Bacillus species obtained from soils and assess whether this diversity affects the enzyme's binding affinity to different substrates and instability index. 130 Bacillus isolates were collected from various cities in Iran. PCR screening revealed that eight isolates contained the aiiA gene (Noor and Almasri, 2022). Sequence alignment with reference sequences from the NCBI database and motif analysis using the MEME Suite tool confirmed the presence of conserved catalytic motifs, including HXHXDH, and critical active site residues (Y194-D191-H169-H235). (Liu and Momb, 2008). The preservation of these residues emphasizes their structural and functional importance. Despite minor changes observed in non-catalytic regions, the integrity of the active site was not disrupted. Estimation of the instability index using the ProtParam tool showed that genetic diversity in the aiiA gene does not significantly affect enzyme stability, with the index ranging between 46.35 and 51.88. Molecular docking studies were performed to evaluate the potential impact of the observed genetic diversity on enzyme-substrate interactions. Four isolates (AK3A, ELM21B, H8A, and NB3C) with the most distinct sequences were selected for further analysis. Homology models of these isolates were generated using the Swiss-Model platform, employing the 3DHB structure as a template. Docking simulations using Autodock Vina were carried out with N-acyl homoserine lactones (AHLs) ligands of varying chain lengths, including C4-HSL, C6-HSL, C8-HSL, C10-HSL, and C12-HSL, to assess binding affinity and enzyme-ligand interactions. The docking results revealed no significant changes in the binding free energy (ΔG) for shorter chain AHLs such as C4-HSL, where all isolates, including the reference 3DHB, maintained identical ΔG values (-5.8 kcal/mol). For longer chain ligands like C6-HSL, C8-HSL, and C10-HSL, minor differences in ΔG values were observed. For instance, with C10-HSL, the ΔG values ranged from -6.1 to -6.4 kcal/mol, showing a slight deviation from the reference value of -7.0 kcal/mol. Importantly, these differences did not disrupt the enzyme's substrate binding efficiency or functionality. Furthermore, the results demonstrated that the ligand chain length did not significantly affect the enzyme's binding affinity. Results obtained emphasize that despite genetic variation in the aiiA gene in Bacillus isolates, catalytic motifs, and active site residues remain conserved, ensuring the robustness of the enzyme’s quorum-quenching activity. Minor amino acid variations outside the active site had no functional impact on enzyme activity, consistent with prior studies (Noor and Almasri, 2022). This study investigates aiiA gene diversity in Bacillus soil isolates, marking the first analysis on these samples, and confirms that variations outside the active site do not affect the enzyme’s binding affinity. These findings contribute valuable insights into the structural and functional stability of the lactonase in Bacillus isolates and its potential applications in disrupting bacterial quorum sensing for controlling biofilm formation and bacterial infections.