Pemrosesan Ulang Struktur Transporter Ekstrusi Senyawa Beracun dan Multi-Obat (ESBM) Halalkalibacterium halodurans C-125

Abstract

Transporter ekstrusi senyawa beracun dan multi-obat (ESBM) diketahui ikut berkontribusi dalam munculnya resistensi antibiotik pada bakteri Halalkalibacterium halodurans. Struktur transporter pada pangkalan data perlu mengalami perbaikan untuk menunjang penelitian resistensi antibiotik akibat ESBM. Penelitian ini bertujuan meningkatkan kualitas struktur tiga dimensi protein ESBM H. halodurans C-125 (PDB Id 5c6o) menggunakan teknik molecular replacement dengan basis struktur hasil pemodelan AlphaFold2 yang diikuti proses refinement. Struktur hasil pemodelan AlphaFold2 menunjukkan tingkat kepercayaan yang tinggi, ditunjukan dari nilai plDDT 89,7 dan pTM 0,874. Struktur AlphaFold2 digunakan sebagai basis molecular replacement menghasilkan nilai top LLG sebesar 407,61 dan top TFZ sebesar 18. Hasil refinement menunjukkan kualitas yang cukup buruk, beberapa parameter mengalami penurunan dan adanya tanda overfitting dari selisih Rworks dan Rfree. Meskipun demikian, beberapa parameter kualitas mengalami peningkatan, sehingga penelitian cukup berpotensi untuk dapat dilanjutkan melalui penggunaan fungsi lanjutan, seperti RefMac CCP4.

Multidrug and toxic compound extrusion (MATE) transporter known to have played a part in the emergence of antibiotic resistance from Halalkalibacterium halodurans bacteria. Research related to antibiotic resistance due to MATE can be supported by improving the structure of transporters in the database. This study aimed to improve the quality of the three-dimensional structure of the MATE protein from H. halodurans C-125 (PDB Id 5c6o) using molecular replacement techniques based on the AlphaFold2 modeling structure followed by a refinement process. The AlphaFold2 modeling structure showed high level of confidence, indicated by a value of 89.7 for plDDT and 0.874 for pTM. The AlphaFold2 structure used as the basis for molecular replacement produced top LLG value of 407.61 and a top TFZ of 18. The refinement results showed poor qualities, some parameters decreased and there were signs of overfitting from the difference between Rworks and Rfree. However, there were several quality parameters that increased, so the research has the potential to be continued through the use of advanced functions, such as RefMac CCP4.