Binding Mode Analysis of Bacillus subtilis Obg with Ribosomal Protein L13 through Computational Docking Study

Lee, Yu-No; Bang, Woo-Young; Kim, Song-Mi; Lazar, Prettina; Bahk, Jeong-Dong; Lee, Keun-Woo

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저자정보: Lee, Yu-No (Division of Applied Life Science [BK21 Program], Environmental Biotechnology National Core Research Center [EB-NCRC], Plant Molecular Biology and Biotechnology Research Center [PMBBRC], Gye) Bang, Woo-Young (Division of Applied Life Science [BK21 Program], Environmental Biotechnology National Core Research Center [EB-NCRC], Plant Molecular Biology and Biotechnology Research Center [PMBBRC]) Kim, Song-Mi (Division of Applied Life Science [BK21 Program], Environmental Biotechnology National Core Research Center [EB-NCRC], Plant Molecular Biology and Biotechnology Research Center [PMBBRC], G) Lazar, Prettina (Division of Applied Life Science [BK21 Program], Environmental Biotechnology National Core Research Center [EB-NCRC], Plant Molecular Biology and Biotechnology Research Center [PMBBRC]) Bahk, Jeong-Dong (Division of Applied Life Science [BK21 Program], Environmental Biotechnology National Core Research) Lee, Keun-Woo

저널정보: 한국생물정보시스템생물학회 Interdisciplinary Bio Central Interdisciplinary Bio Central 제1권 제1호

발행연도: 2009.1

수록면: 31 - 36 (6page)

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Introduction: GTPases known as translation factor play a vital role as ribosomal subunit assembly chaperone. The bacterial Obg proteins ($Spo{\underline{0B}}$-associated ${\underline{G}}TP$-binding protein) belong to the subfamily of P-loop GTPase proteins and now it is considered as one of the new target for antibacterial drug. The majority of bacterial Obgs have been commonly found to be associated with ribosome, implying that these proteins may play a fundamental role in ribosome assembly or maturation. In addition, one of the experimental evidences suggested that Bacillus subtilis Obg (BsObg) protein binds to the L13 ribosomal protein (BsL13) which is known to be one of the early assembly proteins of the 50S ribosomal subunit in Escherichia coli. In order to investigate binding mode between the BsObg and the BsL13, protein-protein docking simulation was carried out after generating 3D structure of the BsL13 structure using homology modeling method. Materials and Methods: Homology model structure of BsL13 was generated using the EcL13 crystal structure as a template. Protein-protein docking of BsObg protein with ribosomal protein BsL13 was performed by DOT, a macro-molecular docking software, in order to predict a reasonable binding mode. The solvated energy minimization calculation of the docked conformation was carried out to refine the structure. Results and Discussion: The possible binding conformation of BsL13 along with activated Obg fold in BsObg was predicted by computational docking study. The final structure is obtained from the solvated energy minimization. From the analysis, three important H-bond interactions between the Obg fold and the L13 were detected: Obg:Tyr27-L13:Glu32, Obg:Asn76-L13:Glu139, and Obg:Ala136-L13:Glu142. The interaction between the BsObg and BsL13 structures were also analyzed by electrostatic potential calculations to examine the interface surfaces. From the results, the key residues for hydrogen bonding and hydrophobic interaction between the two proteins were predicted. Conclusion and Prospects: In this study, we have focused on the binding mode of the BsObg protein with the ribosomal BsL13 protein. The interaction between the activated Obg and target protein was investigated with protein-protein docking calculations. The binding pattern can be further used as a base for structure-based drug design to find a novel antibacterial drug.

#Computational docking #Protein-protein docking calculation #DOT #Bacillus subtilis Obg #Ribosomal protein L13

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