• Interdisciplinary Bio Central
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• v.1 no.1
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• pp.3.1-3.6
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• 2009

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.

• Clean Technology
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• v.28 no.1
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• pp.24-31
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• 2022

Petroleum-based plastics are used for various purposes and pose a significant threat to the earth's environment and ecosystem. Many efforts have been taken globally in different areas to find alternatives. As part of these efforts, this study manufactured alginate-based polyvinyl alcohol (PVA) blended films by casting from an aqueous solution prepared by mixing 10 wt% petroleum-based PVA with biodegradable, marine biomass-derived alginate. Glutaraldehyde was used as a cross-linking agent, and cardanol, an alkyl phenol-based bio-oil extracted from cashew nut shell, was added in the range of 0.1 to 2.0 wt% to grant antibacterial activity to the films. FTIR and TGA were performed to characterize the manufactured blended films, and the tensile strength, degree of swelling, and antibacterial activity were measured. Results obtained from the FTIR, TGA, and tensile strength test showed that alginate, the main component, was well distributed in the PVA by forming a matrix phase. The brittleness of alginate, a known weakness as a single component, and the low thermal durability of PVA were improved by cross-linking and hydrogen bonding of the functional groups between alginate and PVA. Addition of cardanol to the alginate-based PVA blend significantly improved the antibacterial activity against S. aureus and E. coli. The antibacterial performance was excellent with a death rate of 98% or higher for S. aureus and about 70% for E. coli at a contact time of 60 minutes. The optimal antibacterial activity of the alginate-PVA blended films was found with a cardanol content range between 0.1 to 0.5 wt%. These results show that cardanol-containing alginate-PVA blended films are suitable for use as various antibacterial materials, including as food packaging.