September 30, 2024Current Issue Vol. 39 No. 3

September, 2024 | Volume 39, No. 3

• Review Paper 2024-09-30

  

  Recent Research in Plastic Biodegradation Using Microorganisms or Enzymes

  Yeon-Hwa Kim, Ye-Rim Shin, Jeong-Ann Park et al.

  https://doi.org/10.7841/ksbbj.2024.39.3.69

  Abstract : Plastic is one of the fastest-growing consumer goods in modern society, and its usage continues to increase globally. Plastics with high hydrophobicity, such as polyethylene and polypropylene, or those with simple carbon-carbon (C-C) structures like polystyrene, are particularly difficult to degrade. Additionally, the biodegradation mechanisms of plastics such as polyvinyl chloride are not well understood. The widespread use of plastics poses significant environmental and waste management challenges. As an alternative, recent research has focused on the enzymatic degradation of plastics through microorganisms. This study suggests the potential for sustainability in the plastic industry and environmental protection.

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• Research Paper 2024-09-30

  

  Mutation of Orthogonal Aminoacyl-tRNA Synthetase for Incorporating para-azido-L-phenylalanine and Its Structural Modeling

  Euncheol Jung, Yu-bin Lim, and Jong-il Choi

  https://doi.org/10.7841/ksbbj.2024.39.3.78

  Abstract : In this study, we investigated the effect of mutations in orthogonal aminoacyl-tRNA synthetase (aaRS) on the incorporation efficiency of para-azido-L-phenylalanine (AzF), and performed molecular modeling. We targeted three amino acid positions (178, 248, and 256) in the aaRS cloned in the previously reported pEVOL-pAzF-C1-K776 and generated aaRS mutants (M178T, F248L, K256E) using site-directed mutagenesis. Subsequently, we transformed Escherichia coli DH10B (pSEVA631pt-sfGFP204amb) with each of the pEVOL-pAzF-C1 plasmids containing the mutant aaRS and compared the specific fluorescence intensity upon AzF addition. With AzF addition, M178T and F248L mutants exhibited 1.36- and 1.19-fold increases, respectively, in specific fluorescence intensity compared to the control, while K256E mutant showed a 0.46-fold decrease. The selectivity for AzF was 1.987 for M178T, 1.931 for F248L, and 1.619 for K256E, all lower than the control. To interpret these experimental results, modeling and docking using Swiss-Model were performed. The results obtained in this study could be utilized for the development and interpretation of various aaRS for incorporating non-canonical amino acids into proteins.

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• Research Paper 2024-09-30

  

  Identification of Binding between m396 scFv and RBD of SARS-CoV-2 Beta Variant and Molecular Docking Study on Their Binding Mode

  Inji Jung, Dinesh Kumar Sriramulu, Sang Taek Jung et al.

  https://doi.org/10.7841/ksbbj.2024.39.3.83

  Abstract : Development of antibodies neutralizing SARS-CoV-2 variants is very crucial due to their therapeutic potentials and structural study on their binding mode plays an important role in the design of therapeutic antibodies. m396 is an antibody which was originally developed for SARS-CoV-1. The antibody is known to bind to the receptor binding domain (RBD) of SARS-CoV-1 but not to show binding affinity against RBD of SARS-CoV-2. In this study, we demonstrated that m396 scFv exhibited binding affinity to the RBD of SARS-CoV-2 Beta variant. To understand the binding mode of m396 scFv and RBD of SARS-CoV-2 Beta variant, HADDOCK protein-protein docking condition was optimized and employed to model the complex structure of two proteins. Finally, the molecular interactions in the binding interface of the modeled complex were analyzed. This study suggests the possibility that m396 can be an efficient template antibody for SARS-CoV-2 variants. In addition, the optimized docking condition for the HADDOCK docking is expected to be utilized in the various computational studies on the binding of m396 and its variants against the RBDs of SARS-CoV variants.

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• Research Paper 2024-09-30

  

  Utilization of Kifunensine and Sorbitol for Enhanced Production of Glyco-engineered Acid α-Glucosidase in Transgenic Rice Cell Cultures

  Joon-Young Choi, Su-Hwan Cheon, Guewha Lee et al.

  https://doi.org/10.7841/ksbbj.2024.39.3.90

  Abstract : Production of recombinant acid α-glucosidase (GAA) with high-mannose glycan and least plant-specific residues in transgenic rice cell cultures is necessary for effective treatment of Pompe disease, a lysosomal storage disorder, using enzyme replacement therapy. Kifunensine was used as a regulator of N-glycosylation with plant expression system and it showed negative effect on the expression level of GAA. In order to increase protein expression with the presence of kifunensine, sorbitol was used as an alternative carbon source under sugar-depleted environment to enhance both cell viability and GAA production. Concentrations of kifunensine and sorbitol were optimized and the combined use of 2.5 mM kifunensine and 40 mM sorbitol was found to be the best for cell growth, viability and GAA expression. The content of high-mannose type glycan was 3.8% in control culture and 62% in 2.5 mM kifunensine alone. It could be improved up to 77.9% by the combined supplementation of 40 mM sorbitol. Therefore, it was clear that the combined use of kifunensine and sorbitol can improve GAA expression as well as the content of high-mannose type glycan.

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