Structural characterization of iterative polyketide synthases

• Main Author: Tan, Jackie Yen
• Other Authors: Gao Yonggui
• Format: Thesis-Doctor of Philosophy
• Language: English
• Published: Nanyang Technological University 2021
• Subjects: Science::Biological sciences::Molecular biology
• Online Access: https://hdl.handle.net/10356/145736
• Institution: Nanyang Technological University

Polyketide synthases are large multi-domain proteins found in bacterial and fungal species that synthesize structurally complex compounds called polyketides. Polyketides have strong antibacterial, antitumoral, and anticancer effect, and have therapeutic potential. Iterative polyketide synthases (iPKS) are one of the types of polyketide synthase and uses its domain iteratively to synthesize a polyketide chain product. While the individual domains in iPKSs are well studied, the full-length structures of iPKSs remain largely uncharacterized. As such, structural characterization of iPKS for the purpose of rational engineering and fine-tuning polyketide products remains an ongoing effort. The results in this thesis discuss the use of in silico approaches to characterize iPKS. Firstly, the relationship between the physicochemical properties of iPKS ketosynthase domain and its product length was investigated, using multiple linear regression and machine learning. Predictive modelling of iPKS product was achieved by using catalytic site area and volume, and hydropathy scores as features. Secondly, biochemical characterization of partially-reducing iPKS NcsB was performed. Negative stain electron microscopy (EM) was used to elucidate low-resolution structures of monomeric and dimeric NcsB. The proposed domain arrangement in the low-resolution model of NcsB provides an insight into iPKS conformation and architecture. Lastly, biochememical characterization of highly-reducing DynE8 was performed. Optimization of sample preparation was carried out to improve homogeneity for EM experiments. Improved samples of DynE8 was obtained using sucrose gradient ultracentrifugation, which advances efforts in future characterization of iPKS. Negative stain EM models of DynE8 and its overall conformation are shown.