Comparative In Silico Structural Analysis of PHA Synthases from Industrially Prominent PHA Producers

Abstract Environmental issues from petroleum-based plastics have intensified due to long-term accumulation. Their persistence harms marine and terrestrial life, disrupting food chains, and spreading microplastics. Increased plastic usage driven by industrialization, modern lifestyles, and disposable products contributes to this problem. An effective strategy to mitigate plastic’s negative impact includes waste reduction, recycling, and the development of biodegradable biopolymers. In this sense, polyhydroxyalkanoate (PHA) synthase (PhaC) is a vital enzyme for cost-effective biopolymer/bioplastic production. Thus, this study investigated four different genera ( Azotobacter , Bacillus , Cupriavidus , and Halomonas ) that are well-known PHA/Polyhydroxybutyrate (PHB) producers, selected due to their proven industrial capability and metabolic versatility in PHA/PHB biosynthesis. Since there has been inadequate information based on the three-dimensional (3D) structures of PHA synthase(s), this is the first report to assess the PHA synthase(s) of these indicated genera by conducting in silico comparative analyses on AlphaFold predicted structures. Furthermore, frustration analysis revealed structural similarities among Azotobacter , Cupriavidus , and Halomonas PHA synthases, while Bacillus exhibited a distinct profile. Identifying highly frustrated residues in potential substrate-binding regions offers insights into their functional dynamics and engineering potential. Molecular docking analysis was also performed to assess interactions between AlphaFold-predicted enzyme structures and their substrates, quantifying the binding energy of enzyme-substrate complexes. The findings of this work will contribute to the engineering of PHA synthase(s) of PHA/PHB producers with the simultaneous understanding of predicted 3D structures using the advanced capabilities of AlphaFold. This understanding will support the creation of more efficient and sustainable bioplastics for the future. Graphical abstract