Protein Structure and its effects on transcription in Zymobacter palmae and Escherichia coli for ethanol production

Zymobacter palmae, a Gram-negative bacterium from the Halomonadaceae family, is a facultative anaerobic and mesophilic organism. It is extremely rare and has been researched for its unusual capacity to contribute to natural fermentation processes, resulting in different compounds. Z. palmae can efficiently make ethanol by breaking down simple sugars and carbohydrates, such as monosaccharides and oligosaccharides. It also contains enzymes such as cellulase, protease, and lyase, all of which are essential for ethanol formation. The study also examined the stability of these enzymes in a wild E. coli strain and compared the results with Z. palmae. However, structural information on these enzymes remains unavailable. The principal objective of the learning focused onto model and validate three-dimensional (3D) structures of cellulase, protease, and lyase enzymes in Z. palmae, with a focus on understanding their structural characteristics and functional significance in ethanol production. The National Center for Biotechnology Information (NCBI) database provided the annotated genomic sequence of Z. palmae and E. coli for this study. The CGview program revealed the organism's circular genome structure. Protein modeling and secondary structure analysis were done with AlphaFold2 and NetSurfP, respectively. A molecular dynamic simulation (MDS) study was also evaluated using the WebGRO program. The outcomes exhibited excellent confidence on projected local distance difference test (pLDDT) scores: 95.2% for cellulase, 91.9% for lyase, and 93.2% for protease. MDS analysis at 50 nanoseconds (ns) validated the structural stability of cellulase, lyase, and protease, with RMSD values of around 0.2 nm, 0.8 nm, and 0.5 nm respectively. These findings imply that Z. palmae can manufacture stable enzymes, hence contributing to long-term ethanol synthesis. Some of the Z. palmae ethanol production key enzymes were comparable with wild strain of E. coli.