Unveiling the Virtual Blueprint: Exploring the Structural and Functional Analysis of a Novel Endolysin LysSM5 Derived...

Salmonella, a foodborne pathogen, poses a significant threat to public health. This concern is exacerbated by emerging antibiotic resistance. Bacteriophages and their endolysins are promising alternatives to antibiotics. Endolysins play a crucial role in bacterial lysis in the phage life cycle. Leveraging these proteins as antimicrobial agents may offer a potential solution for controlling pathogenic contamination in food. Structural and functional analysis of LysSM5 endolysin derived from vB_SenA_SM5, a Salmonella phage, was studied using computational tools. Functional annotation, physicochemical characteristics, and 3D structure of the LysSM5 were predicted. Validation and quality assessment were performed using various computational tools like Conserved Domain Search, ProtParam, SWISS-Model server, PROCHECK, Verify3D, and ERRAT server. The molecular weight of LysSM5 was 28.8 kDa, 264 amino acids, and an isoelectric point of 8.9. The sequence of LysSM5 comprised of an N-terminal peptidoglycan-binding domain (residues 9-64) and a C-terminal N-acetyl-β-D-muramidase domain (residues 90-263), interconnected by a linker sequence. Phylogenetic analysis using MEGA X revealed that LysSM5 shared similarities with endolysins from phages active against E. coli and various Salmonella serovars. This indicates that LysSM5 may have a broad spectrum of activity, making it a versatile candidate for combating a range of bacterial pathogens. The structure was predicted by using the SWISS-Model server, validated by Ramachandran plot analysis (91.8% residues in favored regions) and quality assessments (ERRAT score: 98.016, Verify3D: 95.44% residues with ≥ 0.1 score). These high-quality scores confirm that LysSM5's predicted structure is accurate and reliable for further analysis. Molecular docking showed a robust binding affinity of LysSM5 to peptidoglycan (- 13.9 kcal/mol), indicating its potential effectiveness in targeting and interacting with bacterial cell walls for antimicrobial applications. Molecular dynamics simulations were performed using the iMODS web server, indicating high stability of the LysSM5-peptidoglycan complex, with an eigenvalue of 8.873650e-05, suggesting that LysSM5 can effectively bind to and disrupt bacterial cell walls, making it a promising candidate for further development in antimicrobial applications.