In Silico Characterization of a Hypothetical Protein from Shigella dysenteriae ATCC 12039 Reveals a Pathogenesis-Related Protein of the Type-VI Secretion System

Shigellosis caused by Shigella dysenteriae is a major public health concern worldwide, particularly in developing countries. The bacterial genome is known, but there are many hypothetical proteins whose functions are yet to be discovered. A hypothetical protein (accession no. WP_128879999.1, 161 residues) of S. dysenteriae ATCC 12039 strain was selected in this study for comprehensive structural and functional analysis. Subcellular localization and different physicochemical properties of this hypothetical protein were estimated indicating it as a stable, soluble, and extracellular protein. Functional annotation tools, such as NCBI-CD Search, Pfam, and InterProScan, predicted our target protein to be an amidase effector protein 4 (Tae4) of type-VI secretion system (T6SS). Multiple sequence alignment of the homologous sequences coincided with previous findings. Random coil was found to be predominant in secondary structure. Three-dimensional (3D) structure of the protein was obtained using homology modeling method by SWISS-MODEL server using a template protein (PDB ID: 4J30) of 80.12% sequence identity. The 3D structure became more stable after YASARA energy minimization and was validated by several quality assessment tools like PROCHECK, QMEAN, Verify3D, and ERRAT. Superimposition of the target with the template protein by UCSF Chimera generated RMSD value of 0.115 Å, suggesting a reliable 3D structure. The active site of the modeled structure was predicted and visualized by CASTp server and PyMOL. Interestingly, similar binding affinity and key interacting residues were found for the target protein and a Salmonella enterica Tae4 protein with the ligand L-Ala D-Glu-mDAP by molecular docking analysis. Protein-protein docking was also performed between the target protein and hemolysin coregulated protein 1 of T6SS. Finally, the protein was found to be a unique protein of S. dysenteriae nonhomologous to human by comparative genomics approach indicating a potential therapeutic target. Most pathogens harboring T6SS in their system pose a significant threat to the human health. Many T6SSs and their effectors are associated with interbacterial competition, pathogenesis, and virulency; however, relationships between these effectors and pathogenicity of S. dysenteriae are yet to be determined. The study findings provide a lucrative platform for future antibacterial treatment.

Fabrication and evaluation of protein imprinted polymer based on magnetic halloysite nanotubes

A novel protein imprinted polymer, which combined the surface imprinting technology and magnetic halloysite nanotubes (MHNTs), was prepared for selective separation of a template protein.

Preparation and Characterize of Konjac Glucomannan-Based Protein Molecularly Imprinted Polymer

Objective: To prepare a novel molecularly imprinted materials for protein recognition. Methods: Konjac glucomannan was used as fundamental materials, after swollen, added 3-Chloro-1,2- epoxypropane and glycerol cross-linked for 3 h at 40 °C. Then added bovine serum albumin (BSA) solution, agitated 1 h at room temperature. Natural dried. Results: After eluted, the imprinted efficiency of the imprinted membrane were (59.27±3.53) % (n=6) with blank membrane as control. The adsorption rate increased from 2 h to 20 h, and reached saturation at 22 to 24 h. The selectively recognition experiment indicated the BSA imprinted membrane have significant selectively recognition abilities for the template protein. Conclusions: konjac glucomannan-based imprinted membrane shows great possibilities to be a promising material for protein molecularly imprinted recognition.

The Rebinding Properties of Bovine Serum Albumin Imprinted Calcium Phosphate/Polyacrylate/Alginate Hybrid Polymer Microspheres

Calcium phosphate/polyacrylate/alginate hybrid polymer microspheres with bovine serum albumin (BSA) embedded and coated on the surface were prepared with (NH4)2HPO4, sodium polyacrylate (SPA) and sodium alginate (SA) via Ca2+ crosslinking in inverse suspension. Rebinding behaviors of the microspheres were evaluated. The factors influencing the imprinting efficiency (IE) of imprinted microspheres were also studied, including the concentration of CaCl2, template content and pH values in rebinding solutions. Selectivity tests showed that the imprinted microspheres exhibited good recognition property for the template protein.

Using Protein Homology Models for Structure-Based Studies: Approaches to Model Refinement

Homology modeling is a computational methodology to assign a 3-D structure to a target protein when experimental data are not available. The methodology uses another protein with a known structure that shares some sequence identity with the target as a template. The crudest approach is to thread the target protein backbone atoms over the backbone atoms of the template protein, but necessary refinement methods are needed to produce realistic models. In this mini-review anchored within the scope of drug design, we show the validity of using homology models of proteins in the discovery of binders for potential therapeutic targets. We also report several different approaches to homology model refinement, going from very simple to the most elaborate. Results show that refinement approaches are system dependent and that more elaborate methodologies do not always correlate with better performances from built homology models.