In silico analysis and molecular identification of an anaphase-promoting complex homologue from human pathogen Entamoeba histolytica

Abstract

Background Amoebiasis, being endemic worldwide, is the second leading cause of parasite-associated morbidity and mortality after malaria. The human parasite Entamoeba histolytica is responsible for the disease. Metronidazole is considered as the gold standard for the treatment of amoebiasis, but this antibiotic is carcinogenic and the development of antibiotic resistance against E. histolytica is a major health concern. Chromosome segregation is irregular in this parasite due to the absence of a few cell cycle checkpoint proteins. Anaphase-promoting complex (APC/C or cyclosome) is an E3 ubiquitin ligase that synchronizes chromosome segregation and anaphase progression via the ubiquitin-proteasome system. Proteasome is considered to be an attractive drug target for protozoan parasites. For the present study, EhApc11 from E. histolytica, a homologue of Apc11 in humans, is selected for elucidating its structural and functional aspects by detailed in silico analysis and molecular methods. Its physicochemical characteristics, identification of probable interactors, 3D model and quality analysis are done using standard bioinformatics tools. cDNA sequence of EhAPC11 has been further cloned for molecular characterization. Result Conserved domain analysis revealed that EhApc11 belongs to the RING (really interesting new gene) superfamily and has ligand binding capacity. Expression study in Escherichia coli BL21 (DE3) revealed that the molecular weight of glutathione S-transferase (GST)-tagged protein is ~ 36 kDa. Conclusion EhApc11 is a hydrophilic, thermostable, extracellular protein with potent antigenicity. The study will serve as a groundwork for future in-depth analysis regarding the validation of protein-protein interaction of EhApc11 with its substrates identified by STRING analysis and the potential of EhApc11 to serve as an anti-amoebic drug target.

Functional, and phylogenetic analysis of maleylacetate reductase of Pseudomonas sp strain PNPG3: An in-silico approach

“…Generally, a good quality model usually shows more than 90% residues in the favored regions (Berman et al 2000;Yadav et al 2013). A similar type of model validation was reported by Pramanik et al (2018) and Pal et al (2021).…”

“…A higher score of ERRAT value indicates the good quality of this model. The accepted threshold value for a high-quality model is >50 (Pal et al 2021). QMEAN is a scoring function that calculates the global as well as local per residue quality analysis of the protein of interest, based on one single model (Benkert et al 2011).…”

“…QMEAN4 score for this predicted protein of MR was -3.64 (Figure 6c). The QMEAN score of less than -4 is an indication of a low-quality model (Pal et al 2021). The Z score of the query protein sequence (MR of strain PNPG3) was within an acceptable range, i.e., 1< [Z score] <2 in comparison with a non-redundant set of PDB structures (Figure 6d).…”