In silico structural and mechanistic sights into the N-glycosidase mechanism of Shiga toxin.

Shiga toxin is the leading cause of food poisoning in the world. It is structurally similar to the plant type II ribosome-inactivating proteins (RIPs) and retains N-glycosidase activity. It acts specifically by depurinating the specific adenine A4605 of human 28S rRNA, ultimately inhibiting translation.

Structural insights into the toxicity of type II ribosome inactivating proteins (RIPs): a molecular dynamics study.

Ribosome Inactivating Proteins (RIPs) act by irreversibly depurinating the 28S rRNA ricin-sarcin loop (SRL) of the eukaryotic ribosome resulting in protein synthesis inhibition. In general, they consist of two variants: Type I which is single chained (∼30 kDa), and Type II, a more toxic variant which is a Type I N-glycosidase chain covalently linked to a lectin chain. These proteins are believed to play a pivotal role in defence mechanisms.

structural studies on anti-inflammatory activity of phytocompounds from the genus Andrographis.

Plant species from the genus were used in Ayurveda and in other folklore medicines for treating ailments for centuries. In this study, we have hypothesized to evaluate the secondary metabolites as potent anti-inflammatory agents from the genus A library of secondary metabolites of the said genus was curated from the PubChem database and was subjected to energy minimization using UCSF Chimera software employing the AMBER force field. Initially, molecular docking was performed to evaluate the binding affinity of the curated library against the enzymes cyclooxygenase-1 (COX-1), cyclooxygenase-2 (COX-2), and 5-Lipoxygenase (5-LOX) using AutoDock Vina.

Insights into the microevolution of SARS-ACE2 interactions: in silico analysis of glycosylation and SNP pattern.

The prefatory protein-glycan interaction and stabilizing protein-protein interaction of severe acute respiratory syndrome viruses with angiotensin-converting enzyme 2 play a significant role in complex formation thereby promoting endocytosis. The microevolution of SARS-CoV-2 over a period of time has a significant role in increasing the affinity of receptor-binding domain against angiotensin converting-enzyme 2. In this study, we have corroborated the vitality of acquired SNPs over a period of time with increased affinity by using docking studies.

Selection of start codon during mRNA scanning in eukaryotic translation initiation.

Accurate and high-speed scanning and subsequent selection of the correct start codon are important events in protein synthesis. Eukaryotic mRNAs have long 5' UTRs that are inspected for the presence of a start codon by the ribosomal 48S pre-initiation complex (PIC). However, the conformational state of the 48S PIC required for inspecting every codon is not clearly understood.

Ligand binding and retention in snake gourd seed lectin (SGSL). A crystallographic, thermodynamic and molecular dynamics study.

Snake gourd seed lectin (SGSL) is a non-toxic homolog of type II ribosome-inactivating proteins (RIPs) which contain a catalytic domain and a lectin domain. Isothermal titration calorimetry (ITC) measurements of the interactions of the protein with LacNAc, Lac, Gal, Me-α-Gal were carried out and the crystal structures of the native protein and its complex with Lac were determined. The crystal structure of the Me-α-Gal complex has already been determined.

Structural studies on a non-toxic homologue of type II RIPs from bitter gourd: Molecular basis of non-toxicity, conformational selection and glycan structure.

The structures of nine independent crystals of bitter gourd seed lectin (BGSL), a non-toxic homologue of type II RIPs, and its sugar complexes have been determined. The four-chain, two-fold symmetric, protein is made up of two identical two-chain modules, each consisting of a catalytic chain and a lectin chain, connected by a disulphide bridge. The lectin chain is made up of two domains.

Generation of ligand specificity and modes of oligomerization in β-prism I fold lectins.

β-Prism I fold lectins constitute one of the five widely occurring structural classes of plant lectins. Each single domain subunit is made up of three Greek key motifs arranged in a threefold symmetric fashion. The threefold symmetry is not reflected in the sequence except in the case of the lectin from banana, a monocot, which carries two sugar-binding sites instead of the one in other lectins of known three-dimensional structure, all from dicots.

The sequence and structure of snake gourd (Trichosanthes anguina) seed lectin, a three-chain nontoxic homologue of type II RIPs.

The sequence and structure of snake gourd seed lectin (SGSL), a nontoxic homologue of type II ribosome-inactivating proteins (RIPs), have been determined by mass spectrometry and X-ray crystallography, respectively. As in type II RIPs, the molecule consists of a lectin chain made up of two β-trefoil domains. The catalytic chain, which is connected through a disulfide bridge to the lectin chain in type II RIPs, is cleaved into two in SGSL.

Crystallization and preliminary X-ray studies of a galactose-specific lectin from the seeds of bitter gourd (Momordica charantia).

A galactose-specific lectin from the seeds of bitter gourd (Momordica charantia) is a four-chain type II ribosome-inactivating protein (RIP) resulting from covalent association through a disulfide bridge between two identical copies of a two-chain unit. The available structural information on such four-chain RIPs is meagre. The bitter gourd lectin was therefore crystallized for structural investigation and the crystals have been characterized.

A novel Plasmodium falciparum erythrocyte binding protein associated with the merozoite surface, PfDBLMSP.

Proteins on the surface of the merozoite, the invasive form of the malaria parasite Plasmodium falciparum,and those secreted from its apical secretory organelles are promising vaccine candidates against blood stage malaria. In the present study, we have identified a novel parasite protein (PfDBLMSP; Gene IDPF10_0348), that harbors a predicted signal sequence, a central Duffy binding-like (DBL) domain and a secreted polymorphic antigen associated with merozoites (SPAM) domain in its C-terminal half. Transcription and translation of pfdblmsp is up-regulated specifically in schizont stage parasites, similar to other well-chararacterized merozoite proteins involved in invasion of red blood cells (RBCs).