‘Proof of concept’ of how tube-net diameter affects growth and agar content in industrially important farmed red seaweed Gracilaria dura

Journal of Applied Phycology - Several emerging therapeutic applications of agar and its derivatives make it one of the sought-after hydrocolloids, commanding the highest price in global markets....     

Conformation and stability of the Streptococcus pyogenes pSM19035-encoded site-specific beta recombinase, and identification of a folding intermediate

Solution properties of beta recombinase were studied by circular dichroism and fluorescence spectroscopy, size exclusion chromatography, analytical ultracentrifugation, denaturant-induced unfolding and thermal unfolding experiments. In high ionic strength buffer (1 M NaCl) beta recombinase forms mainly dimers, and strongly tends to aggregate at ionic strength lower than 0.3 M NaCl. Urea and guanidinium chloride denaturants unfold beta recombinase in a two-step process. The unfolding curves have bends at approximately 5 M and 2.2 M in urea and guanidinium chloride-containing buffers. Assuming a three-state unfolding model (N2-->2I-->2U), the total free energy change from 1 mol of native dimers to 2 mol of unfolded monomers amounts to deltaG(tot) = 17.9 kcal/mol, with deltaG(N2-->2I) = 4.2 kcal/mol for the first transition and deltaG(I-->U) = 6.9 kcal/mol for the second transition. Using sedimentation-equilibrium analytical ultracentrifugation, the presence of beta recombinase monomers was indicated at 5 M urea, and the urea dependence of the circular dichroism at 222 nm strongly suggests that folded monomers represent the unfolding intermediate.     

The polybasic insert,the RBD of the SARS-CoV-2 spike protein,and the feline coronavirus – evolved or yet to evolve

Recent research on the SARS-CoV-2 pandemic has exploded around the furin-cleavable polybasic insert PRRAR↓S, found within the spike protein. The insert and the receptor-binding domain, (RBD), are vital clues in the Sherlock Holmes-like investigation into the origin of the virus and in its zoonotic crossover. Based on comparative analysis of the whole genome and the sequence features of the insert and the RBD domain, the bat and the pangolin have been proposed as very likely intermediary hosts. In this study, using the various databases, in-house developed tools, sequence comparisons, structure-guided docking, and molecular dynamics simulations, we cautiously present a fresh, theoretical perspective on the SARS-CoV-2 virus activation and its intermediary host. They are a) the SARS-CoV-2 has not yet acquired a fully optimal furin binding site or this seemingly less optimal sequence, PRRARS, has been selected for survival; b) in structural models of furin complexed with peptides, PRRAR↓S binds less well and with distinct differences as compared to the all basic RRKRR↓S; c) these differences may be exploited for the design of virus-specific inhibitors; d) the novel polybasic insert of SARS-CoV-2 may be promiscuous enough to be cleaved by multiple enzymes of the human airway epithelium and tissues which may explain its unexpected broad tropism; e) the RBD domain of the feline coronavirus spike protein carries residues that are responsible for high-affinity binding of the SARS-CoV-2 to the ACE 2 receptor; f) en route zoonotic transfer, the virus may have passed through the domestic cat whose very human-like ACE2 receptor and furin may have played some role in optimizing the traits required for zoonotic transfer.     

Prion metal interaction: Is prion pathogenesis a cause or a consequence of metal imbalance?

Functional role of cellular prion protein (PrPc) has been hypothesized to be in metal homeostasis and providing cells with a superoxide dismutase (SOD)-like activity to escape damage by reactive oxygen species (ROS). PrPc interacts with a range of divalent metal ions and undergoes Cu²⁺ as well as Zn²⁺-associated endocytosis, thereby maintaining homeostasis of these and other metal ions. Conformational change to a β-sheet rich, protease resistant entity, reminiscent of the disease-associated scrapie form called PrPsc, has been found to be induced by interaction of PrPc with metal ions like Cu²⁺, Zn²⁺, Mn²⁺ and Fe²⁺. This review compiles data from various experimental studies of the interaction of metals with PrPc. The effect of metal ions on the expression and conformation of the prion protein is described in detail with emphasis on their possible physiological and pathogenic role. Further, a hypothesis is presented where attainment of altered conformation by metal-bound PrPc has been viewed as a deleterious consequence of efforts made by cells to maintain metal homeostasis. Thus, PrPc presumably sacrifices itself by converting into PrPsc form in an attempt to protect cells from the toxicity of metal imbalance. Finally, possible reasons for contradictions reported in the literature on the subject are explored and experimental approaches to resolve the same are suggested.     

Protein–ligand interaction studies of retinol-binding protein 3 with herbal molecules using AutoDock for the management of Eales’ disease

Eales’ disease is an idiopathic retinal vasculitis of the eye. The disease is predominantly characterized by recurrent vitreous hemorrhage. Interphotoreceptor retinol-binding protein 3 plays a significant role in the etiopathogenesis of this condition. It transports retinoids between the retinal pigment epithelium and the photoreceptors; hence, this protein is a potential target for docking studies. In silico data reveal that herbal molecules interact with regulatory domains of interphotoreceptor retinol-binding protein 3 (IRBP-3), resulting into significant docking score and also forms H-bond and several hydrophobic interactions between active residues of IRBP-3. These interactions between the active residues may lead to significant conformational change in that particular portion of the protein. This efficacy and suitability of ligand was determined on the basis of binding energy calculations. Ginkgolide showed minimum binding energy calculations among selected 10 other natural ligands. This fact of virtual screening for potential ligand can give new insights toward the therapeutic intonations and alterations toward the advances in treatment for Eales’ disease.