Poly (N-vinylpyrrolidone) modification mitigates plasma protein corona formation on phosphomolybdate-based nanoparticles

Phosphomolybdate-based nanoparticles (PMo12-based NPs) have been commonly applied in nanomedicine. However, upon contact with biofluids, proteins are quickly adsorbed onto the NPs surface to form a protein corona, which induces the opsonization and facilitates the rapid clearance of the NPs by macrophage uptake. Herein, we introduce a family of structurally homologous PMo12-based NPs (CDS-PMo12@PVPx(x = 0 ~ 1) NPs) capping diverse content of zwitterionic polymer poly (N-vinylpyrrolidone) (PVP) to regulate the protein corona formation on PMo12-based NPs. The fluorescence quenching data indicate that the introduction of PVP effectively reduces the number of binding sites of proteins on PMo12-based NPs. Molecular docking simulations results show that the contact surface area and binding energy of proteins to CDS-PMo12@PVP1 NPs are smaller than the CDS-PMo12@PVP0 NPs. The liquid chromatography-tandem mass spectrometry (LC–MS/MS) is further applied to analyze and quantify the compositions of the human plasma corona formation on CDS-PMo12@PVPx(x = 0 ~ 1) NPs. The number of plasma protein groups adsorption on CDS-PMo12@PVP1 NPs, compared to CDS-PMo12@PVP0 NPs, decreases from 372 to 271. In addition, 76 differentially adsorption proteins are identified between CDS-PMo12@PVP0 and CDS-PMo12@PVP1 NPs, in which apolipoprotein is up-regulated in CDS-PMo12@PVP1 NPs. The apolipoprotein adsorption onto the NPs is proposed to have dysoponic activity and enhance the circulation time of NPs. Our findings demonstrate that PVP grafting on PMo12-based NPs is a promising strategy to improve the anti-biofouling property for PMo12-based nanodrug design. Graphical Abstract

CircRNA75 and CircRNA72 Function as the Sponge of MicroRNA-200 to Suppress Coelomocyte Apoptosis Via Targeting Tollip in Apostichopus japonicus

Circular RNAs (circRNAs) act as essential regulators in many biological processes, especially in mammalian immune response. Nonetheless, the functions and mechanisms of circRNAs in the invertebrate immune system are largely unclarified. In our previous work, 261 differentially expressed circRNAs potentially related to the development of Apostichopus japonicus skin ulceration syndrome (SUS), which is a major problem restricting the sea cucumber breeding industry, were identified by genome-wide screening. In this study, via miRanda analysis, both circRNA75 and circrRNA72 were shown to share the miR-200 binding site, a key microRNA in the SUS. The two circRNAs were verified to be increased significantly in LPS-exposed primary coelomocytes, similar to the results of circRNA-seq in sea cucumber under Vibrio splendidus-challenged conditions. A dual-luciferase assay indicated that both circRNA75 and circRNA72 could bind miR-200 in vivo, in which circRNA75 had four binding sites of miR-200 and only one for circRNA72. Furthermore, we found that miR-200 could bind the 3’-UTR of Toll interacting protein (Tollip) to negatively mediate the expression of Tollip. Silencing Tollip increased primary coelomocyte apoptosis. Consistently, inference of circRNA75 and circRNA72 could also downregulate Tollip expression, thereby increasing the apoptosis of primary coelomocytes, which could be blocked by miR-200 inhibitor treatment. Moreover, the rate of si-circRNA75-downregulated Tollip expression was higher than that of si-circRNA72 under an equivalent amount. CircRNA75 and circRNA72 suppressed coelomocyte apoptosis by sponging miR-200 to promote Tollip expression. The ability of circRNA to adsorb miRNA might be positively related to the number of binding sites for miRNA.

Interaction of Carrier Protein with Potential Metallic Drug Candidate N-Glycoside ‘GATPT’: Validation by Multi-Spectroscopic and Molecular Docking Approaches

Lysozyme is often used as a model protein to study interaction with drug molecules and to understand biological processes which help in illuminating the therapeutic effectiveness of the drug. In the present work, in vitro interaction studies of 1-{(2-hydroxyethyl)amino}-2-amino-1,2-dideoxy-d-glucose triphenyl tin (IV) (GATPT) complex with lysozyme were carried out by employing various biophysical methods such as absorption, fluorescence, and circular dichroism (CD) spectroscopies. The experimental results revealed efficient binding affinity of GATPT with lysozyme with intrinsic binding (Kb) and binding constant (K) values in the order of 105 M−1. The number of binding sites and thermodynamic parameters ΔG, ΔH, and ΔS at four different temperatures were also calculated and the interaction of GATPT with lysozyme was found to be enthalpy and entropy driven. The CD spectra revealed alterations in the population of α–helical content within the secondary structure of lysozyme in presence of GATPT complex. The morphological analysis of the complex with lysozyme and lysozyme-DNA condensates was carried out by employing confocal and SEM studies. Furthermore, the molecular docking studies confirmed the interaction of GATPT within the larger hydrophobic pocket of the lysozyme via several non-covalent interactions.

Poly (N-vinylpyrrolidone) Modification Mitigates Plasma Protein Corona Formation on Phosphomolybdate-based Nanoparticles

Phosphomolybdate-based nanoparticles (PMo12-based NPs) have been commonly applied in nanomedicine. However, upon contact with biofluids, proteins are quickly adsorbed onto the NPs surface to form a protein corona, which induces the opsonization and facilitates the rapid clearance of the NPs by macrophage uptake. Herein, we introduce a family of structurally homologous PMo12-based NPs (CDS-PMo12@PVPx(x = 0 ~ 1) NPs) capping diverse content of zwitterionic polymer poly (N-vinylpyrrolidone) (PVP) to regulate the protein corona formation on PMo12-based NPs. The fluorescence quenching data indicate that the introduction of PVP effectively reduces the number of binding sites of proteins on PMo12-based NPs. Molecular docking simulations results show that the contact surface area and binding energy of proteins to CDS-PMo12@PVP1 NPs are smaller than the CDS-PMo12@PVP0 NPs. The liquid chromatography-tandem mass spectrometry (LC-MS/MS) is further applied to analyze and quantify the compositions of the human plasma corona formation on CDS-PMo12@PVPx(x = 0 ~ 1) NPs. The number of plasma protein groups adsorption on CDS-PMo12@PVP1 NPs, compared to CDS-PMo12@PVP0 NPs, decreases from 372 to 271. In addition, 76 differentially adsorption proteins are identified between CDS-PMo12@PVP0 and CDS-PMo12@PVP1 NPs, in which apolipoprotein is up-regulated in CDS-PMo12@PVP1 NPs. The apolipoprotein adsorption onto the NPs is proposed to have dysoponic activity and enhance the circulation time of NPs. Our findings demonstrate that PVP grafting on PMo12-based NPs is a promising strategy to improve the anti-biofouling property for PMo12-based nanodrug design.

Target-Dependent Coordinated Biogenesis Ensure Cascaded Expression of miRNAs in Activated Macrophage

miRNA represses protein expression by binding to the the target mRNAs. We have noted miRNA with higher number of binding sites (primary miRNA) coordinates the biogenesis and activity of another miRNA (secondary miRNA) having binding sites on the 3' UTR of a common target mRNA. From the quantitative data obtained from macrophage cells, we detected miR-146a-5p as a "primary" miRNA that coordinates biogenesis of "secondary" miR-125b, miR-21 or miR-142-3p to target new sets of mRNAs to balance the immune response in activated macrophage cells. Interestingly, target dependent coordinated biogenesis of miRNAs, happening on the rough endoplasmic reticulum attached membrane, ensures a cumulative mode of action of primary and secondary miRNAs on the secondary target mRNAs where a cascaded effect of primary miRNA on its secondary targets has been detected. Extensive computational analysis for the presence of coordinated biogenesis pairs of miRNAs in mammalian cells has also allowed us to construct a coordinate biogenesis repository to determine context specific coordinated biogenesis relationships exists for specific pairs of miRNAs in mammalian cells.

The nucleoid-associated protein Gbn binds to GATC sequences and affects sporulation and antibiotic production in Streptomyces

ABSTRACTBacterial chromosome structure is organized by a diverse group of proteins collectively called nucleoid-associated proteins (NAPs). Many NAPs have been studied in detail in Streptomyces, including Lsr2, HupA, HupS, and sIHF. Here, we show that SCO1839 represents a novel family of small NAPs unique to Actinobacteria and recognizes a consensus sequence consisting of GATC followed by (A/T)T. The protein was designated Gbn for GATC-binding NAP. Chromatin immunoprecipitation sequencing (ChIP-Seq) detected more than 2800 binding regions, encompassing some 3600 GATCWT motifs, which comprise 55% of all motifs in the S. coelicolor genome. DNA binding of Gbn in vitro increased DNA stiffness but not compaction, suggesting a role in regulation rather than chromosome organization. Despite the huge number of binding sites, the DNA binding profiles were nearly identical during vegetative and aerial growth. The exceptions were SCO1311 and SCOt32, for a tRNA editing enzyme and a tRNA that recognises the rare leucine codon CUA, respectively, which were nearly exclusively bound during vegetative growth. Deletion of gbn led to pleiotropic alterations in developmental timing, morphogenesis and antibiotic production. Taken together, our data show that Gbn is a highly pleiotropic NAP that impacts growth and development in streptomycetes.

BINDING OF 17-SUBSTITUTED 16-NITRILE 16,17-SECOESTRANE COMPOUNDS TO ESTROGEN RECEPTORS – „IN VITRO“ AND „IN SILICO“ STUDY

About 75% of breast cancers express estrogen receptors (ERs), which is a good base for an efficient endocrine therapy. This gives the opportunity for the treatment of patients with antiestrogens, compounds that bind to the ERs and thus compete to estradiol (E2), preventing its action in progression of estrogen-depending cancers. Here we present results of testing the effect of the modified steroids, namely 17-substituted 16-nitrile 16,17-secoestrane compounds on the E2-ER complex forming, its stability, nuclear translocation and binding to DNA. Almost all compounds in moderate to high rate induced lower forming of this complex, destabilizing it – they increased Kd of this complex and decreased number of binding sites. Complex formed in the presence of some test secosteroids could pass to the nucleus, while other compounds inhibited translocation. In the presence of some compounds binding of the formed complex E2-ER to DNA was noticed. Docking followed molecular dynamics simulation was performed to reveal binding mode of E2 to ER in the presence of test secosteroids. Amino acids important for binding process and complex stabilization were detected. Analysis of the simulation data allowed identifying key amino acids and type of binding of the secoestrane compounds, important for high affinity binding of the steroidal compounds.

ACEII Gene Analysis Exposes SARS-CoV-2 As A Potential Threat to Agricultural and National Security

Coronavirus is now a significant human pathogen with the emergence of SARS-CoV-2. Until now there has been no data to support a threat to agricultural industries. Using a comparative genomic protein analysis, this study examined the angiotensin-converting enzyme II (ACEII) gene of 17 animal species with an emphasis on agriculture. To determine viral vulnerability the 20 known SARS-CoV-2 receptor-binding domain (RBD)/ACEII receptor interaction sites were compared to determine their potential susceptibility to the SARS-CoV-2 virus. With the known bat host’s (XP_032963186) number of binding sites as a threshold, we note that ALL animal species examined in this study contained significant numbers (≥10) of SARS-CoV-2 binding sites and could be at risk for SARS-CoV-2 infection. The data from this study suggest SARS-CoV-2 imposes a grave threat to the safety and security of the agricultural industry. Urgent studies are needed to determine if infected animals can transmit SARS-CoV-2 before and/or after processing.

Development of Nano-KIT for Synthesis of Silver and Gold Nanostructures with Emphasis on Biological Applications

Nano-KIT consist of few standard chemicals (solvents)/constitutes that can be added sequentially by given protocol. Spherical silver (30 nm) and gold (25–30 nm) nanostructure were synthesized instantly in (5–10 min). Surface plasmon resonance for silver 413 nm and gold 545 nm were confirmed synthesis. Synthesized silver has stability more than 36 months in cold condition. Dynamic Light Scattering (DLS), X-ray Diffraction (XRD) and High Resolution-Transmission Electron Microscopy (HR-TEM) revealed 30 nm (silver) and 25–30 nm (gold). Nano-KIT can be used for variety of application in Nano research areas like biomedical and industrial. Synthesized silver nanostructure were analysed with its molecular interaction between Bovine Serum Albumin (BSA). Biocompatibility assays with Red Blood Cells (RBC), number of binding sites, thermodynamic parameters i.e., free energy, enthalpy and entropy were studied.

Modelling cytoskeletal transport by clusters of non-processive molecular motors with limited binding sites

Molecular motors are responsible for intracellular transport of a variety of biological cargo. We consider the collective behaviour of a finite number of motors attached on a cargo. We extend previous analytical work on processive motors to the case of non-processive motors, which stochastically bind on and off cytoskeletal filaments with a limited number of binding sites available. Physically, motors attached to a cargo cannot bind anywhere along the filaments, so the number of accessible binding sites on the filament should be limited. Thus, we analytically study the distribution and the velocity of a cluster of non-processive motors with limited number of binding sites. To validate our analytical results and to go beyond the level of detail possible analytically, we perform Monte Carlo latticed based stochastic simulations. In particular, in our simulations, we include sequence preservation of motors performing stepping and binding obeying a simple exclusion process. We find that limiting the number of binding sites reduces the probability of non-processive motors binding but has a relatively small effect on force–velocity relations. Our analytical and stochastic simulation results compare well to published data from in vitro and in vivo experiments.