Protein surface topography as a tool to enhance the selective activity of a potassium channel blocker.

Tk-hefu is an artificial peptide designed based on the α-hairpinin scaffold, which selectively blocks voltage-gated potassium channels K1.3. Here we present its spatial structure resolved by NMR spectroscopy and analyze its interaction with channels using computer modeling.

Confined Dynamics of Water in Transmembrane Pore of TRPV1 Ion Channel.

Solvation effects play a key role in chemical and biological processes. The microscopic properties of water near molecular surfaces are radically different from those in the bulk. Furthermore, the behavior of water in confined volumes of a nanometer scale, including transmembrane pores of ion channels, is especially nontrivial.

Structure, Function, and Therapeutic Potential of Marine Bioactive Peptides.

In recent years, bioactive peptides from marine organisms have gained increasing attention in the field of pharmaceutical, cosmeceutical, and nutraceutical product development owing to their interesting biological properties [...

Redesigning Arenicin-1, an Antimicrobial Peptide from the Marine Polychaeta , by Strand Rearrangement or Branching, Substitution of Specific Residues, and Backbone Linearization or Cyclization.

Arenicin-1, a β-sheet antimicrobial peptide isolated from the marine polychaeta coelomocytes, has a potent, broad-spectrum microbicidal activity and also shows significant toxicity towards mammalian cells. Several variants were rationally designed to elucidate the role of structural features such as cyclization, a certain symmetry of the residue arrangement, or the presence of specific residues in the sequence, in its membranolytic activity and the consequent effect on microbicidal efficacy and toxicity. The effect of variations on the structure was probed using molecular dynamics simulations, which indicated a significant stability of the β-hairpin scaffold and showed that modifying residue symmetry and β-strand arrangement affected both the twist and the kink present in the native structure.

Heat Shock Protein 70 kDa as a Target for Diagnostics and Therapy of Cardiovascular and Cerebrovascular Diseases.

Acute focal ischemia is a main factor of pathogenesis of a number of widespread cardiovascular and cerebrovascular diseases, in particular, myocardial infarction and ischemic stroke. It is known that under the conditions of ischemia expression of intracellular heat shock proteins (HSPs), especially HSP70, grows greatly irrespective of the cell type. This stress-induced cell response is connected with cytoprotective properties of HSP70.

Specific refolding pathway of viscumin A chain in membrane-like medium reveals a possible mechanism of toxin entry into cell.

How is a water-soluble globular protein able to spontaneously cross a cellular membrane? It is commonly accepted that it undergoes significant structural rearrangements on the lipid-water interface, thus acquiring membrane binding and penetration ability. In this study molecular dynamics (MD) simulations have been used to explore large-scale conformational changes of the globular viscumin A chain in a complex environment - comprising urea and chloroform/methanol (CHCl/MeOH) mixture. Being well-packed in aqueous solution, viscumin A undergoes global structural rearrangements in both organic media.

Cytotoxic Potential of the Novel Horseshoe Crab Peptide Polyphemusin III.

Biological activity of the new antimicrobial peptide polyphemusin III from the horseshoe crab was examined against bacterial strains and human cancer, transformed, and normal cell cultures. Polyphemusin III has the amino acid sequence RRGCFRVCYRGFCFQRCR and is homologous to other β-hairpin peptides from the horseshoe crab. Antimicrobial activity of the peptide was evaluated and MIC (minimal inhibitory concentration) values were determined.

Carbon Nanospikes: Synthesis, characterization and application for high resolution AFM.

We present a detailed study of synthesis, structural characterization of sharp, spike-like carbon structures and its application for high-resolution atomic-force microscopy (AFM) measurements of biological molecules. The probes are obtained by chemical vapor deposition of spike-like carbon structures on the apexes of common AFM silicon probes. The deposition process is carried out in carbonaceous gas mixture activated by a direct-current discharge.

Novel Antimicrobial Peptides from the Arctic Polychaeta Provide New Molecular Insight into Biological Role of the BRICHOS Domain.

Endogenous antimicrobial peptides (AMPs) are among the earliest molecular factors in the evolution of animal innate immunity. In this study, novel AMPs named nicomicins were identified in the small marine polychaeta in the Maldanidae family. Full-length mRNA sequences encoded 239-residue prepropeptides consisting of a putative signal sequence region, the BRICHOS domain within an acidic proregion, and 33-residue mature cationic peptides.

Radioactive (Y) upconversion nanoparticles conjugated with recombinant targeted toxin for synergistic nanotheranostics of cancer.

We report combined therapy using upconversion nanoparticles (UCNP) coupled to two therapeutic agents: beta-emitting radionuclide yttrium-90 (Y) fractionally substituting yttrium in UCNP, and a fragment of the exotoxin A derived from genetically fused with a targeting designed ankyrin repeat protein (DARPin) specific to HER2 receptors. The resultant hybrid complex UCNP-R-T was tested using human breast adenocarcinoma cells SK-BR-3 overexpressing HER2 receptors and immunodeficient mice, bearing HER2-positive xenograft tumors. The photophysical properties of UCNPs enabled background-free imaging of the UCNP-R-T distribution in cells and animals.

Receptor-binding properties of influenza viruses isolated from gulls.

Ducks, gulls and shorebirds represent the major hosts of influenza A viruses (IAVs) in nature, but distinctions of IAVs in different birds are not well defined. Here we characterized the receptor specificity of gull IAVs with HA subtypes H4, H6, H14, H13 and H16 using synthetic sialylglycopolymers. In contrast to duck IAVs, gull IAVs efficiently bound to fucosylated receptors and often preferred sulfated and non-sulfated receptors with Galβ1-4GlcNAc cores over the counterparts with Galβ1-3GlcNAc cores.

A Highly Productive CHO Cell Line Secreting Human Blood Clotting Factor IX.

Hemophilia B patients suffer from an inherited blood-clotting defect and require regular administration of blood-clotting factor IX replacement therapy. Recombinant human factor IX produced in cultured CHO cells is nearly identical to natural, plasma-derived factor IX and is widely used in clinical practice. Development of a biosimilar recombinant human factor IX for medical applications requires the generation of a clonal cell line with the highest specific productivity possible and a high level of specific procoagulant activity of the secreted factor IX.

Design of polymer particle dispersions (latexes) in the course of radical heterophase polymerization for biomedical applications.

Dispersions of polymer particle (DPPs) are increasingly being exploited both as biomolecule carriers, and as markers in various DPP biomedical applications related to cell and molecular biology, enzymology, immunology, diagnostics, in vitro and in vivo visualization, bioseparation, etc. Their potential to reduce reaction scales, lower costs, improve the rate, sensitivity, selectivity, stability and reproducibility of assays governs the diversity of their bioapplications. This review focuses on the design of DPPs with innovative special properties in the course of free radical heterophase polymerization that provides careful control of both macromolecular and colloidal properties.

Genomic characteristics of vB_PpaP_PP74, a T7-like Autographivirinae bacteriophage infecting a potato pathogen of the newly proposed species Pectobacterium parmentieri.

Bacteriophage vB_PpaP_PP74 (PP74) is a novel virulent phage that infects members of the species Pectobacterium parmentieri, a newly established species of soft-rot-causing bacteria in the family Pectobacteriaceae, derived from potato-specific Pectobacterium wasabiae. vB_PpaP_PP74 was identified as a member of the family Podoviridae by transmission electron microscopy. The phage has a 39,790-bp dsDNA genome containing 50 open reading frames (ORFs).

Sorption of nucleic acids and proteins on polyaniline and polyaramide nano-coatings as studied by spectral-correlation interferometry in a real time mode.

Polyaniline (PANI) and polyaramides deposited on the surfaces of glass slides and particulate silica were studied as adsorbents of nucleic acids and proteins by flow-through spectral correlation interferometry and solid-state extraction using spin-cartridges. Double stranded DNA from E. coli as well as pepsin, bovine serum albumin and lysozyme were the analytes studied in contact with the polymer nanolayers in phosphate buffer solution, pH 7.

Pharmacological analysis of Poecilotheria spider venoms in mice provides clues for human treatment.

Bites of tiger spiders belonging to Poecilotheria genus cause moderate to severe pain and long-lasting local or generalized muscle cramps in humans. Bites occur in regions of the spiders' natural habitat, India and Sri Lanka, but the popularity of these colorful tarantulas as pets leads to reports of envenomation cases worldwide. Treatment is predominantly symptomatic and often inadequate since there is almost no clinical or toxicology research data available, and physicians outside India or Sri Lanka typically have no experience in treating such cases.

Multicomponent nanocrystals with anti-Stokes luminescence as contrast agents for modern imaging techniques.

Lanthanide-doped upconversion nanoparticles (UCNPs) have recently attracted great attention in theranostics due to their exceptional optical and physicochemical properties, which enable the design of a novel UCNP-based nanoplatform for luminescent imaging, temperature mapping, sensing, and therapy. In addition, UCNPs are considered to be ideal building blocks for development of multimodal probes for cells and whole body imaging, exploiting simple variation of host matrix, dopant ions, and surface chemistry. Modalities responsible for magnetic resonance imaging (MRI), computed tomography (CT), and positron emission tomography (PET)/single-photon emission computed tomography (SPECT) are embedded in a single UC nanocrystal, providing integrating effect over any modality alone in terms of the efficiency and sensitivity for clinical innovative diagnosis through multimodal bioimaging.

Molecular markers of paragangliomas/pheochromocytomas.

Paragangliomas/pheochromocytomas comprise rare tumors that arise from the extra-adrenal paraganglia, with an incidence of about 2 to 8 per million people each year. Approximately 40% of cases are due to genetic mutations in at least one out of more than 30 causative genes. About 25-30% of pheochromocytomas/paragangliomas develop under the conditions of a hereditary tumor syndrome a third of which are caused by mutations in the VHL gene.

Structural basis of the high thermal stability of the histone-like HU protein from the mollicute Spiroplasma melliferum KC3.

The three-dimensional structure of the histone-like HU protein from the mycoplasma Spiroplasma melliferum KC3 (HUSpm) was determined at 1.4 Å resolution, and the thermal stability of the protein was evaluated by differential scanning calorimetry. A detailed analysis revealed that the three-dimensional structure of the HUSpm dimer is similar to that of its bacterial homologues but is characterized by stronger hydrophobic interactions at the dimer interface.

Temperature-sensitive gating of TRPV1 channel as probed by atomistic simulations of its trans- and juxtamembrane domains.

Heat-activated transient receptor potential channel TRPV1 is one of the most studied eukaryotic proteins involved in temperature sensation. Upon heating, it exhibits rapid reversible pore gating, which depolarizes neurons and generates action potentials. Underlying molecular details of such effects in the pore region of TRPV1 is of a crucial importance to control temperature responses of the organism.

Sorption behavior of polyaramides in relation to isolation of nucleic acids and proteins.

The effect of chemical composition and morphology of the surface layers of new polyaramide-containing sorbents on the mechanism of selective sorption of nucleic acids and proteins was investigated as compared to the previously studied sorbents modified with fluoropolymers and polyaniline (high-throughput materials providing one-step isolation of DNA from biological mixtures). A series of silica-based sorbents modified with polyaramides having consistently varying structure and containing the set of "key" structural elements (aromatic units and nitrogen atoms in the backbone, fluorinated groups), and various donor and acceptor moieties was prepared. The chemical composition of the polymer coatings was evaluated by X-ray photoelectron spectroscopy.

CrossHub: a tool for multi-way analysis of The Cancer Genome Atlas (TCGA) in the context of gene expression regulation mechanisms.

The contribution of different mechanisms to the regulation of gene expression varies for different tissues and tumors. Complementation of predicted mRNA-miRNA and gene-transcription factor (TF) relationships with the results of expression correlation analyses derived for specific tumor types outlines the interactions with functional impact in the current biomaterial. We developed CrossHub software, which enables two-way identification of most possible TF-gene interactions: on the basis of ENCODE ChIP-Seq binding evidence or Jaspar prediction and co-expression according to the data of The Cancer Genome Atlas (TCGA) project, the largest cancer omics resource.

GMDP: unusual physico-chemical and biological properties of the anomeriс forms.

Disaccharide containing unit of peptidoglycan from bacterial cell wall, N-acetyl-d-glucosaminyl-N-acetylmuramyl-l-alanyl-d-glutaminamide (gluсosaminyl-muramyl-dipeptide) registered in Russia as an immunomodulatory drug, is shown to participate in slow equilibrium of α and β anomeric forms. Data of NMR spectra and molecular dynamics indicate that the α-anomer predominantly acquires a folded conformation stabilized by intramolecular hydrogen bond between the alanyl carbonyl and muramyl NH proton. The β-form displays a considerable fraction of extended, non-hydrogen bonded structures.

Low doses of mercuric chloride cause the main features of anti-nucleolar autoimmunity in female outbred CFW mice.

The growth of the influence of anthropogenic factors aimed on the improvement of human life has its side effect, for example, living organisms receive increasing exposure to toxic mercuric compounds. Experimental data show that mercury (Hg) salts are able to induce systemic autoimmunity in rodents. This Hg-induced autoimmune process (HgIA) is characterized by T cell-dependent polyclonal activation of B lymphocytes, increased level of serum immunoglobulin G1 (IgG1) and immunoglobulin E (IgE), production of antinucleolar autoantibodies (ANoA), and immune complex deposition in multiple organs.