Fusion Peptide Interaction with Lipid Bilayer: Modeling with Monte Carlo Simulation and Continuum Electrostatics Calculation

Abstract

Conformation of 20-residue peptide E5, an analog of the fusion peptide of influenza virus hemagglutinin, was explored by Monte-Carlo technique starting with the fully buried in the membrane ideal α-helix. The lipid bilayer (of 30 Å width) together with surrounding water were modeled by the atomic solvation parameters. During the simulation, residues 2–18 of the peptide retained α-helical conformation, and the peptide was found to be partially immersed into the bilayer. In the resulting low-energy conformers, the N-terminus was buried inside the membrane, its position with respect to the bilayer surface (Z_NT) being varied from 2.5 to 7.5 Å, and the orientation of the helical axis relative to the membrane plane (Θ) – from 10 to 35°. The low-energy conformers (below -200kcal/mol) were clustered in the space (Z_NT, Θ) into 4 groups. To select low-energy states of the peptide compatible with NMR data, we calculated pKa values of E5 ionizable groups and compared them with the experimental values. It was shown that the best correlation coefficient (0.87) and rmsd (0.68 in pH units) were obtained for the group of states which is characterized by Θ = 15–19° and Z_NT = 3.5–4.5Å.     

Atomic Force Microscopy Imaging of Double Stranded DNA and RNA

Abstract

A procedure for imaging long DNA and double stranded RNA (dsRNA) molecules using Atomic Force Microscopy (AFM) is described. Stable binding of double stranded DNA molecules to the flat mica surface is achieved by chemical modification of freshly cleaved mica under mild conditions with 3-aminopropyltriethoxy silane. We have obtained striking images of intact lambda DNA, Hind III restriction fragments of lambda DNA and dsRNA from reovirus. These images are stable under repeated scanning and measured contour lengths are accurate to within a few percent. This procedure leads to strong DNA attachment, allowing imaging under water. The widths of the DNA images lie in the range of 20 to 80nm for data obtained in air with commercially available probes. The work demonstrates that AFM is now a routine tool for simple measurements such as a length distribution. Improvement of substrate and sample preparation methods are needed to achieve yet higher resolution.     

Structural analysis of the envelope gp120 V3 loop for some HIV-1 variants circulating in the countries of Eastern Europe

The V3 loop on gp120 from human immunodeficiency virus type 1 (HIV-1) is a focus of many research groups involved in anti-AIDS drug development because this region of the protein is a principal target for neutralizing antibodies and a major determinant for cell tropism and syncytium formation. In this study, the nucleotide sequences of the env gene region coding the V3 loop were determined by DNA sequencing methods for four novel HIV-1 strains that circulate in the countries of Eastern Europe, such as Russia, Belarus, Ukraine, etc. Based on the empirical data obtained, the 3D structures of the V3 loops associated with these viral modifications were generated by computer modeling and then compared to discover similarities in the spatial arrangement of this functionally important site of gp120. Despite the HIV-1 genetic variety, several regions of the V3 loop that contain residues critical for cell tropism were shown to be structurally invariant, which may explain its exceptional role in a co-receptor usage. These data together with those on the biological activity of the V3 individual residues clearly show that these conserved structural motifs of gp120 represent potential HIV-1 weak points most suitable for therapeutic intervention.     

Virulence and pathogenicity of Candida albicans is enhanced in biofilms containing oral bacteria

This study examined the influence of bacteria on the virulence and pathogenicity of candidal biofilms. Mature biofilms (Candida albicans-only, bacteria-only, C. albicans with bacteria) were generated on acrylic and either analysed directly, or used to infect a reconstituted human oral epithelium (RHOE). Analyses included Candida hyphae enumeration and assessment of Candida virulence gene expression. Lactate dehydrogenase (LDH) activity and Candida tissue invasion following biofilm infection of the RHOE were also measured. Candida hyphae were more prevalent (p < 0.05) in acrylic biofilms also containing bacteria, with genes encoding secreted aspartyl-proteinases (SAP4/SAP6) and hyphal-wall protein (HWP1) up-regulated (p < 0.05). Candida adhesin genes (ALS3/EPA1), SAP6 and HWP1 were up-regulated in mixed-species biofilm infections of RHOE. Multi-species infections exhibited higher hyphal proportions (p < 0.05), up-regulation of IL-18, higher LDH activity and tissue invasion. As the presence of bacteria in acrylic biofilms promoted Candida virulence, consideration should be given to the bacterial component when managing denture biofilm associated candidoses.     

Functional and Structural Characterization of Neutralizing Epitopes of Measles Virus Hemagglutinin Protein

Effective vaccination programs have dramatically reduced the number of measles-related deaths globally. Although all the available data suggest that measles eradication is biologically feasible, a structural and biochemical basis for the single serotype nature of measles virus (MV) remains to be provided. The hemagglutinin (H) protein, which binds to two discrete proteinaceous receptors, is the major neutralizing target. Monoclonal antibodies (MAbs) recognizing distinct epitopes on the H protein were characterized using recombinant MVs encoding the H gene from different MV genotypes. The effects of various mutations on neutralization by MAbs and virus fitness were also analyzed, identifying the location of five epitopes on the H protein structure. Our data in the present study demonstrated that the H protein of MV possesses at least two conserved effective neutralizing epitopes. One, which is a previously recognized epitope, is located near the receptor-binding site (RBS), and thus MAbs that recognize this epitope blocked the receptor binding of the H protein, whereas the other epitope is located at the position distant from the RBS. Thus, a MAb that recognizes this epitope did not inhibit the receptor binding of the H protein, rather interfered with the hemagglutinin-fusion (H-F) interaction. This epitope was suggested to play a key role for formation of a higher order of an H-F protein oligomeric structure. Our data also identified one nonconserved effective neutralizing epitope. The epitope has been masked by an N-linked sugar modification in some genotype MV strains. These data would contribute to our understanding of the antigenicity of MV and support the global elimination program of measles.     

Biomineralization of Poorly Crystalline Fe(III) Oxides by Dissimilatory Metal Reducing Bacteria (DMRB)

Dissimilatory metal reducing bacteria (DMRB) catalyze the reduction of Fe(III) to Fe(II) in anoxic soils, sediments, and groundwater. Two-line ferrihydrite is a bioavailable Fe(III) oxide form that is exploited by DMRB as a terminal electron acceptor. A wide variety of biomineralization products result from the interaction of DMRB with 2-line ferrihydrite. Here we describe the state of knowledge on the biotransformation of synthetic 2-line ferrihydrite by laboratory cultures of DMRB using select published data and new experimental results. A facultative DMRB is emphasized ( Shewanella putrefaciens ) upon which most of this work has been performed. Key factors controlling the identity of the secondary mineral suite are evaluated including medium composition, electron donor and acceptor concentrations, ferrihydrite aging/recrystallization status, sorbed ions, and co-associated crystalline Fe(III) oxides. It is shown that crystalline ferric (goethite, hematite, lepidocrocite), ferrous (siderite, vivianite), and mixed valence (magnetite, green rust) iron solids are formed in anoxic, circumneutral DMRB incubations. Some products are well rationalized based on thermodynamic considerations, but others appear to result from kinetic pathways driven by ions that inhibit interfacial electron transfer or the precipitation of select phases. The primary factor controlling the nature of the secondary mineral suite appears to be the Fe(II) supply rate and magnitude, and its surface reaction with the residual oxide and other sorbed ions. The common observation of end-product mineral mixtures that are not at global equilibrium indicates that microenvironments surrounding respiring DMRB cells or the reaction-path trajectory (over Eh-pH space) may influence the identity of the final biomineralization suite.     

Tracing the Origin and Diversification of Dipodoidea (Order: Rodentia): Evidence from Fossil Record and Molecular Phylogeny

Dipodoidea are a diverse rodent group whose earliest known record is from the Middle Eocene. The evolution and diversification of this superfamily have been documented by fossils and comparative morphology, but have not yet been studied from the perspective of molecular phylogeny. This study is the first attempt to reconstruct an extensive phylogeny of Dipodidae and estimate divergence times based on a nuclear gene coding for interphotoreceptor retinoid-binding protein. We found that there is a wide measure of agreement with the fossil record. Each of the three ecological groups of the extant Dipodoidea (sicistines, zapodines, and jerboas) has its distinctive distribution; the distribution patterns have been shaped by the dispersal events. The key events of paleogeographic distribution coincided with major paleoenvironmental events in the Cenozoic. The first important diversification phase occurred during the period from the Oligocene to Early Miocene, when global climate underwent major changes beginning with the Eocene/Oligocene boundary. The second adaptive radiation occurred within jerboas and was associated with the expansion of open habitat starting with the late Middle Miocene. The diversification of jerboas can be correlated with habitat changes in response to global and regional climatic events.     

萨哈林岛舞蛛属一新种记述

记述了采自萨哈林岛1新种,Alopecosa mikhailovi sp.nov.,2♂♂,新种与solivaga种团近似.     

Composition,diversity and distribution of microbenthos across the intertidal zones of Ryazhkov Island (the White Sea)

The composition and distribution of the main unicellular eukaryotic groups (diatom algae, ciliates, dinoflagellates (DF), other phototrophic (PF) and heterotrophic flagellates (HF)) were investigated in sandy sediments at five stations allocated across the tidal sheltered beach of the White Sea. Overall, 75 diatoms, 98 ciliates, 16 DF, 3 PF and 34 HF species were identified; some are new records for the White Sea. Common species for each group are illustrated. Diatoms and ciliates showed high alpha-diversity (species richness per sample), whereas flagellates were characterized by high beta-diversity (species turnover across the intertidal flat). Each group demonstrated its own spatial pattern that was best matched with its own subset of abiotic variables, reflecting group-specific responses to environmental gradients. Species richness increased from the upper intertidal zone seaward for ciliates but decreased for HF, whereas autotrophs showed a relatively uniform pattern with a slight peak at the mid-intertidal zone. Across the littoral zone, all groups showed distinct compositional changes; however, the position of the boundary between “upper” and “lower” intertidal communities varied among groups. Most of the species found at Ryazhkov Island are known from many other regions worldwide, indicating a wide geographic distribution of microbial eukaryotic species.