Investigation of Binding Affinity Between Prokaryotic Proteins (AHU-IHF) and DNAs: Steered Molecular Dynamics Approach

The aim of this work is to investigate the binding affinity between the prokaryotic proteins—AHU-IHF proteins (AHU (AHU2, TR3, and AHU6) and IHF (IHF-WT and IHF-βE44A))—and DNAs (DNA, H′-DNA, and H′44A-DNA) by using the steered molecular dynamics (SMD) simulation and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method. The gained results show that although the fluctuation of the pulling force yielded the change of the pulling work, the higher pulling work of the AHU/DNA complexes in comparison to those of the IHF/DNA complexes is not only dependent on the pulling force but also controlled by the change of the trajectory in SMD simulation process. In this study, the pulling work profile not only described the pulling pathway of the complexes but also reflected the hindered process of DNAs when AHU-IHF proteins come out from the binding pocket of DNAs. Additionally, the binding free energy (estimated by the MM-PBSA method) is more confident in giving a true effect to the experimental results in comparison to the pulling force and the pulling work values. These results have also shown a fact that the AHU/DNA complexes were more stable than the IHF/DNA complexes.     

Stabilization centers and protein stability

The well-balanced stability of protein structures allows large-scale fluctuations, which are indispensable in many biochemical functions, ensures the long-term persistence of the equilibrium structure and it regulates the degradation of proteins to provide amino acids for biosynthesis. This balance is studied in the present work with two sets of proteins by analyzing stabilization centers, defined as certain clusters of residues involved in cooperative long-range interactions. One data set contains 56 proteins, which belong to 16 families of homologous proteins, derived from organisms of various physiological temperatures. The other set is composed of 31 major histocompatibility complex (MHC)–peptide complexes, which represent peptide transporters complexed with peptide ligands that apparently contribute to the stabilization of the MHC proteins themselves. We show here that stabilization centers, which had been identified as special clusters of residues that protect the protein structure, evolved to serve also as regulators of function – related degradation of useless protein as part of protein housekeeping. Received: 25 August 2000 / Accepted: 6 September 2000 / Published online: 21 December 2000     

Proteomics of snake venoms from Elapidae and Viperidae families by multidimensional chromatographic methods

Snake venoms contain a large number of biologically active substances and the venom components are very useful for pharmaceutical applications. Our goal is to separate and identify components of snake venoms in ten snake species from the Elapidae and Viperidae families using multidimensional chromatographic methods. The multidimensional chromatographic methods include reversed-phase high-performance liquid chromatography (RP-HPLC), sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), lab-on-a-chip, two-dimensional electrophoresis (2-DE), and mass spectrometry. The venoms of eight snake species demonstrated major differences in hydrophobicity, molecular weight separations, and 2-DE protein distribution patterns. The 2-DE images showed major differences between families, within each family and even between the same species. Venoms of the Elapidae family showed many basic proteins with a wide range of molecular weights, while venoms of the Viperidae family showed wide ranges of pI and molecular weights, especially for Trimeresurus sp. The multidimensional chromatographic methods revealed specific differences in venom proteins intra-species as well as between species and families. We have isolated and identified proteins that may be unique for each species for further studies in the proteome of snake venoms and their potentially use in the pharmaceutical applications.     

Influence of mobile DNA-protein-DNA bridges on DNA configurations: coarse-grained Monte-Carlo simulations

A large literature exists on modeling the influence of sequence-specific DNA-binding proteins on the shape of the DNA double helix in terms of one or a few fixed constraints. This approach is inadequate for the many proteins that bind DNA sequence independently, and that are present in very large quantities rather than as a few copies, such as the nucleoid proteins in bacterial cells. The influence of such proteins on DNA configurations is better modeled in terms of a great number of mobile constraints on the DNA. Types of constraints that mimic the influence of various known non-specifically DNA binding proteins include DNA bending, wrapping, and bridging. Using Monte-Carlo simulations, we here investigate the influence of (non-interacting) mobile DNA-protein-DNA bridges on the configurations of a 1000 bp piece of linear DNA, for both homogeneous DNA and DNA with an intrinsic planar bend. Results are compared to experimental data on the bacterial nucleoid protein H-NS that forms DNA-protein-DNA bridges. In agreement with data on H-NS, we find very strong positioning of DNA-protein-DNA bridges in the vicinity of planar bends. H-NS binds to DNA very cooperatively, but for non-interacting bridges we only find a moderate DNA-induced clustering. Finally, it has been suggested that H-NS is an important contributor to the extreme condensation of bacterial DNA into a nucleoid structure, but we find only a moderate compaction of DNA coils with increasing numbers of non-interacting bridges. Our results illustrate the importance of quantifying the various effects on DNA configurations that have been proposed for proteins that bind DNA sequence independently.     

HYDROGEN PEROXIDE MEDIATES UV-INDUCED IMPAIRMENT OF ANTIGEN PRESENTATION IN A MURINE EPIDERMAL-DERIVED DENDRITIC CELL LINE

Abstract— Ultraviolet-B (290–320 nm) radiation is known to impair the antigen-presenting cell (APC) function of Langerhans cells (LC), skin-specific members of the dendritic cell (DC) family. We sought to address mechanisms of this effect, focusing on the role played by hydrogen peroxide. For this purpose, we used a newly established murine DC line, XS52, which resembles epidermal LC in several respects. The APC capacity of XS52 cells, using two different CD4* T cell clones as responders, was inhibited significantly (>50%) by exposure to UV radiation (unfiltered FS20 sunlamps) at relatively small fluences (50–100 J/m²). Ultraviolet radiation also inhibited growth factor-dependent proliferation of XS52 cells. On the other hand, cell surface phenotype was relatively well preserved after irradiation; expression levels of B7-1 and B7-2 were reduced slightly, while other molecules ( e.g. Ia, CD54, CD1 la and CD18) were not affected. With respect to the role played by hydrogen peroxide, pretreatment with purified catalase (900 U/mL) prevented UV-induced inhibition of APC function. Short-term exposure to 3 miM H₂0₂ or f-butyl H₂0₂ mimicked UV radiation by inhibiting APC function. Finally, intrinsic catalase activity was substantially lower in XS52 cells compared with Pam 212 keratinocytes. These results indicate that the generation of hydrogen peroxide alone is sufficient to produce some, but not all, of the deleterious effects of UV radiation on DC derived from the skin.     

Discovery of the archaeal chemical link between glycogen (starch) synthase families using a new mass spectrometry assay

Starch and its analogue glycogen are biosynthesized by enzymes that have been classified by sequence similarities into two families that have no significant sequence overlap: the animal/fungal glycogen synthases and the plant/bacterial glycogen (starch) synthases. Recent gene sequence analysis of putative archaea enzymes implicates them as a third family that links the structural and functional features of the other two classes. Herein, we present the first rapid electrospray ionization mass spectrometry-based assay to quantify any carbohydrate-polymerizing activity, the first cloning and recombinant expression as well as verification of the putative function of a glycogen synthase from the hyperthermophilic archaea Pyrococcus furiosus, and the characterization of a variety of glycogen synthases with the new assay. The new assay allowed the determination of Km and Vmax values for the rabbit, yeast, and P. furiosus glycogen synthases. Most surprisingly, unlike the synthases from rabbit or yeast and in contradiction to what would be expected from structural studies of other nucleotide-sugar binding proteins, the synthase from the archaea source accepts both uridine- and adenine-diphosphate activated glucose competitively and with comparable affinities to form a glucose polymer. This loose substrate specificity implicates this protein as the chemical link between the two branches of glycogen synthases that have evolved to accept primarily one or the other nucleotide as well as a good source enzyme for polymer bioengineering efforts.     

Adrenocorticotropic Hormone and Cyclic Adenosine Monophosphate are Involved in the Control of Shark Bioluminescence

Among Etmopteridae and Dalatiidae, luminous species use hormonal control to regulate bioluminescence. Melatonin (MT) triggers light emission and, conversely, alpha melanocyte-stimulating hormone (α-MSH) actively reduces ongoing luminescence. Prolactin (PRL) acts differentially, triggering light emission in Etmopteridae and inhibiting it in Dalatiidae. Interestingly, these hormones are also known as regulators of skin pigment movements in vertebrates. One other hormone, the adrenocorticotropic hormone (ACTH), also members of the skin pigmentation regulators, is here pharmacologically tested on the light emission. Results show that ACTH inhibits luminescence in both families. Moreover, as MT and α-MSH/ACTH receptors are members of the G-protein coupled receptor (GPCR) family, we investigated the effect of hormonal treatments on the cAMP level of photophores through specific cAMP assays. Our results highlight the involvement of ACTH and cAMP in the control of light emission in sharks and suggest a functional similarity between skin pigment migration and luminescence control, this latter being mediated by pigment movements in the light organ-associated iris-like structure cells.     

Influence of Triarylamine and Indoline as Donor on Photovoltaic Performance of Dye-Sensitized Solar Cells Employing Cobalt Redox Shuttle

Two organic dyes XS51 and XS52 derivated from triarylamine and indoline are synthesized for dye-sensitized solar cells (DSCs) employing cobalt and iodine redox shuttles. The effects of dye structure upon the photophysical, electro-chemical characteristics and cell performance are investigated. XS51 with four hexyloxyl groups on triarylamine performs better steric hindrance and an improvement of photovoltage. XS52 provides higher short-circuit photocurrent density due to the strong electron-donating capability of indoline unit. The results from the redox electrolyte on cell performances indicate that the synthesized dyes are more suitable for tris(1,10-phenanthroline)cobalt(II/III) redox couple than I^?/I₃^? redox couple in assembling DSCs. Application of XS52 in the cobalt electrolyte yields a DSC with an overall power conversion efficiency of 6.58% under AM 1.5 (100 mW/cm²) irradiation.     

Intercellular communication: the Drosophila innexin multiprotein family of gap junction proteins

Gap junctions belong to the most conserved cellular structures in multicellular organisms, from Hydra to man. They contain tightly packed clusters of hydrophilic membrane channels connecting the cytoplasms of adjacent cells, thus allowing direct communication of cells and tissues through the diffusion of ions, metabolites, and cyclic nucleotides. Recent evidence suggests that gap junctions are constructed by three different families of four transmembrane proteins: the Connexins and the Innexins found in vertebrates and in invertebrates, respectively, and the Innexin-like Pannexins, which were recently discovered in humans. This article focuses on the Drosophila Innexin multiprotein family, which is comprised of eight members. We highlight common structural features and discuss recent findings that suggest close similarities in cellular distribution, function, and regulation of Drosophila Innexins and vertebrate gap junction proteins.     

Synthesis and Crystal Structure of α-Mo4XS3(μ-dtp)3(dtp)3 (X=0.6S + 0.4O)

The title compound (Mo4XS15P6O12C24H30), α-Mo4XS3(μ-dtp)3(dtp)3 (X=0.6S+0.4O; dtp=-S2P[OEt]2), isolated as a prismatic black crystal, was prepared from ethanolic solution of Mo(CO)6, MoCl5 and P2S5. It crystallizes in triclinic system, space group P with a=14.031(4), b=13.372(2), c=16.270(8)(A), α=92.15(2), β = 72.91(3), γ = 95.20(2)°, V = 2905.4(2)(A)3, Z = 2, Dc = 1.82 g/cm3, Mr=1598.93, F(000)=1564.8, λ=0.71069(A)(MoKα), μ=1.584 mm-1. The final R=0.058, Rw=0.057 for 5016 observed reflections with I≥3.0σ(I). The structure analysis reveals that the title compound has a [Mo4XS3] core, belonging to the cubane-type tetranuclear molybdenum clusters family, with one of its four μ3-caps being statistically occupied by S and O. Three dtp ligands chelated three μ-X capped Mo atoms as terminal ligands, while another three dtp bridged these three Mo atoms and the fourth one, forming an α-type cluster compound.     

Human Blue-light Photoreceptor hCRY2 Specifically Interacts with Protein Serine/Threonine Phosphatase 5 and Modulates Its Activity

Abstract— Photolyase/blue-light photoreceptor family of proteins includes cyclobutane pyrimidine dimer photolyase, (6-4) photolyase and blue-light photoreceptors that were recently discovered in Arabidopsis thaliana, Sinapis alba and Chlamydomonas reinhardtii. Recently, we identified two human genes, hCRYl and hCRY2, belonging to this family. The proteins encoded by these genes have no DNA repair activity and therefore were hypothesized to function in human blue-light response reactions. To identify downstream targets for these putative blue-light photoreceptors we searched for interacting proteins by the yeast two-hybrid method. We found that the tetratricopeptide repeat protein 1, Tpr1, and the protein serine/ threonine phosphatase 5 (PP5) that contains the TPR motif specifically interacted with hCRY2. The effect of the hCRY2-PP5 interaction on the protein phosphatase activity was investigated. We found that hCRY2, but not the highly homologous (6-4) photolyase, inhibits the phosphatase activity of PP5. This inhibition may be on the pathway of blue-light signal transduction reaction in humans.