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Helicobacter pylori (H. pylori) have a unique ability to survive in extreme acidic environments and to colonize the gastric mucosa. It can cause diverse gastric diseases such as peptic ulcers, chronic gastritis, mucosa-associated lymphoid tissue (MALT) lymphoma, gastric cancer, etc. Based on genomic research of H. pylori, over 1600 genes have been functionally identified so far. However, H. pylori possess some genes that are uncharacterized since: (i) the gene sequences are quite new; (ii) the function of genes have not been characterized in any other bacterial systems; and (iii) sometimes, the protein that is classified into a known protein based on the sequence homology shows some functional ambiguity, which raises questions about the function of the protein produced in H. pylori. Thus, there are still a lot of genes to be biologically or biochemically characterized to understand the whole picture of gene functions in the bacteria. In this regard, knowledge on the 3D structure of a protein, especially unknown or hypothetical protein, is frequently useful to elucidate the structure-function relationship of the uncharacterized gene product. That is, a structural comparison with known proteins provides valuable information to help predict the cellular functions of hypothetical proteins. Here, we show the 3D structures of some hypothetical proteins determined by NMR spectroscopy and X-ray crystallography as a part of the structural genomics of H. pylori. In addition, we show some successful approaches of elucidating the function of unknown proteins based on their structural information. [ABSTRACT FROM AUTHOR]

The article discusses a research that describes the structural analysis of residual dipolar couplings (RDCs) with dipolar waves and delta maps. It states that the measurement enables the phage-induced alignment of membrane proteins. Illustration of measurements of RDCs for three different phage-aligned membrane proteins is presented.

The metal-ligand complexes, [Ru(bpy)(dppz)] (bpy = 2,2′-bipyridine, dppz = dipyrido[3,2-a:2′,3′-c]phenazine) (RuBD) and [Ru(phen)(dppz)] (phen = 1,10-phenanthroline) (RuPD), display favorable photophysical properties including long lifetime, polarized emission, and very little background fluorescence. To check if RuBD and RuPD reflect the overall rotational mobility of small nucleic acid, we measured the intensity and anisotropy decays of RuBD and RuPD when intercalated into tRNA using pBC SK(+) phagemid as a control. We used frequency-domain fluorometry with a blue light-emitting diode (LED) as the modulated light source. We observed shorter lifetimes for tRNA than those for the pBC SK(+) phagemid for both probes, however, RuPD showed much larger decrease in the mean lifetime values (64%). The slow rotational correlation time of RuBD (31.3 ns) and the fast rotational correlation time of RuPD (26.0 ns) reflected the overall rotational mobility of tRNA. In addition, the steady-state anisotropy and time-resolved anisotropy decay data showed a clear difference between tRNA and pBC SK(+) phagemid. This suggests the possibility of a homogeneous assay for identifying target nucleic acids and/or nucleic acid binding proteins. [ABSTRACT FROM AUTHOR]

The HP0062 gene encodes a small acidic protein of 86 amino acids with a theoretical pI of 4.6. The crystal structure of hypothetical protein HP0062 from Helicobacter pylori has been determined at 1.65 Å by molecular-replacement method. The crystallographic asymmetric unit contains dimer, in which HP0062 monomer folds into a helix–hairpin–helix structure. The two protomers are primarily held together by extensive hydrophobic interactions in an antiparallel arrangement, forming a four helix bundle. Aromatic residues located at a or g position in the heptad leucine zipper are not major contributor required for HP0062 dimerization but important for the thermostability of this protein. [ABSTRACT FROM PUBLISHER]

Acyl carrier protein (ACP) is a small acidic protein and its primary structure is highly conserved in various bacterial sources. Despite its small size, it interacts with diverse proteins associated with many biosynthetic pathways. The three-dimensional structure of H. pylori ACP and its structural characteristics were clarified using NMR and CD spectroscopy. H. pylori ACP consists of four helices connected by different sized loops. The helices correspond to residues L3-Q14 (αI), S36-G50 (αII), D56-E60 (αIII), and V65-K76 (αVI). The size of each helix differs slightly from that of homologous ACPs. However, H. pylori ACP showed a distinct pH-dependent conformational characteristic: at neutral pH, it adopts a partially unfolded structure, while it has a tight fold at pH 6. The chemical shift perturbation and 1H-15N steady state NOE analysis at both pH 6 and 7 showed that the local change of structural components occurred mainly around loop II, and this change was reflected by the changes of the residues Ile 54 and Asp 56. Examination of the structure showed that the network of Glu 47, Ile 54, Asn 75, and Lys 76 is very important for the structural stability. The pH-dependent folding process shows a kind of cooperativity, since all the residues involved in the conformational transitions are contiguous and in spatial proximity. [ABSTRACT FROM PUBLISHER]

The versatile synthesis of (-)-6-desmethyl-fluvirucinine A1 was accomplished at a 24% overall yield through a thirteen-step process from a known vinylpiperidine. The key part involved the elaboration of the distal stereocenters and a macrolactam skeleton via conformationally-induced diastereocontrol and the iterative aza-Claisen rearrangements of lactam precursors. [ABSTRACT FROM AUTHOR]

White spot lesions (WSLs) are irreversible damages in orthodontic treatment due to excessive etching or demineralization by microorganisms. In this study, we conducted a mechanical and cell viability test to examine the antibacterial properties of 0.2% and 1% bioactive glass (BAG) and silver-doped and zinc-doped BAGs in a primer and evaluated their clinical applicability to prevent WSLs. The microhardness statistically significantly increased in the adhesive-containing BAG, while the other samples showed no statistically significant difference compared with the control group. The shear bond strength of all samples increased compared with that of the control group. The cell viability of the control and sample groups was similar within 24 h, but decreased slightly over 48 h. All samples showed antibacterial properties. Regarding remineralization property, the group containing 0.2% of the samples showed remineralization properties compared with the control group, but was not statistically significant; further, the group containing 1% of the samples showed a significant difference compared with the control group. Among them, the orthodontic bonding primer containing 1% silver-doped BAG showed the highest remineralization property. The new orthodontic bonding primer used in this study showed an antimicrobial effect, chemical remineralization effect, and WSL prevention as well as clinically applicable properties, both physically and biologically. [ABSTRACT FROM AUTHOR]

Hepatitis C virus (HCV) nonstructural protein 5B (NS5B), an RNA-dependent RNA polymerase (RdRp), is the key enzyme for HCV RNA replication. We previously showed that HCV RdRp is phosphorylated by protein kinase C-related kinase 2 (PRK2). In the present study, we used biochemical and reverse-genetics approaches to demonstrate that HCV NS5B phosphorylation is crucial for viral RNA replication in cell culture. Two-dimensional phosphoamino acid analysis revealed that PRK2 phosphorylates NS5B exclusively at its serine residues in vitro and in vivo. Using in vitro kinase assays and mass spectrometry, we identified two phosphorylation sites, Ser29 and Ser42, in the 1 finger loop region that interacts with the thumb subdomain of NS5B. Colonyforming assays using drug-selectable HCV subgenomic RNA replicons revealed that preventing phosphorylation by Ala substitution at either Ser29 or Ser42 impairs HCV RNA replication. Furthermore, reverse-genetics studies using HCV infectious clones encoding phosphorylation-defective NS5B confirmed the crucial role of these PRK2 phosphorylation sites in viral RNA replication. Molecular-modeling studies predicted that the phosphorylation of NS5B stabilizes the interactions between its 1 loop and thumb subdomain, which are required for the formation of the closed conformation of NS5B known to be important for de novo RNA synthesis. Collectively, our results provide evidence that HCV NS5B phosphorylation has a positive regulatory role in HCV RNA replication. [ABSTRACT FROM AUTHOR]

Matrix metalloproteinases (MMPs) play important roles in normal brain development and synaptic plasticity, although aberrant expression of MMPs leads to brain damage, including blood–brain barrier disruption, inflammation, demyelination, and neuronal cell death. In this article, we report that MMP-8 is upregulated in LPS-stimulated BV2 microglial cells and primary cultured microglia, and treatment of MMP-8 inhibitor (M8I) or MMP-8 short hairpin RNA suppresses proinflammatory molecules, particularly TNF-α secretion. Subsequent experiments showed that MMP-8 exhibits TNF-α–converting enzyme (TACE) activity by cleaving the prodomain of TNF-α (A74/Q75, A76/V77 residues) and, furthermore, that M8I inhibits TACE activity more efficiently than TAPI-0, a general TACE inhibitor. Biochemical analysis of the underlying anti-inflammatory mechanisms of M8I revealed that it inhibits MAPK phosphorylation, NF-κB/AP-1 activity, and reactive oxygen species production. Further support for the proinflammatory role of microglial MMP-8 was obtained from an in vivo animal model of neuroinflammatory disorder. MMP-8 is upregulated in septic conditions, particularly in microglia. Administration of M8I or MMP-8 short hairpin RNA significantly inhibits microglial activation and expression/secretion of TNF-α in brain tissue, serum, and cerebrospinal fluid of LPS-induced septic mice. These results demonstrate that MMP-8 critically mediates microglial activation by modulating TNF-α activity, which may explain neuroinflammation in septic mouse brain. [ABSTRACT FROM AUTHOR]

An NMR method for determining the three-dimensional structures of membrane proteins in proteoliposomes is demonstrated by determining the structure of MerFt, the 60-residue helix-loop-helix integral membrane core of the 81-residue mercury transporter MerF. The method merges elements of oriented sample (OS) solid-state NMR and magic angle spinning (MAS) solid-state NMR techniques to measure orientation restraints relative to a single external axis (the bilayer normal) from individual residues in a uniformly 13C/15N labeled protein in unoriented liquid crystalline phospholipid bilayers. The method relies on the fast (>105 Hz) rotational diffusion of membrane proteins in bilayers to average the static chemical shift anisotropy and heteronuclear dipole-dipole coupling powder patterns to axially symmetric powder patterns with reduced frequency spans. The frequency associated with the parallel edge of such motionally averaged powder patterns is exactly the same as that measured from the single line resonance in the spectrum of a stationary sample that is macroscopically aligned parallel to the direction of the applied magnetic field. All data are collected on unoriented samples undergoing MAS. Averaging of the homonuclear 13C/13C dipolar couplings, by MAS of the sample, enables the use of uniformly 13C/15N labeled proteins, which provides enhanced sensitivity through direct 13C detection as well as the use of multidimensional MAS solid-state NMR methods for resolving and assigning resonances. The unique feature of this method is the measurement of orientation restraints that enable the protein structure and orientation to be determined in unoriented proteoliposomes. [ABSTRACT FROM AUTHOR]

The aim of this study was to investigate the effects of low-level laser (LLL) irradiation on the turnover of fibronectin and collagen type I in periodontal tissue during tooth movement in rats by immunohistochemistry. Thirty male Sprague-Dawley rats aged 15 weeks were assigned to either an experimental group (n = 15) that underwent LLL irradiation during tooth movement, or a control group (n = 15). In the experimental group, the gallium-aluminum-arsenide (Ga-Al-As) diode LLL (wavelength 808 nm; output 96 mW) was used to irradiate three areas on both the palatal side and the labial side of the maxillary incisor. The radiation was administered by the contact method for 10 s at 0.83 J/cm(2) energy dose, once a day for 7 days. Total energy dose over the complete schedule was 34.86 J/cm(2). The animals were killed on days 1, 3, 7, 14 and 21. There was no difference between the two groups in the amount of tooth movement. The immunohistochemistry results showed that the expression of fibronectin and collagen type I in the experimental group had significantly increased from day 1, with a more even distribution than in the control group, and that this difference was maintained until the end of the experiment. These results suggest that LLL irradiation facilitates the reorganization of the connective tissues during tooth movement in rats. [ABSTRACT FROM AUTHOR]

The anuran (frogs and toads) skin is a rich source of antimicrobial peptides that can be developed therapeutically. We searched the skin secretions of Korean Rana esculenta for antimicrobial peptides, and isolated two cationic peptides with antimicrobial activity and little hemolytic activity: a 46-residue peptide of the esculentin-1 family and a 24-residue peptide of the brevinin-1 family. Their sequences showed some differences from the esculentins-1 and brevinins-1 of European Rana esculenta, indicating that sequence diversification of anuran skin antimicrobial peptides can arise from differences in habitat as well as from species differences. The 46-residue peptide named es-culentin-1c had broad antimicrobial activity, while the 24-residue peptide named brevinin-lEd exhibited limited activity. The solution structure of brevinin-1Ed was in good agreement with that of other brevinin-1-like peptides, with an amphipathic a-helix spanning residues 3-20, stabilized in membrane-mimetic environments. The weak bioactivity of brevinin-1Ed was attributable to the unusual presence of an anionic amino acid in the middle of the helical hydrophilic face. This report contributes to world-wide investigations of the structure-activity relationships and evolutional diversification of anuran-skin antimicrobial peptides. [ABSTRACT FROM AUTHOR]

Human immunodeficiency virus type 1 (HIV-1) integrase is an essential enzyme in the life cycle of the virus. It is responsible for catalyzing the insertion of the viral genome into the host cell chromosome. This integrase is an attractive target for the design of a HIV antiviral drug, because integrase has no human counterpart. In order to know the interaction mode of HIV-1 integrase with its inhibitor, we investigated the effect of the inhibitor, baicalein, on the conformation of the HIV-1 integrase catalytic domain [IN-(50- 212/F185K)] using fluorescence and circular dichroism (CD) spectroscopy. We found that baicalein binds to the hydrophobic region of the HIV-1 integrase catalytic core domain. This binding of baicalein induces the conformational change of the enzyme. We also found that the binding ratio of baicalein to the HIV-1 integrase catalytic domain is 2:1. [ABSTRACT FROM AUTHOR]