Historic nucleic acids isolated by Friedrich Miescher contain RNA besides DNA.

One hundred fifty years ago, Friedrich Miescher discovered DNA when he isolated "Nuclein"-as he named it-from nuclei of human pus cells. Miescher recognized his isolate as a new type of molecule equal in importance to proteins. He realised that it is an acid of large molecular weight and high phosphorus content. Subsequently, he discovered Nuclein also in the nuclei of other cell types, realised that it chemically defines the nucleus, and speculated on its role in proliferation, heredity and fertilisation. While now universally recognised as the discoverer of DNA, whether Miescher also discovered RNA has not yet been addressed. To determine whether his isolation also yielded RNA, we first reproduced his historic protocols. Our resulting modern Nuclein contained a significant percentage of RNA. Encouraged by this result, we then analysed a sample of Nuclein isolated by Miescher from salmon sperm. Assuming that the RNA present in this sample had degraded to nucleobases, we tested for the presence of uracil in the historic Nuclein. Detection of significant levels of uracil by LC-UV-MS demonstrates that Miescher isolated both forms of nucleic acid-DNA and RNA-and underlines the fundamental nature of his discovery for the field of molecular genetics.

Bidirectional binding of invariant chain peptides to an MHC class II molecule.

T-cell recognition of peptides bound to MHC class II (MHCII) molecules is a central event in cell-mediated adaptive immunity. The current paradigm holds that prebound class II-associated invariant chain peptides (CLIP) and all subsequent antigens maintain a canonical orientation in the MHCII binding groove. Here we provide evidence for MHCII-bound CLIP inversion. NMR spectroscopy demonstrates that the interconversion from the canonical to the inverse alignment is a dynamic process, and X-ray crystallography shows that conserved MHC residues form a hydrogen bond network with the peptide backbone in both orientations. The natural catalyst HLA-DM accelerates peptide reorientation and the exchange of either canonically or inversely bound CLIP against antigenic peptide. Thus, noncanonical MHC-CLIP displays the hallmarks of a structurally and functionally intact antigen-presenting complex.

HLA-DQ2 and -DQ8 signatures of gluten T cell epitopes in celiac disease.

Celiac disease is associated with HLA-DQ2 and, to a lesser extent, HLA-DQ8. Type 1 diabetes is associated with the same DQ molecules in the opposite order and with possible involvement of trans-encoded DQ heterodimers. T cells that are reactive with gluten peptides deamidated by transglutaminase 2 and invariably restricted by DQ2 or DQ8 can be isolated from celiac lesions. We used intestinal T cells from celiac patients to map DQ2 and DQ8 epitopes within 2 representative gluten proteins, alpha-gliadin AJ133612 and gamma-gliadin M36999. For alpha-gliadin, DQ2- and DQ8-restricted T cells recognized deamidated peptides of 2 separate regions. For gamma-gliadin, DQ2- and DQ8-restricted T cells recognized deamidated peptides of the same region. Some gamma-gliadin peptides were recognized by T cells in the context of DQ2 or DQ8 when bound in exactly the same registers, but with different requirements for deamidation; deamidation at peptide position 4 (P4) was important for DQ2-restricted T cells, whereas deamidation at P1 and/or P9 was important for DQ8-restricted T cells. Peptides combining the DQ2 and DQ8 signatures could be presented by DQ2, DQ8, and trans-encoded DQ heterodimers. Our findings shed light on the basis for the HLA associations in celiac disease and type 1 diabetes.

Heterodimerization of TLR2 with TLR1 or TLR6 expands the ligand spectrum but does not lead to differential signaling.

TLR are primary triggers of the innate immune system by recognizing various microorganisms through conserved pathogen-associated molecular patterns. TLR2 is the receptor for a functional recognition of bacterial lipopeptides (LP) and is up-regulated during various disorders such as chronic obstructive pulmonary disease and sepsis. This receptor is unique in its ability to form heteromers with TLR1 or TLR6 to mediate intracellular signaling. According to the fatty acid pattern as well as the assembling of the polypeptide tail, LP can signal through TLR2 in a TLR1- or TLR6-dependent manner. There are also di- and triacylated LP, which stimulate TLR1-deficient cells and TLR6-deficient cells. In this study, we investigated whether heterodimerization evolutionarily developed to broaden the ligand spectrum or to induce different immune responses. We analyzed the signal transduction pathways activated through the different TLR2 dimers using the three LP, palmitic acid (Pam)octanoic acid (Oct)(2)C-(VPGVG)(4)VPGKG, fibroblast-stimulating LP-1, and Pam(2)C-SK(4). Dominant-negative forms of signaling molecules, immunoblotting of MAPK, as well as microarray analysis indicate that all dimers use the same signaling cascade, leading to an identical pattern of gene activation. We conclude that heterodimerization of TLR2 with TLR1 or TLR6 evolutionarily developed to expand the ligand spectrum to enable the innate immune system to recognize the numerous, different structures of LP present in various pathogens. Thus, although mycoplasma and Gram-positive and Gram-negative bacteria may activate different TLR2 dimers, the development of different signal pathways in response to different LP does not seem to be of vital significance for the innate defense system.

Complementary strategies to elucidate T helper cell epitopes in myasthenia gravis.

CD4(+) T cells specific for the acetylcholine receptor (AChR) are assumed to play an important role in pathogenesis of myasthenia gravis (MG). A large and diverse number of potential T cell epitopes have been reported for different experimental setups aiming at the identification of disease-relevant T cells in MG. Investigating the T cell response to the epsilon subunit of human AChR, we explore complementary in vitro and in vivo approaches (PBMC from MG patients and mice transgenic for HLA-DR3 and human CD4) to address the possibilities and limitations of different strategies for elucidating natural autoimmune T cell epitopes.

Insecticidal activity of 12-epi-hapalindole J isonitrile.

12-epi-Hapalindole J isonitrile (1) and three previously described hapalindoles, 12-epi-hapalindole C isonitrile (2), hapalindole L (3) and 12-epi-hapalindole E isonitrile (4) were isolated and identified as insecticidal alkaloids of the biofilm-forming freshwater cyanobacterium Fischerella ATCC 43239 (Stigonematales). The structures of the purified compounds were elucidated by ESI-FTICR-MS, GC-EI-MS and various 2D NMR experiments. At 26 microM hapalindole 1 killed 100% of the larvae of the dipteran Chironomus riparius within 48h. Insecticidal activities were also found at similar concentration for the hapalindoles 2-4. The bioactivity of hapalindoles demonstrates that cyanobacterial biofilms can be considered as promising sources of insecticidal metabolites which might be useful for the biocontrol of dipterans.

Lipolanthionine peptides act as inhibitors of TLR2-mediated IL-8 secretion. Synthesis and structure-activity relationships.

Lipoproteins from gram-positive and -negative bacteria, mycoplasma, and shorter synthetic lipopeptide analogues activate cells of the innate immune system via the Toll-like receptor TLR2/TLR1 or TLR2/TLR6 heterodimers. For this reason, these compounds constitute highly active adjuvants for vaccines either admixed or covalently linked. The lanthionine scaffold has structural similarity with the S-(2,3-dihydroxypropyl)cysteine core structure of the lipopeptides. Therefore, lanthionine-based lipopeptide amides were synthesized and probed for activity as potential TLR2 agonists or antagonists. A collection of analytically defined lipolanthionine peptide amides exhibited an inhibitory effect of the TLR2-mediated IL-8 secretion when applied in high molar excess to the agonistic synthetic lipopeptide Pam3Cys-Ser-(Lys)4-OH. Structure-activity relationships revealed the influence of the chirality of the two alpha-carbon atoms, the chain lengths of the attached fatty acids and fatty amines, and the oxidation level of the sulfur atom on the inhibitory activity of the lipolanthionine peptide amides.

Characterization of the ribonuclease activity on the skin surface.

The rapid degradation of ribonucleic acids (RNA) by ubiquitous ribonucleases limits the efficacy of new therapies based on RNA molecules. Therefore, our aim was to characterize the natural ribonuclease activities on the skin and in blood plasma i.e. at sites where many drugs in development are applied. On the skin surfaces of Homo sapiens and Mus musculus we observed dominant pyrimidine-specific ribonuclease activity. This activity is not prevented by a cap structure at the 5'-end of messenger RNA (mRNA) and is not primarily of a 5'- or 3'-exonuclease type. Moreover, the ribonuclease activity on the skin or in blood plasma is not inhibited by chemical modifications introduced at the 2'OH group of cytidine or uridine residues. It is, however, inhibited by the ribonuclease inhibitor RNasin although not by the ribonuclease inhibitor SUPERase* In. The application of our findings in the field of medical science may result in an improved efficiency of RNA-based therapies that are currently in development.

Immunocytochemical analysis of rat vagus nerve by antibodies against glycogen phosphorylase isozymes.

Glycogen is an endogenous store of glucose equivalents for energy metabolism in many tissues. The brain contains a significant amount of glycogen the role of which as an energy reserve is currently under debate. Apparently little is known concerning a possible role of glycogen in peripheral nerves. We have demonstrated immunocytochemically the presence of glycogen phosphorylase (GP), a key enzyme in glycogen metabolism, in large and small axons of the rat vagus nerve, but not in Schwann cells. Furthermore, the isozyme-specific antibodies applied detected only the presence of the brain isoform BB of GP, but not the muscle isoform MM. This is in agreement with the occurrence of solely the BB isoform in the few brain and spinal cord neurons that contain GP. In contrast, astroglial cells in brain and spinal cord have previously been shown to contain both isoforms. Since GP isozymes are regulated differentially, the expression of isoform BB may provide hints to possible functions of glycogen in the vagus nerve.

Lipopeptide structure determines TLR2 dependent cell activation level.

Bacterial lipoproteins/peptides are composed of di-O-acylated-S-(2,3-dihydroxypropyl)-cysteinyl residues N-terminally coupled to distinct polypeptides, which can be N-acylated with a third fatty acid. Using a synthetic lipopeptide library we characterized the contribution of the lipid portion to the TLR2 dependent pattern recognition. We found that the two ester bound fatty acid length threshold is beyond eight C atoms because almost no response was elicited by cellular challenge with analogues carrying shorter acyl chains in HEK293 cells expressing recombinant human TLR2. In contrast, the amide bound fatty acid is of lesser importance. While two ester-bound palmitic acids mediate a high stimulatory activity of the respective analogue, a lipopeptide carrying one amide-bound and another ester-bound palmitic acid molecule was inactive. In addition, species specific LP recognition through murine and human TLR2 depended on the length of the two ester bound fatty acid chains. In conclusion, our results indicate the responsibility of both ester bound acyl chains but not of the amide bound fatty acid molecule for the TLR dependent cellular recognition of canonical triacylated LP, as well as a requirement for a minimal acyl chain length. Thus they might support the explanation of specific immuno-stimulatory potentials of different microorganisms and provide a basis for rational design of TLR2 specific adjuvants mediating immune activation to distinct levels.

Peptide inhibitors of G protein-coupled receptor kinases.

G protein-coupled receptor kinases (GRKs) are regulatory enzymes involved in the modulation of seven-transmembrane-helix receptors. In order to develop specific inhibitors for these kinases, we synthesized and investigated peptide inhibitors derived from the sequence of the first intracellular loop of the beta2-adrenergic receptor. Introduction of changes in the sequence and truncation of N- and C-terminal amino acids increased the inhibitory potency by a factor of 40. These inhibitors not only inhibited the prototypical GRK2 but also GRK3 and GRK5. In contrast there was no inhibition of protein kinase C and protein kinase A even at the highest concentration tested. The peptide with the sequence AKFERLQTVTNYFITSE inhibited GRK2 with an IC50 of 0.6 microM, GRK3 with 2.6 microM and GRK5 with 1.6 microM. The peptide inhibitors were non-competitive for receptor and ATP. These findings demonstrate that specific peptides can inhibit GRKs in the submicromolar range and suggest that a further decrease in size is possible without losing the inhibitory potency.

Glycopeptide biosynthesis in Amycolatopsis mediterranei DSM5908: function of a halogenase and a haloperoxidase/perhydrolase.

Glycopeptides are important clinical emergency antibiotics consisting of a glycosylated and chlorinated heptapeptide backbone. The understanding of the biosynthesis is crucial for development of new glycopeptides. With balhimycin as a model system, this work focuses on the investigation of the putative halogenase gene (bhaA) and the putative haloperoxidase/perhydrolase gene (bhp) of the balhimycin biosynthesis gene cluster. An in-frame deletion mutant in the haloperoxidase/perhydrolase gene bhp (OP696) did not produce balhimycin. Feeding experiments revealed that bhp is involved in the biosynthesis of beta-hydroxytyrosine, a precursor of balhimycin. A bhaA in-frame deletion mutant (PH4) accumulated glycosylated but nonchlorinated balhimycin variants. The mutants indicated that only the halogenase BhaA is required for chlorination of balhimycin. Nonglycosylated and/or nonhalogenated metabolites can serve as starting points for combinatorial approaches for novel glycopeptides.

The molecular basis for oat intolerance in patients with celiac disease.

BACKGROUND: Celiac disease is a small intestinal inflammatory disorder characterized by malabsorption, nutrient deficiency, and a range of clinical manifestations. It is caused by an inappropriate immune response to dietary gluten and is treated with a gluten-free diet. Recent feeding studies have indicated oats to be safe for celiac disease patients, and oats are now often included in the celiac disease diet. This study aimed to investigate whether oat intolerance exists in celiac disease and to characterize the cells and processes underlying this intolerance. METHODS AND FINDINGS: We selected for study nine adults with celiac disease who had a history of oats exposure. Four of the patients had clinical symptoms on an oats-containing diet, and three of these four patients had intestinal inflammation typical of celiac disease at the time of oats exposure. We established oats-avenin-specific and -reactive intestinal T-cell lines from these three patients, as well as from two other patients who appeared to tolerate oats. The avenin-reactive T-cell lines recognized avenin peptides in the context of HLA-DQ2. These peptides have sequences rich in proline and glutamine residues closely resembling wheat gluten epitopes. Deamidation (glutamine-->glutamic acid conversion) by tissue transglutaminase was involved in the avenin epitope formation. CONCLUSIONS: We conclude that some celiac disease patients have avenin-reactive mucosal T-cells that can cause mucosal inflammation. Oat intolerance may be a reason for villous atrophy and inflammation in patients with celiac disease who are eating oats but otherwise are adhering to a strict gluten-free diet. Clinical follow-up of celiac disease patients eating oats is advisable.

Coordination Chemistry of the Carboxylate Type Siderophore Rhizoferrin: The Iron(III) Complex and Its Metal Analogs.

Rhizoferrin is a member of a new class of siderophores (microbial iron transport compounds) based on carboxylate and hydroxy donor groups rather than the commonly encountered hydroxamates and catecholates. We have studied the coordination chemistry of rhizoferrin (Rf), as a representative of this group, with Fe(3+), Rh(3+), Cr(3+), Al(3+), Ga(3+), VO(2+), and Cu(2+). The metal complexes have been studied by UV-vis, CD, NMR, and EPR spectroscopies and mass spectrometry. The formation constants for the iron complex have also been measured and yield a log K(LFe) of 25.3. The Rh and Cr rhizoferrin complexes are unusual in that they appear to adopt a chirality about the metal center that is the opposite of the native iron analog. Several of the alternative metal ion complexes are found to have biological activity toward Morganella morganii in a plate type assay.

Aspochalamins A-D and aspochalasin Z produced by the endosymbiotic Fungus Aspergillus niveus LU 9575. II. Structure elucidation.

The structures of new cytochalasan fungal metabolites aspochalamins A-D have been elucidated by ESI-FTICR-MS, NMR spectroscopy, and chiral amino acid analysis. Aspochalamins A-D consist of different aspochalasin skeletons connected at position C-19 to the N terminus of the tripeptidic moiety amide anthranoyl-L-alanine-E-didehydrotryptamide. Furthermore, the structure of a new aspochalasin analog, aspochalasin Z, was derived from its molecular mass and NMR data as 10-isopropyl-14-methyl[11]-cytochalasa-6Z,13E,19E-triene-1,21-dione.

Arylomycins A and B, new biaryl-bridged lipopeptide antibiotics produced by Streptomyces sp. Tü 6075. II. Structure elucidation.

The structures of new lipopeptide antibiotics, arylomycins A and B, were elucidated by a combination of ESI-FTICR-mass spectrometry, NMR spectroscopy, Edman sequencing, and fatty acid and chiral amino acid analyses. The colourless arylomycins A share the peptide sequence of D-N-methylseryl2(D-MeSer2)-D-alanyl3-glycyl4-N-methyl- 4-hydroxyphenylglycyl5(MeHpg5)-L-alanyl6-tyrosine7 cyclised by a [3,3]biaryl bond between MeHpg5 and Tyr7. The yellow arylomycins B differ from arylomycins A by nitro substitution of Tyr7. The N-termini of arylomycins A and B are acylated with saturated C11-C15 fatty acids (fa1) comprising n, iso, and anteiso isomers. Arylomycins A and B represent the first examples of biaryl-bridged lipopeptides.

Small interacting peptides. Part II: Interaction of cyclohexapeptides with immobilised model peptides. Comparison of infrared investigations, principal components analysis and force field calculations.

The interaction of cyclic peptides with surface-bound model peptides was investigated by ATR-FTIR spectroscopy, principal components analysis and force field calculations. Information about the interacting functional COOH, COO-, and NH3+ groups and the peptide backbone was gained through a set of cyclohexapeptides (seven of the type c(X1KX2KX3K) (K = L-lysine) and one of the type c(X1KX2KX3k) (k = D-lysine), which are interacting with L-arginine- or tripeptide-coated Si-ATR crystals. All measurements were performed in aqueous solutions. Spectra evaluation in the range 1800-1500 cm(-1) was done by band and principal components analysis (PCA). Only adsorbed molecules were present in these spectra. The coatings were investigated by ATR-FTIR spectroscopy too in order to characterise their functional groups. Based on this knowledge, the spectra of the interacting partners could be evaluated in relation to cyclohexapeptides and coatings. As a result, it was possible to identify the distinct differences in the bonding behaviour of the various peptides.

Small interacting peptides. Part I. Interaction of cyclohexapeptides with an unspecific SiOH surface: comparison of infrared investigations and force field calculations.

The interaction of cyclohexapeptides c(X(1)(1)K(2)X(2)(3)K(4)X(3)(5)K(6)) in water with hydrolysed silicon surfaces were studied by attenuated total reflection Fourier transform infrared (ATR FTIR) spectroscopy and by force field calculations. The band sequences (1800-1500 cm(-1)) for dissolved and adsorbed cyclohexapeptides were recorded and compared with those obtained after flushing with distilled water in order to eliminate the background signal of the peptides in solution. Band analyses and principal component analyses were carried out for the characteristic peptide vibrations in order to evaluate the spectra. In addition, force field calculations were performed to study the binding energies to the surface and to illustrate the possible structures of the cyclohexapeptides. The positively charged lysine side chains of the cyclohexapeptides interact with the OH groups of the surface, as indicated by band shifts. This also was verified by the force field calculations. The bonding stability increases with the number of interacting sites (lysine side chains and other peptide residues) to the surface. These sites are determined by structure and polarity of the cyclohexapeptides.

Oxoammonium Resins as Metal-Free, Highly Reactive, Versatile Polymeric Oxidation Reagents.

Polymer-supported oxidation of alcohols was conducted very efficiently by employing oxoammonium salts, the reactive intermediates in TEMPO oxidations (TEMPO=2,2,6,6-tetramethylpiperidinoxyl). These highly reactive salts (see scheme; X=Br, Cl) could be prepared and isolated on the polymeric support, and were used for the conversion of single compounds as well as of complex mixtures of alcohols.

FT-IR Mapping-A New Tool for Spatially Resolved Characterization of Polymer-Bound Combinatorial Compound Libraries with IR Microscopy.

In the search for selective receptors, a promising approach is provided by immobilization of cyclopeptides on sensor surfaces (see picture) and subsequent detection of low molecular weight analytes with reflectometric interference spectroscopy (RIfS). Together with combinatorial chemistry, this innovative method offers a great potential for applications as sensors.