Mass Spectrometric and Bio-Computational Binding Strength Analysis of Multiply Charged RNAse S Gas-Phase Complexes Obtained by Electrospray Ionization from Varying In-Solution Equilibrium Conditions

We investigated the influence of a solvent’s composition on the stability of desorbed and multiply charged RNAse S ions by analyzing the non-covalent complex’s gas-phase dissociation processes. RNAse S was dissolved in electrospray ionization-compatible buffers with either increasing organic co-solvent content or different pHs. The direct transition of all the ions and the evaporation of the solvent from all the in-solution components of RNAse S under the respective in-solution conditions by electrospray ionization was followed by a collision-induced dissociation of the surviving non-covalent RNAse S complex ions. Both types of changes of solvent conditions yielded in mass spectrometrically observable differences of the in-solution complexation equilibria. Through quantitative analysis of the dissociation products, i.e., from normalized ion abundances of RNAse S, S-protein, and S-peptide, the apparent kinetic and apparent thermodynamic gas-phase complex properties were deduced. From the experimental data, it is concluded that the stability of RNAse S in the gas phase is independent of its in-solution equilibrium but is sensitive to the complexes’ gas-phase charge states. Bio-computational in-silico studies showed that after desolvation and ionization by electrospray, the remaining binding forces kept the S-peptide and S-protein together in the gas phase predominantly by polar interactions, which indirectly stabilized the in-bulk solution predominating non-polar intermolecular interactions. As polar interactions are sensitive to in-solution protonation, bio-computational results provide an explanation of quantitative experimental data with single amino acid residue resolution.

A Highly Specific DNA Aptamer for RNase H2 from Clostridium difficile

Molecular recognition elements with high specificity are of great importance for the study of molecular interactions, accurate diagnostics, drug design, and personalized medicine. Herein, a highly specific DNA aptamer for RNase H2 from Clostridium difficile (C. difficile) was generated by SELEX and minimized to 40 nucleotides. The aptamer exhibits a dissociation constant (K_d) of 1.8 ± 0.5 nM and an inhibition constant (IC₅₀) of 7.1 ± 0.6 nM for C. difficile RNase H2, both of which are 2 orders of magnitude better for the same enzyme from other control bacteria. The fluorescent version of the aptamer can distinguish C. difficile from several other control bacteria in a cell lysate assay. This work demonstrates that a ubiquitous protein like RNase H2 can still be used as the target for the development of highly specific aptamers and the combination of the protein and the aptamer can achieve the recognition specificity needed for a diagnostic test and drug development.

Quantitative Evaluation of Native Protein Folds and Assemblies by Hydrogen Deuterium Exchange Mass Spectrometry (HDX-MS)

Hydrogen deuterium exchange mass spectrometry (HDX-MS) has significant potential for protein structure initiatives but its relationship with protein conformations is unclear. We report on the efficacy of HDX-MS to distinguish between native and non-native proteins using a popular approach to calculate HDX protection factors (PFs) from protein structures. The ability of HDX-MS to identify native protein conformations is quantified by binary structural classification such that merits of the approach for protein modelling can be quantified and better understood. We show that highly accurate PF calculations are not a prerequisite for HDX-MS simulations that are capable of effectively discriminating between native and non-native protein folds. The simulations can also be performed directly on unique structures facilitating high-throughput evaluation of many alternate conformations. The ability of HDX-MS to classify the conformations of homo-protein assemblies is also investigated. In contrast to protein monomers, we show a significant lack of correspondence between the simulated and experimental HDX-MS data for these systems with a subsequent decrease in the ability of HDX-MS to identify native states. However, we demonstrate surprisingly high diagnostic ability of the simulated data for assemblies in which a significant proportion of the individual chains occupy protein-protein interfaces. We relate this to the number of peptides that can sample alternate subunit orientations and discuss these observations within the larger context of applying HDX-MS to evaluate protein structures. Graphical Abstract.

MCPIP1 contributes to the inflammatory response of UVB-treated keratinocytes

BACKGROUND

Monocyte chemoattractant protein-1-induced protein-1 (MCPIP1), also known as regnase-1, negatively regulates many cellular processes including the cellular response to inflammatory agents, differentiation, viability, and proliferation. It possesses a PilT N-terminus (PIN) domain that is directly involved in regulating the stability of transcripts and miRNAs by recognizing stem loop structures and degrading them by endonucleolytic cleavage.

OBJECTIVE

We investigated the role of MCPIP1 in the response of human primary keratinocytes to UVB stress.

METHODS

Keratinocytes were treated with UVB, siRNA against MCPIP1, pharmacological inhibitors of signaling pathways, or subjected to control treatments. The mRNA and protein levels of MCPIP1 and MCPIP1-dependent changes gene expression were analyzed by quantitative (Q)-RT-PCRs and Western blots. Secretion of TNFα and IL-8 was determined by ELISA.

RESULTS

UVB treatment of keratinocytes induced upregulation of MCPIP1 at the mRNA level after 4-8h and at the protein level after 8-16h. MCPIP1 abundance depended on NF-κB activity. Using an siRNA strategy, we found that diminished MCPIP1 resulted in an up-regulation of transcripts coding for IL-8, TNFα, COX-2, and BCL-2, as well as an enhanced release of IL-8. Moreover, decreased phosphorylation of NF-κB and p38 signaling pathways were observed in addition to a slight up-regulation of ERK1/2 directly after UVB treatment. Twenty-four hours later, decreased phosphorylation was observed only for NF-κB and p38. Furthermore, in MCPIP1-suppressed cells, the levels of pro-apoptotic Puma, the phosphorylated form of p53 and the abundance of its target p21 as well as the activity of caspase 3 decreased, while the level of cyclin D1 increased.

CONCLUSION

MCPIP1 contributes to the UVB response of keratinocytes by altering metabolic and apoptotic processes and the release of inflammatory mediators.

RNase 7 in Cutaneous Defense

RNase 7 belongs to the RNase A superfamily and exhibits a broad spectrum of antimicrobial activity against various microorganisms. RNase 7 is expressed in human skin, and expression in keratinocytes can be induced by cytokines and microbes. These properties suggest that RNase 7 participates in innate cutaneous defense. In this review, we provide an overview about the role of RNase 7 in cutaneous defense with focus on the molecular mechanism of the antimicrobial activity of RNase 7, the regulation of RNase 7 expression, and the role of RNase 7 in skin diseases.

[Cytochemical localization and properties of selected nucleolytic enzymes]

In the article there are shortly outlined studies on cytochemical localization of selected nucleolytic enzymes carried out between 1957-1986 by David Shugar and his coworkers. The histochemical localization of several nucleolytic enzymes in animal and plant tissues was determined by synthesis of specific substrates, alpha-naphthyl esters of 5'- and 3'-nucleotides and their derivatives. In rat tissues phosphodiesterase I was localized in the plasma membrane whereas phosphodiesterase II in the lizosomes, reflecting their physiological roles. The localization of pancreatic type ribonuclease in animal tissues was determined, indicating its role in extracellular digestion. Plant nucleotide pyrophosphatase was localized in several tissues, purified to near homogeneity from potato tubers and its properties and substrate specificity were determined. Application of this enzyme for removal of m7GMP from the "cap" of eukaryotic mRNA allowed to elucidate the role of "cap" in mRNA binding to ribosomes in the process of translation. Furthermore, cyclic nucleotide phosphodiesterase was isolated from potato tubers and its physicochemical properties, oligomeric structure and substrate specificity were elucidated.

Modular structure of HEL protein from Arabidopsis reveals new potential functions for PR-4 proteins

Plants possess an innate immune system enabling them to defend themselves against pathogen attack.The accumulation of newly synthesized pathogenesis related proteins (PRs) is one of the most studied inducible plant defence response. In this paper, we report on the characterization of a class I PR4 vacuolar protein from Arabidopsis, named At HEL. The protein has a modular structure consisting of an N-terminal hevein-like domain(CB-HEL) and a C-terminal domain (CD-HEL) that are posttranslationally processed. Both domains show a strong antifungal activity, but they do not have chitinolitic properties.CD-HEL was found to be endowed with RNase, but not DNase activity. Molecular modeling carried out on both domains revealed that CB-HEL possesses a chitin binding site strictly conserved between hevein-type peptides and that the cavity involved in substrate interaction of CD-HEL do not show any residue substitution with respect to the orthologous wheatwin1 from wheat. Using a fishing for partners approach, CB-HEL was found to interact with a fungal fruiting body lectin. According to literature, we can hypothesize that CB-HEL could cross the pathogen hyphal membrane and that its interaction with a fungal lectin could knock out one of the weapons that the fungus uses.

Constrained Multiple Sequence Alignment Tool Development and Its Application to RNase Family Alignment

In this paper, we design a heuristic algorithm of computing a constrained multiple sequence alignment (CMSA for short) for guaranteeing that the generated alignment satisfies the user-specified constraints that some particular residues should be aligned together. If the number of residues needed to be aligned together is a constant α, then the time-complexity of our CMSA algorithm for aligning K sequences is O(αKn4), where n is the maximum of the lengths of sequences. In addition, we have built up such a CMSA software system and made several experiments on the RNase sequences, which mainly function in catalyzing the degradation of RNA molecules. The resulting alignments illustrate the practicability of our method.

EFFICIENT CONSTRAINED MULTIPLE SEQUENCE ALIGNMENT WITH PERFORMANCE GUARANTEE

The constrained multiple sequence alignment problem is to align a set of sequences of maximum length n subject to a given constrained sequence, which arises from some knowledge of the structure of the sequences. This paper presents new algorithms for this problem, which are more efficient in terms of time and space (memory) than the previous algorithms,15 and with a worst-case guarantee on the quality of the alignment. Saving the space requirement by a quadratic factor is particularly significant as the previous O(n4)-space algorithm has limited application due to its huge memory requirement. Experiments on real data sets confirm that our new algorithms show improvements in both alignment quality and resource requirements.

Label-free quantitation: a new glycoproteomics approach

We demonstrate herein a method for quantifying glycosylation changes on glycoproteins. This novel method uses MS data of characterized glycopeptides to analyze glycosylation profiles, and several quality control tests were done to demonstrate that the method is reproducible, robust, applicable to different types of glycoproteins, and tolerant of instrumental variability during ionization of the analytes. This method is unique in that it is the first label-free quantitative method specifically designed for glycopeptide analysis. It can be used to monitor changes in glycosylation in a glycosylation site-specific manner on a single glycoprotein, or it can be used to quantify glycosylation in a glycoprotein mixture. During mixture analysis, the method can discriminate between changes in glycosylation of a given protein, and changes in the glycoprotein's concentration in the mixture. This method is useful for quantitative analyses in biochemical studies of glycoproteins, where changes in glycosylation composition can be linked to functional differences; it could also be implemented in the pharmaceutical industry, where glycosylation profiles of glycoprotein-based therapeutics must be quantified. Finally, quantification of glycopeptides is an important aspect of glycopeptide-based biomarker discovery, and our quantitative approach could be a valuable asset to this field as well, provided the compositions of the glycopeptides to be quantified are identifiable using other methods.

Deamidated active intermediates in the irreversible acid denaturation of ribonuclease-A

A study has been made on the changes in the enzymatic activity of Ribonuclease-A**-(RNase-A) exposed to highly acidic (pH less than 1) acqueous environment. Irreversible alterations of activity were observed when the protein was exposed to an acidic medium for a long period (20 to 60 h). Even prior to these changes in activity RNase-A was found to form intermediates which had very nearly the same activity as the native protein. The primary process in the acid denaturation of RNase-A was observed to be deamidation of the protein leading to the formation of active chromotographically distinct derivatives. The initial product of deamidation, a monodeamidated derivative, has been isolated by chromatography on Amberlite XE-64. This initial deamidation reaction proceeded with very high specificity. The subsequent deamidation reaction is comparatively slower, so that nearly 50% of the native protein could be converted to this derivative before any subsequent deamidation took place. This monodeamidated derivative has been designated RNase-Aa1. The conversion of RNase-A to RNase-Aa1 was not accompanied by any changes in the primary structure other than the observed deamidation. Apart from the differences in chromatographic and electrophoretic mobilities, RNase-Aa1 was found to have very nearly the same activity and physicochemical properties as the native enzyme. Significance of this specific and faster deamidation of RNase-A in this denaturing medium as well as the biological significance of such deamidation reactions of proteins are discussed.

Kinetic and conformational studies on some partially synthetic ribonuclease S' analogues modified in position 8

Syntheses are described of two S-peptide analogues where the arginyl residue in position 10 has been replaced by ornithine and the phenylalanine in position 8 has been substituted by the unnatural amino acids cyclohexylalanine or p-fluorophenylalanine. In order to regenerate the arginyl residue, which is present in position 10 in the natural sequence, the S-peptide analogues beloning to the [Orn10]-series are transformed into the corresponding guanidinated derivatives by treatment with O-methylisourea. 1epsilon, 7epsilon, 10delta triguan-[Cha8, Orn10]-, 1epsilon, 7epsilon, 10delta-triguan-[pF-Phe8, Orn10]- and 1epsilon, 7epsilon, 10delta-triguan-[Tyr8, Orn10]-S-peptides were prepared. The ability to bind to and activate the S-protein of the synthetic S-peptide analogues, before and after guanidination, was tested by exploring their capacity to generate ribonuclease activity using RNA and C greater than p as substrates. The affinity of the different peptides for the S-protein in the absence of substrate was evaluated by difference spectroscopy.

On the reactivity of carboxyl groups of ribonuclease-A in anhydrous methanol

The esterification of Ribonuclease-A in methanol/0.1 M hydrochloric acid has been studied by measuring the decrease in the number of titratable groups of the protein and estimating the amount of methanol incorporated. Esterification of nearly five of the 11 free carboxyl groups of the protein resulted in almost complete inactivation of the enzyme. The initial products of esterification have been chromatographed on Amberlite columns, and five partially active methyl ester derivatives of Ribonuclease-A have been isolated. The dimethyl ester, the initial product of esterification with reduced catalytic activity, has the carboxyl groups of Glu-49 and Asp-53 modified. Even in the non-aqueous solvent, as in the native structure of the protein in aqueous solution, these carboxyl groups are the fast reacting ones. Subsquently, the esterification reaction appears to proceed preferentially at the C-terminal region of the molecule. Comparison of the reactivities of carboxyl groups of Ribonuclease-A in acidic methanol to that known in aqueous solutions (with carbodiimides) suggests that the structure of Ribonuclease-A in the non-aqueous solvent resembles, at least in part, the structure in aqueous environment.

A new arylating agent, 2-carboxy-4,6-dinitrochlorobenzene. Reaction with model compounds and bovine pancreatic ribonuclease

The reagent 2-carboxy-4,6-dinitrochlorobenzene (CDNCB) reacts with the imino, amino and sulfhydryl groups of model compounds. At pH 8.2, sulfhydryl groups react much faster than do amines. N alpha-Acetylhistidine, N alpha-acetyltyrosine and N alpha-acetyltryptophan do not react. Poly(L-Lysine) and poly(DL-lysine) react about 50 times as fast as does N alpha-acetyllysine. A dichloroanalog, 6-carboxy-2,4-dinitro-1,3-dichlorobenzene, shows stepwise reactivity with amines. With bovine pancreatic ribonuclease, which contains no sulfhydryl, CDNCB reacts preferentially with the epsilon-amino of Lys-41 at 450 times the rate with the epsilon-amino of N alpha-acetyllysine. The preferential reactivity at Lys-41 is discussed in relation to the pK of Ly-41, the cationic character of the active site cleft, and the mechanism of RNAase action on substrates.

Studies on the primary structure of bison pancreatic ribonuclease

Bison pancreatic ribonuclease was isolated by affinity chromatography. Thermolysin and tryptic digestion of denaturated protein, and subtilisin digestion of native protein yielded peptides, which were purified and submitted to amino acid analysis. These peptides, together with partial sequence data obtained by Stewart & Stevenson (16) overlap the entire amino acid sequence of bison ribonuclease. No differences with bovine ribonuclease were found, although there may be differences in state of amidation of some residues.

The primary structure of muskrat pancreatic ribonuclease

Pancreatic ribonuclease from muskrat (Ondatra zibethica) was isolated and its amino acid sequence was determined from tryptic digests of the performic acid-oxidized and the reduced and aminoethylated enzyme. The peptides have been positioned in the sequence by homology with other ribonucleases. This could be done unambiguously for all peptides except Arg-Arg (tentative position 32-33) and Ser-Arg (tentative position 75-76). The amino acid sequences of the peptides were determined by the dansyl-Edman method, with the exception of residues 23-25 and 99-102, which were positioned by homology. The enzyme differs in 38 positions from the enzyme from rat and in 31-42 positions from other mammalian pancreatic ribonucleases, while rat ribonuclease differs at 44-52 positions from the other enzymes. These data point to a common ancestry of the enzymes from muskrat and rat and an increased evolution rate of rat ribonuclease after divergence of the ancestors of both species. Muskrat ribonuclease contains no carbohydrate, although the enzyme possesses a recognition site for carbohydrate attachment in the sequence Asn-Val-Thr (62-64).

Targeted acquisition for real-time NMR spectroscopy

A target-oriented approach for the acquisition of information in biomolecular NMR spectroscopy is being developed. This approach combines concurrent data accumulation, processing, and monitoring of spectral quality. Real-time estimation of parameters allows acquisition to be stopped when results are complete and have a specified precision. The technique is based on multidimensional decomposition, which can process incomplete data. An incremental nonuniform sampling scheme ensures the optimization of resolution sensitivity. To validate this method, 3D HNCO spectra of three biomolecular systems (8 kDa ubiquitin, 22 kDa barstar-barnase complex, and 82 kDa malate synthase G) are processed incrementally at small acquisition time steps. The range of molecular sizes illustrates applicability in both sample- and sensitivity-limited regimes. In each case, the target was to acquire all backbone resonances in the spectra. For the three systems, the targets are achieved after 4.5 min, 1.6 h, and 22 h of acquisition time, respectively. A number of other targets that can be similarly monitored as a function of time are discussed.

The modulator effect of GH on skeletal muscle lysosomal enzymes is dietary protein dependent

OBJECTIVE

The purpose of this work is to determine whether changes in dietary protein level could alter the modulator effect that GH has on the muscle lysosomal system by influencing the hydrolytic activities of cathepsin D, acid RNase and DNase II and the participation of these enzymes in muscle growth.

DESIGN

BALB/c female mice were fed a diet containing 20% (HP) or 12% (MP) protein ad libitum and were treated with either saline (s) or rhGH (GH) (74 ng/g) for 29 days. Body weight and feed intake were recorded daily. At 25, 30, 35, 40, 45 and 50 days of age, five mice from each group were slaughtered and nucleic acids and protein concentrations and cathepsin D, acid RNase and DNase II activities in gastrocnemius muscle were analysed. Correlation coefficients were used to analyse the links between the activity of each enzyme with its substrate.

RESULTS

GH-treatment induced a depletion-recovery response in muscle growth through a compensatory mechanism. Changes in protein content, DNA and RNA concentrations were related to changes in lysosomal enzyme activities. Muscle cathepsin D activity in saline mice fell as the dietary protein concentration increased. GH-treatment reversed this effect by enhancing the proteolytic activity in muscle of well-fed mice and inhibiting it in mice fed a 12% protein diet. This inversion appears to be related to the different mechanism elicited by GH-treatment on skeletal muscle protein growth in each dietary group. An opposite trend was observed in muscle acid nuclease activities. Acid RNase and DNase II increased according to the dietary protein concentration, since a 12% protein diet induced a lower catabolism, especially on muscle DNA of saline mice. In contrast, GH-treatment decreased acid RNase and DNase II activities, but only in mice fed a 20% protein diet, perhaps leading to spare muscle RNA for protein synthesis, as well as to the inhibition of DNA degradation during catch-up growth. A lower dietary protein concentration appeared to reverse the GH protective effect on nucleic acids.

CONCLUSIONS

GH seems to act as a dietary protein-dependent modulator of the skeletal muscle lysosomal enzyme activity. These lysosomal enzymes play a role during muscle growth in GH-treated post-weaning mice by modifying muscle protein and DNA and RNA degradation.

New small-scale cross-axis coil planet centrifuge. Partition efficiency and application to purification of bullfrog ribonuclease

The new small-scale cross-axis coil planet centrifuge (X-axis CPC) previously designed and fabricated in our laboratory has a distinctive feature such that four separation columns of similar weight are mounted symmetrically around the rotary frame to achieve stable balancing of the centrifuge under a high revolution speed. In this column layout, neighboring columns must be rotated in the opposite direction if viewed from the center of the centrifuge to avoid twisting the interconnecting flow tubes. The effect of rotational direction of the columns on the partition efficiency was evaluated with separation of a set of test samples such as cytochrome c, myoglobin, and lysozyme using an aqueous-aqueous polymer phase system composed of 12.5% (w/w) polyethylene glycol (PEG) 1000 and 12.5% (w/w) dibasic potassium phosphate under 1000 rpm of column revolution. A series of experiments was performed using a set of two diagonally located columns (connected in series) each consisting of five coiled layers of 1 mm I.D. with a total capacity of 27.0 mL. Both right- and left-handed coils were tested each under the optimized conditions for choice of mobile phase and direction of the column rotation so that the satisfactory volume of the mobile phase was retained in the column by the aid of Archimedean screw effect. The results of these studies showed that one particular combination of handedness of the coil and direction of the rotation yielded the best peak resolution for each mobile phase. In order to demonstrate the capability of the apparatus, the purification of ribonuclease (RNase) from the extract of bullfrog egg, sialic acid binding lectin (cSBL), was carried out using both organic-aqueous and aqueous-aqueous polymer phase systems. When using the 16.0% (w/w) PEG 1000-6.3% (w/w) dibasic potassium phosphate-6.3% (w/w) monobasic potassium phosphate system, cSBL was successfully separated from other proteins present in the extract while commercial RNase A was eluted at near the solvent front by the lower phase mobile. The cSBL retained its native RNase activity. The overall results demonstrated that the present new small-scale X-axis CPC is useful for the purification of bioactive compounds without loss of their native activities.

Pronase-immobilized enzyme reactor: an approach for automation in glycoprotein analysis by LC/LC-ESI/MSn

An automated analytical approach is proposed for simultaneous characterization of glycan and peptide moieties in pronase-generated glycopeptides. The proposed method is based on the use of a new pronase-immobilized enzyme reactor for the on-line rapid digestion of the target glycoprotein. By coupling the bioreactor to a Hypercarb chromatographic trap column, on-line selective glycopeptide enrichment prior to normal-phase liquid chromatography-mass spectrometry was obtained. A detailed study was carried out for integration and automation of each phase of the proposed analytical procedure. On-line digestion allowed extensive cleavage of the model protein (ribonuclease B), yielding to glycopeptides with peptide moieties up to eight amino acids, carrying the Man5-Man9 N-glycans each, selectively resolved on an Amide-80 column. The use of a linear ion trap instrument resulted in efficient ion capture and led to MS3 acquisition times and spectra quality similar to those for MS2, allowing the unambiguous identification of glycan (MS2) and peptide (MS3) sequences. The proposed procedure reduces the glycoprotein analysis time from approximately 3 days, as in most of the traditional off-line methods, to approximately 1 h.

Intracellular route and mechanism of action of ERB-hRNase, a human anti-ErbB2 anticancer immunoagent

Human anti-ErbB2 immunoRNase with Erbicin fused to HP-RNase (ERB-hRNase) is a fully human immunoRNase made up of human pancreatic RNase fused to a human anti-ErbB2 scFv. It binds selectively with high affinity to ErbB2-positive cells, and specifically inhibits their proliferation, in vitro and in vivo. An investigation of its mechanism of action and its intracellular destination has revealed that ERB-hRNase depends on its RNase activity for cytotoxic action; it reaches the cytosol directly from the endosomal compartment; it is inhibited by the cytosolic RNase inhibitor (cRI), but the levels that ERB-hRNase reaches in the cytosol neutralize cRI, thus inducing cell death by apoptosis.

Electrochemical RNase detection using ferrocenylnaphthalene diimide

To develop a conventional RNase detecting system, an RNA electrode was constructed by the immobilization of poly(A)+RNA from mouse kidney on the glassy carbon electrode. Electrochemical measurement using this RNA electrode in the electrolyte containing ferrocenylnaphthalene diimide (1) was carried out and showed the electrochemical signal depending on the amount of the immobilized RNA. After this electrode was treated with water, the differential pulse voltammetric (DPV) measurement was subsequently conducted in the electrolyte containing 1. When RNase is contained in the water, the electrochemical signal decreased with an increase of the amount of RNase. This is derived from the decreasing amount of RNA on the electrode by RNase. In DPV measurement, the concentration of RNaseA was linear in the range of 10(-10) - 10(-8) M and the amount of RNase in the tap water could be estimated.

Insulin-like growth factor binding protein 5 induces skin fibrosis: A novel murine model for dermal fibrosis

OBJECTIVE

To determine the role of insulin-like growth factor binding protein 5 (IGFBP-5) in the development of skin fibrosis in vivo, by examining the effect of overexpression of IGFBP-5 in mouse skin.

METHODS

Wild-type C57BL/6J mice were injected subcutaneously with replication-deficient serotype 5 adenovirus expressing human IGFBP-3 (Ad3), IGFBP-5 (Ad5), or no complementary DNA (cAd). Mice were killed 3, 8, or 22 days postinjection. The dermal thickness and dermal collagen bundle thickness in skin sections were measured. The deposition of collagen in the extracellular matrix (ECM) was quantified using the Sircol assay. Expression of proliferating cell nuclear antigen (PCNA) and fibronectin, as determined by immunohistochemical analysis, was used to evaluate fibroblast activation, and vimentin and alpha-smooth muscle actin (alpha-SMA) were used to evaluate the fibroblast phenotype.

RESULTS

Adenovirally expressed IGFBP was detected in dermal fibroblasts, endothelial cells, epithelial cells, and muscle bundles in Ad3- and Ad5-injected mice. Increased collagen deposition, denser dermal connective tissue, and increased collagen bundle thickness were observed in IGFBP-5-overexpressing mice. Dermal thickness and collagen bundle thickness were significantly increased in Ad5-injected mice compared with cAd- and Ad3-injected mice. Treatment with Ad5 resulted in a dose-dependent increase in dermal and collagen bundle thickness. Increased deposition of collagen and fibronectin, increased numbers of PCNA-positive fibroblasts, as well as increased numbers of vimentin- and alpha-SMA-double-positive fibroblasts were detected in the dermis of IGFBP-5-overexpressing mouse skin.

CONCLUSION

IGFBP-5 is a key mediator of fibrosis. IGFBP-5 mediates its profibrotic effects through fibroblast activation, increased ECM deposition, and myofibroblastic transformation of dermal fibroblasts. Overexpression of IGFBP-5 provides a novel model for studying the pathogenesis of skin fibrosis in systemic sclerosis.

[Preparation of a concanavalin A immobilized affinity column and its application in the structural analysis of ribonuclease B]

The research on glycoproteomes represents an interesting field in the functional proteomics research. Affinity chromatography and mass spectrometry are powerful techniques that are used for gaining valuable information on glycoproteomes because glycoproteins and their unusual forms resulting from protein glycosylation can be important indicators of several diseases. In this study, the concanavalin A (Con A) immobilized silica packing was prepared and used for the separation of glycoprotein and glycopeptides. A very low, non-specific adsorption on the Con A affinity column was demonstrated by mass recovery of bovine serum albumin at more than 98.5%. The effect of concentration of methyl-alpha-D-mannopyranoside (alpha-Me-D-Man) in the mobile phase and the effect of flow rate on the retention behavior of ribonuclease B (RNase B) were also investigated. The standard glycoprotein RNase B was separated under optimized conditions using 0.2 mol/L alpha-Me-D-Man in the mobile phase at a flow rate of 0.5 mL/min. Meanwhile, the oligosaccharides and glycopeptides were enriched using a Con A column after digestion of the purified RNase B with peptide-N-glycosidase F (PNGase F) and trypsin. The structure of N-linked glycan and the rate and the site of glycosylation of RNase B were determined by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). Glycoproteins and glycopeptides in human serum and digest solution could be separated by this method. The results showed that this method is rapid and sensitive for the purification and characterization of glycoproteins and glycopeptides.

The Complete Amino Acid Sequence of Green Turtle (Chelonia mydas) Egg White Ribonuclease

Egg white ribonuclease was first found in green turtle eggs. This enzyme has been purified by CM-toyopearl cation exchange. Two isoforms (GTRNase-1 and GTRNase-2) were further separated by RP-HPLC, with the same M.W. (13 kDa) and activity. These isoforms carried one amino acid exchange of Ser and Leu at the position 37. The N-terminal sequence, ETRYEKF, was determined for the transblotted protein. Internal sequences were analyzed by protein sequencer and ESI-Q-TOF mass spectrometry for tryptic peptides (Ts). The overlapping sequences were obtained from chymotryptic peptides, CNBr fragments and ISD-MS/MS analysis. The C-terminal Ile was identified by CPase-Y. The established sequence composed of 119 residues with the molecular mass of 12,942.1 Da for GTRNase-1 and 12,967.8 Da for GTRNase-2. The comparison of sequence with known pancreatic RNases, 27 positions including catalytic residues at the position 11 and 114 were conserved. Also basic residues contributed to phosphate binding residues were conserved with the exception of Lys 66. One insertion at the position 14, and 3 deletions at the position-1, between position 64-65, and 110 and 111 were found. Two Cys residues at position 65 and 72 that form a disulfide bond in mammalian RNase were deleted and exchanged. All these difference in the sequence were similar to reptile pancreatic RNase.

In contrast to specific B cells, human basophils are unaffected by the toxic activity of an allergen toxin due to lack of internalization of immunoglobulin E-bound allergen

BACKGROUND

Specific immunotherapy is the only curative therapy for type I allergies and the alarming increase in allergy prevalence emphasizes the need for additional/alternative strategies for curative treatment. Allergen toxins (AT), fusion products of an allergen with an apoptosis inducing cytotoxin, are a new kind of immunotoxin.

OBJECTIVE

AT should allow allergen-specific targeting and elimination of allergy-relevant cells, with B cells being the primary target. An important question is the fate of the effector cells, e.g. mast cells and basophils, which carry allergen-specific IgE: the immunotoxin might even prove to be harmful.

METHODS

We established a reliable in vitro B cell model (using two mouse hybridoma cell lines) for testing specificity and toxicity of P5-ETA', a fusion protein of the major timothy grass pollen allergen Phl p 5b and truncated Pseudomonas Exotoxin A. In a second step, we investigated the impact of the AT on human basophils.

RESULTS

P5-ETA' reliably eliminated Phl p 5-specific cells in the in vitro B cell model, leaving unspecific B cells unharmed. Human basophils of grass pollen allergic donors specifically bound P5-ETA', released IL-4 and up-regulated the activation marker CD203c, but were not subject to the toxic effect because of lack of internalization of IgE-bound allergen.

CONCLUSION

According to our data, basophils are pure effector cells in the context of IgE-bound allergen and not involved in classical antigen presentation.

Spatial and temporal expression of the response regulators ARR22 and ARR24 in Arabidopsis thaliana

ARR22 (At3g04280) is a novel Type A response regulator whose function in Arabidopsis is unknown. RT-PCR analysis has shown that expression of the gene takes place in flowers and developing pods with the tissues accumulating different proportions of splice variants. Spatial analysis of expression, using ARR22::GUS plants as a marker, has revealed that the reporter protein accumulates specifically at the junction between the funiculus and the chalazal tissue. Expression can be up-regulated at this location by wounding the developing seed. A detailed analysis has failed to detect ARR22 expression at any other sites and, to support this assertion, the only evidence for tissue ablation in ARR22::Barnase plants is during seed development, with the consequence that embryo growth is attenuated. Ectopic expression of ARR22, driven by either the CaMV 35S or the pea plastocyanin (PPC) promoters, resulted in the generation of plants exhibiting extremely stunted root and shoot growth. No viable progeny could be isolated from the PPC::ARR22 transgenic lines. An RT-PCR analysis of a recently annotated gene (ARR24-At5g26594), that exhibits 66% amino acid similarity to ARR22, has shown that expression is also predominantly in floral and silique tissues. Examination of ARR24::GUS plants has revealed that the activity of the promoter is primarily restricted to pollen grains indicating that this gene is unlikely to display an overlapping function with ARR22. Analyses of individual KO lines of either ARR22 or ARR24 have failed to identify a mutant phenotype under the growth conditions employed and the double knockout ARR22/ARR24 line is also indistinguishable from wild-type plants. These results are discussed in the light of the proposed role of response regulators in plant growth and development.

[Eosinophil cationic protein as a marker of eosinophil activity]

Eosinophil cationic protein (ECP) is one of the markers released by eosinophils. It suggests that ECP can be a good laboratory measurement for late allergic phase assessment. ECP can be measured in serum, BAL, sputum or nasal lavage. There are many studies that document the use of ECP in such diseases like: bronchial asthma, pollinosis or food allergy, but their results are not uniform.

Ratiometric fluorescence detection of a tag fused protein using the dual-emission artificial molecular probe

We have successfully developed a ratiometric detection system for protein of interest using the complementary recognition pair of the tetra-aspartate peptide tag and the SNARF-appended Zn(ii)-DpaTyr probe.

Genome-wide transcriptional analysis of the phosphate starvation stimulon of Bacillus subtilis

Bacillus subtilis responds to phosphate starvation stress by inducing the PhoP and SigB regulons. While the PhoP regulon provides a specific response to phosphate starvation stress, maximizing the acquisition of phosphate (P(i)) from the environment and reducing the cellular requirement for this essential nutrient, the SigB regulon provides nonspecific resistance to stress by protecting essential cellular components, such as DNA and membranes. We have characterized the phosphate starvation stress response of B. subtilis at a genome-wide level using DNA macroarrays. A combination of outlier and cluster analyses identified putative new members of the PhoP regulon, namely, yfkN (2',3' cyclic nucleotide 2'-phosphodiesterase), yurI (RNase), yjdB (unknown), and vpr (extracellular serine protease). YurI is thought to be responsible for the nonspecific degradation of RNA, while the activity of YfkN on various nucleotide phosphates suggests that it could act on substrates liberated by YurI, which produces 3' or 5' phosphoribonucleotides. The putative new PhoP regulon members are either known or predicted to be secreted and are likely to be important for the recovery of inorganic phosphate from a variety of organic sources of phosphate in the environment.

Degradation of RNA during the autolysis of Saccharomyces cerevisiae produces predominantly ribonucleotides

Autolytic degradation of yeast RNA occurs in many foods and beverages and can impact on the sensory quality of the product, but the resulting complex mixture of nucleotides, nucleosides and nucleobases has not been properly characterised. In this study, yeast autolysis was induced by incubating cell suspensions of Saccharomyces cerevisiae at 30-60 degrees C (pH 7.0), and at pH 4.0-7.0 (40 degrees C) for 10-14 days, and the RNA degradation products formed during the process were determined by reversed-phase HPLC. Up to 95% of cell RNA was degraded, with consequent leakage into the extracellular environment of mainly 3'-, 5'- and 2'-ribonucleotides, and lesser amounts of polynucleotides, ribonucleosides and nucleobases. The rate of RNA degradation and the composition of the breakdown products varied with temperature and pH. RNA degradation was fastest at 50 degrees C (pH 7.0). Autolysis at lower temperatures (30 degrees C and 40 degrees C) and at pH 5.0 and 6.0 favoured the formation of 3'-nucleotides, whereas autolysis at 40 degrees C and 50 degrees C (pH 7.0) favoured 5'- and 2'-nucleotides. The best conditions for the formation of the two flavour-enhancing nucleotides, 5'-AMP and 5'-GMP, were 50 degrees C (pH 7.0) and pH 4.0 (40 degrees C), respectively.

Purification, kinetic and thermodynamic studies of a new ribonuclease from a mutant of Aspergillus niger

Ribonuclease was purified from Aspergillus niger SA-13-20 to homogeneity level by using (NH(4))(2)SO(4) precipitation, DEAE-cellulose anion-exchange chromatography, ultrafiltration and Sephacryl HR-200 chromatography. The molecular weight and isoelectric point of the enzyme was 40.1kDa and 5.3, respectively. The pH- and temperature-dependent kinetic parameters were determined. The RNase showed the strongest affinity with RNA as the substrate, and the highest catalytic efficiency for hydrolysis of the substrate at pH 3.5 and 65 degrees C. It exhibited Michaelis-Menten Kinetics with k(cat) of 118.1s(-1) and K(m) of 57.0 microg ml(-1), respectively. Thermodynamic parameters for catalysis and thermal denaturation were also determined. Activation energy (E(a)) for catalysis of A. niger SA-13-20 RNase was 50.31 kJ mol(-1) and free energy (DeltaG(#)), enthalpy (DeltaH(#)) and entropy (DeltaS(#)) of activation for catalysis of the enzyme at 65 degrees C were 69.76, 47.50 and -65.83 Jmol(-1)K(-1), respectively. Activation energy (E(a,d)) for denaturation of the enzyme was 200.53 kJ mol(-1) and free energy (DeltaG(d)(#)), enthalpy (DeltaH(d)(#)) and entropy (DeltaS(d)(#)) of activation for denaturation of the enzyme at 45 degrees C were 79.18 kJ mol(-1), 197.88 and 373.09 Jmol(-1)K(-1), respectively.

Analysis of non-suspect samples lacking visually identifiable sperm using a Y-STR 10-plex

Y-STRs are valuable in the investigation of sexual assaults in which autosomal STR genotype interpretation is challenging. To detect male DNA from compromised sexual assault evidence, 45 non-suspect samples were differentially extracted and analyzed with 10 Y-STRs. These samples were positive for the presence of human seminal fluid, but were negative for spermatozoa by microscopic examination. Y-STR data were obtained in approximately 86.2% of the epithelial or sperm fractions. On samples yielding incomplete profiles, results were obtained on an average of 5 loci per sample. The inability to obtain results may be due to insufficient amplifiable male DNA, PCR inhibition, or unfounded accusations of sexual assault. This study indicates that it is possible to obtain a male STR profile even in the absence of visually identifiable spermatozoa. Furthermore, Y-STR loci should become components of CODIS if they are to be used in solving non-suspect sexual assaults.

Calmodulin interaction with peptides from G-protein coupled receptors measured with S-Tag labeling

We have developed a quantitative assay of calmodulin (CaM) binding to S-Tag labeled peptides derived from G-protein coupled receptor (GPCR) sequences. CaM binding of peptides derived from the third intracellular loop (i3) of mu opioid receptor (MOR) was confirmed and the CaM-binding motif refined. A MORi3 peptide with a Lys > Ala substitution--shown to reduce CaM-binding of intact MOR--bound fivefold less avidly than the wild-type peptide. Screening peptides derived from i3 loops of other GPCR families confirmed 5HT1A, and identified muscarinic receptor 3, and melanocortin receptor 1, as proteins carrying CaM-binding domains. The use of S-Tag labeling can serve for rapid screening of putative CaM-binding domains in GPCRs.

Protein glycosylation analyzed by normal-phase nano-liquid chromatography--mass spectrometry of glycopeptides

A new method for the mass spectrometric characterization of site-specific protein glycosylation is presented. Glycoprotein samples were subjected to unspecific proteolysis by Pronase, resulting in glycopeptides with peptide moieties of mostly two to eight amino acids. Resulting (glyco-)peptide samples were resolved by nanoscale normal-phase liquid chromatography (LC)-online mass spectrometry (MS). Retention depended on the size of the glycan chain and allowed the separation of identical peptide moieties containing different N-glycan structures. Glycopeptides were analyzed in an ion trap instrument performing repetitive ion isolation/fragmentation cycles. While the MS/MS spectra were dominated by fragmentations of glycosidic linkages, MS(3) spectra exhibited cleavages of the peptide backbone and provided information on the peptide sequence and glycan attachment site. When applied to the model glycoproteins ribonuclease B and horseradish peroxidase (HRP), the method provided detailed insights into protein glycosylation and revealed some new features of site-specific glycosylation of HRP. Application of the method to Dolichos biflorus lectin, which has hitherto not been studied with respect to its glycosylation, identified two glycans attached alternatively to its single glycosylation site. Thus, the presented, unique combination of Pronase digestion of glycoproteins, normal-phase nano-LC, and multistage MS provides a method for the facile characterization of site-specific protein glycosylation.

Labeling ribonuclease S with a 3 nm Au nanoparticle by two-step assembly

We label ribonuclease S with a 3 nm Au nanoparticle (NP) by utilizing its two-piece structure. One portion, S-peptide, is mutated with a unique NP attachment site. NP-peptide self-assembles with the other portion, S-protein, to form an active enzyme. NP mobility decreases with peptide labeling and S-protein association. Surface plasmon shifts support conjugation. Higher S-peptide coverages on the NP surface reduce nonspecific adsorption, while sterically hindering assembly of RNaseS. Thiols displace nonspecific adsorption, maximizing site-specific labeling.

Analysis of the major proteins secreted by the human opportunistic pathogenAspergillus fumigatusunderin vitroconditions

Although secreted proteins of pathogenic microorganisms often represent potential virulence factors, so far only limited information has been available on the proteins secreted by Aspergillus fumigatus. We therefore analysed supernatant proteins after growth in different media. In serum-free cell culture medium A. fumigatus growth was limited and no protein secretion was detectable, whereas distinct protein patterns were detectable after growth in either aspergillus minimal medium (AMM) or the more complex yeast glucose medium (YG). The three major proteins secreted under these conditions were identified as the ribotoxin mitogillin, a chitosanase and the aspergillopepsin i. Mitogillin and chitosanase were secreted in AMM, whereas aspergillopepsin i was especially prominent after growth in YG. When the AMM cultures reached stationary phase, seven additional major proteins were detectable. Two of them were identified as the chitinase chiB1 and a beta(1-3) endoglucanase. Conditioned medium containing mitogillin and chitosanase did not have a detectable cytotoxic effect on A549 and Vero cells. Using recombinant mitogillin and chitosanase we detected anti-chitosanase and antimitogillin antibodies in sera of patients suffering from invasive aspergillosis or aspergilloma, but not in control sera of healthy individuals. This suggests that chitosanase, like mitogillin, is expressed during infection and might therefore be of diagnostic relevance.

Purification and Partial Characterization of an Extracellular Ribonuclease From a Mutant of Aspergillus niger

A new extracellular ribonuclease (RNase) from a mutant of Aspergillus niger, named A. niger SA-13-20 RNase, was purified to homogeneity by (NH4)2SO4 fractionation (50-85%), DEAE-cellulose anion-exchange chromatography, ultrafiltration and Sephacryl HR-200 chromatography. The enzyme was purified up to 54.4-fold with a final yield of 24.5%. There were differences in the molecular weight, pI value and some physico-chemical properties between A. niger SA-13-20 RNase and that from the parent strain. The enzyme is monomeric and its molecular weight and isoelectric point were 40.1 kDa and 5.3, respectively. The N-terminal amino acid sequence of A. niger SA-13-20 RNase was TIDTYSSDSP. The optimum pH, temperature and buffer concentration for the enzymatic reaction were 3.5, 65 degrees C, and 0.175 M, respectively. Metal ions, such as K+, NH4+, Mg2+, and Ca2+ at the concentration of 1.0 mM had a slight activation effect on the enzyme activity and (NH4)2SO4 activated the enzyme significantly. The enzyme was stable at pH lower than 8.5 and was easy to inactivate in strong alkali solution.

Effect of anti-immunoglobulin E on nasal inflammation in patients with seasonal allergic rhinoconjunctivitis

BACKGROUND

Binding of allergens to IgE on mast cells and basophils causes release of inflammatory mediators in nasal secretions.

OBJECTIVE

The combined effect of specific immunotherapy (SIT) and omalizumab, a humanized monoclonal anti-IgE antibody, on release of eosinophilic cationic protein (ECP), tryptase, IL-6, and IL-8 in nasal secretion was evaluated.

METHODS

Two hundred and twenty five children (aged 6-17 years) with a history of seasonal allergic rhinoconjunctivitis induced by birch and grass pollen were randomized into four groups: either birch- or grass-pollen SIT in combination with either anti-IgE or placebo. Complete sets of nasal secretion samples before treatment Visit 1 (V1), during birch- (V2) and grass (V3)-pollen season and after the pollen season (V4) were collected from 53 patients.

RESULTS

A significant reduction in tryptase only was seen in the anti-IgE-treated group at V2 (P<0.05) and V4 (P<0.05) compared with the placebo group. During the pollen season, patients with placebo showed an increase of ECP compared with baseline (V2: +30.3 microg/L; V3: +134.2 microg/L, P< 0.005; V4: +79.0 microg/L, P< 0.05), and stable levels of tryptase, IL-6 and IL-8. Treatment with anti-IgE resulted in stable ECP values and a significant decrease of tryptase compared with V1 (baseline): V2: -80.0 microg/L (P< 0.05); V3: -56.3 microg/L, which persisted after the pollen season with V4: -71.6 microg/L (P< 0.05). After the pollen season, a decrease of IL-6 was observed in both groups (V4 placebo group: -37.5 ng/L; V4 anti-IgE group: -42.9 ng/L, P< 0.01).

CONCLUSION

The combination of SIT and anti-IgE is associated with prevention of nasal ECP increase and decreased tryptase levels in nasal secretions.