Identification of low molecular weight proteins isolated by 2-D liquid separations

Proteins with molecular mass (M(r)) <20 kDa are often poorly separated in 2-D sodium dodecyl sulfate polyacrylamide gel electrophoresis. In addition, low-M(r) proteins may not be readily identified using peptide mass fingerprinting (PMF) owing to the small number of peptides generated in tryptic digestion. In this work, we used a 2-D liquid separation method based on chromatofocusing and non-porous silica reversed-phase high-performance liquid chromatography to purify proteins for matrix-assisted laser desorption/ionization time-of-flight mass spectrometric (MALDI-TOFMS) analysis and protein identification. Several proteins were identified using the PMF method where the result was supported using an accurate M(r) value obtained from electrospray ionization TOFMS. However, many proteins were not identified owing to an insufficient number of peptides observed in the MALDI-TOF experiments. The small number of peptides detected in MALDI-TOFMS can result from internal fragmentation, the few arginines in its sequence and incomplete tryptic digestion. MALDI-QTOFMS/MS can be used to identify many of these proteins. The accurate experimental M(r) and pI confirm identification and aid in identifying post-translational modifications such as truncations and acetylations. In some cases, high-quality MS/MS data obtained from the MALDI-QTOF spectrometer overcome preferential cleavages and result in protein identification.     

不同孔径硅胶聚合物键合相对蛋白质分离的影响

介绍了不同孔径的硅胶聚合物键合相的合成，比较了其对蛋白质的分离特性。结果表明，大孔径的硅胶聚合物键合相比表面积小，易于获得生物大了分子的快速分离。     

Fractionation and purification of antioxidant peptides from Chinese sturgeon (Acipenser sinensis) protein hydrolysates prepared using papain and alcalase 2.4L

Protein hydrolysates have the potential to be natural and safer sources of bioactive peptides. In this study, two proteases were used to hydrolyze Chinese sturgeon (Acipenser sinensis) protein, and the hydrolysates were then purified to yield antioxidant peptides. The degree of hydrolysis of 23.56 % and 18.14 % was obtained using papain and alcalase 2.4L, respectivly, and hydrolysates had 96.80 % and 87.24 % total amino acid content, respectivly. The papain hydrolysate (PH) and alcalase 2.4L hydrolysate (AH) showed good antioxidant activity against DPPH^? (IC₅₀ of 3.64 and 3.15 mg/mL) and ABTS^?+ (IC₅₀ of 1.92 and 1.58 mg/mL), respectively. The low-molecular-weight (<1000 Da) fraction of both hydrolysates demonstrated the highest antiradical activity (IC₅₀ of 2.59 and 2.31 mg/mL, DPPH) and (IC₅₀ of 1.54 and 1.36 mg/mL, ABTS), respectively. Nine peptides were separated from both hydrolysates using reverse phase high performance liquid chromatography (RP-HPLC). The IC₅₀ for ABTS^?+ scavenging activity of peptide P5 with valine, glycine and asparagine (MW of 282.13 Da) from PH, and peptide P3 with histidine, glycine and alanine (MW of 302.74 Da) from AH was 0.89 and 0.72 mg/mL, respectively. The fractions and purified peptides obtained from Chinese sturgeon hydrolysates could be utilized as natural antioxidant substitutes in pharmaceuticals and food products.     

Cross-Talk between Overlap Interactions in Biomolecules: A Case Study of the β-Turn Motif

Noncovalent interactions play a pivotal role in regulating protein conformation, stability and dynamics. Among the quantum mechanical (QM) overlap-based noncovalent interactions, n→π* is the best understood with studies ranging from small molecules to β-turns of model proteins such as GB1. However, these investigations do not explore the interplay between multiple overlap interactions in contributing to local structure and stability. In this work, we identify and characterize all noncovalent overlap interactions in the β-turn, an important secondary structural element that facilitates the folding of a polypeptide chain. Invoking a QM framework of natural bond orbitals, we demonstrate the role of several additional interactions such as n→σ* and π→π* that are energetically comparable to or larger than n→π*. We find that these interactions are sensitive to changes in the side chain of the residues in the β-turn of GB1, suggesting that the n→π* may not be the only component in dictating β-turn conformation and stability. Furthermore, a database search of n→σ* and π→π* in the PDB reveals that they are prevalent in most proteins and have significant interaction energies (∼1 kcal/mol). This indicates that all overlap interactions must be taken into account to obtain a comprehensive picture of their contributions to protein structure and energetics. Lastly, based on the extent of QM overlaps and interaction energies, we propose geometric criteria using which these additional interactions can be efficiently tracked in broad database searches.     

Inhomogeneity in Distribution and Conformation of Bovine Serum Albumin in Sol–Gel: A Closer Look with a Near-Infrared Multispectral Imaging Technique

Concentration distributions and conformations of bovine serum albumin (BSA) entrapped in sol–gels were successfully determined for the first time by use of the recently developed NIR multispectral imaging instrument. It was found that BSA molecules were inhomogeneously distributed within the sol–gel matrix, independent of its concentration. At relatively high concentration (366 mg/mL) the encapsulation process does not seem to produce any observable changes in the conformation of BSA. However, when the concentration of BSA was decreased to 220 mg/mL, pronounced changes in the spectra of the protein were observed as a function of (sol–gel reaction) time. The observed inhomogenity might be traced to both a non-uniform concentration distribution of BSA and changes in protein native conformation resulting from interactions between the charged protein and the silicate anions. Results obtained seem to suggest that the protein molecules might adapt themselves to accommodate evolving geometry and sites of the silica network.     

Anti-Inflammatory Effects of Spiramycin in LPS-Activated RAW 264.7 Macrophages

Drug repurposing is a simple concept with a long history, and is a paradigm shift that can significantly reduce the costs and accelerate the process of bringing a new small-molecule drug into clinical practice. We attempted to uncover a new application of spiramycin, an old medication that was classically prescribed for toxoplasmosis and various other soft-tissue infections; specifically, we initiated a study on the anti-inflammatory capacity of spiramycin. For this purpose, we used murine macrophage RAW 264.7 as a model for this experiment and investigated the anti-inflammatory effects of spiramycin by inhibiting the production of pro-inflammatory mediators and cytokines. In the present study, we demonstrated that spiramycin significantly decreased nitric oxide (NO), interleukin (IL)-1β, and IL-6 levels in lipopolysaccharide (LPS)-stimulated RAW 264.7 cells. Spiramycin also inhibited the expression of NO synthase (iNOS), potentially explaining the spiramycin-induced decrease in NO production. In addition, spiramycin inhibited the phosphorylation of mitogen-activated protein kinases (MAPKs); extracellular signal-regulated kinase (ERK) and c-Jun N terminal kinase (JNK) as well as the inactivation and subsequent nuclear translocation of nuclear factor κB (NF-κB). This indicated that spiramycin attenuates macrophages’ secretion of IL-6, IL-1β, and NO, inducing iNOS expression via the inhibition of the NF-κB and MAPK signaling pathways. Finally, we tested the potential application of spiramycin as a topical material by human skin primary irritation tests. It was performed on the normal skin (upper back) of 31 volunteers to determine whether 100 μM and μM of spiramycin had irritation or sensitization potential. In these assays, spiramycin did not induce any adverse reactions. In conclusion, our results demonstrate that spiramycin can effectively attenuate the activation of macrophages, suggesting that spiramycin could be a potential candidate for drug repositioning as a topical anti-inflammatory agent.     

A Novel Strategy for Regulating mRNA’s Degradation via Interfering the AUF1’s Binding to mRNA

The study on the mechanism and kinetics of mRNA degradation provides a new vision for chemical intervention on protein expression. The AU enrichment element (ARE) in mRNA 3′-UTR can be recognized and bound by the ARE binding protein (AU-rich Element factor (AUF1) to recruit RNase for degradation. In the present study, we proposed a novel strategy for expression regulation that interferes with the AUF1-RNA binding. A small-molecule compound, JNJ-7706621, was found to bind AUF1 protein and inhibit mRNA degradation by screening the commercial compound library. We discovered that JNJ-7706621 could inhibit the expression of AUF1 targeted gene IL8, an essential pro-inflammatory factor, by interfering with the mRNA homeostatic state. These studies provide innovative drug design strategies to regulate mRNA homeostasis.     

Essential Oils in Respiratory Mycosis: A Review

Respiratory mycosis is a major health concern, due to the expanding population of immunosuppressed and immunocompromised patients and the increasing resistance to conventional antifungals and their undesired side-effects, thus justifying the development of new therapeutic strategies. Plant metabolites, namely essential oils, represent promising preventive/therapeutic strategies due to their widely reported antifungal potential. However, regarding fungal infections of the respiratory tract, information is disperse and no updated compilation on current knowledge is available. Therefore, the present review aims to gather and systematize relevant information on the antifungal effects of several essential oils and volatile compounds against the main type of respiratory mycosis that impact health care systems. Particular attention is paid to Aspergillus fumigatus, the main pathogen involved in aspergillosis, Candida auris, currently emerging as a major pathogen in certain parts of the world, and Cryptococcus neoformans, one of the main pathogens involved in pulmonary cryptococcosis. Furthermore, the main mechanisms of action underlying essential oils’ antifungal effects and current limitations in clinical translation are presented. Overall, essential oils rich in phenolic compounds seem to be very effective but clinical translation requires more comprehensive in vivo studies and human trials to assess the efficacy and tolerability of these compounds in respiratory mycosis.