Protein and Peptide Letters - Volume 23, Issue 9, 2016

The design and synthesis of modified pentapeptides based on a truncated version of the substrate for KDM4C, a histone lysine demethylase (KDM), and investigation of their inhibitory activity at KDM4C is reported. By modifying the lysine residue corresponding to lysine 9 at histone 3 (H3K9), three different series of peptides were designed and synthesized. One series contained N-acylated H3K9 and two series introduced triazoles in this position via click chemistry to enable facile variation of headgroups. The click reaction is compatible with free amino acids and this was performed on an azido containing deprotected pentapeptide demonstrating a highly facile and convergent synthetic strategy for making substrate-based inhibitors. One of the 14 peptides showed inhibitory activity at KDM4C demonstrating the need for an iron chelator in the pentapeptide series.

The canine metabolic diseases, such as obesity and diabetes, have become a worldwide problem. Fibroblast growth factor 21 (FGF21) is a potent regulator which has many biological functions relative to metabolism regulation. It suggests that FGF21 plays important roles in regulating canine metabolic diseases. To acquire the recombinant canine FGF21 (rcFGF21) in Escherichia coli, the recombinant bacteria were induced by 0.5 mM IPTG for 16 hours at 16 °C, and the rcFGF21 protein was purified by Ni-NTA. 8 mg rcFGF21 was acquired from one liter bacteria. The rcFGF21 protein has specific immunoblot reactivity against anti-FGF21 and anti-His antibody. The in vivo experimental result showed that rcFGF21 can significantly reduce plasma glucose of STZ-induced diabetic mice.

Investigating interactions of designed peptide-based biomaterials with lipid membranes is important for applications in nanobiotechnology. Here the interaction of an ornithine-rich pH-responsive peptide called P11-5 with a model membrane was investigated employing Fourier transform infrared spectroscopy (FTIR). The results showed that in the range of pH 6.0-8.0 the peptide P11-5 shows spectral features which are evidence of the presence of peptides with antiparallel beta-sheet conformation (bands in the range 1625-1615 cm-1), as also spectral features which indicate the existence of random coil conformation (bands in the range 1640-1648 cm-1). Two types of membranes were used, 1,2- dipalmitoyl-sn-3-glycero-phosphocholine (DPPC) membranes with zwitterionic head groups and 1,2-dipalmitoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] (sodium salt) (DPPG) membranes with anionic head groups. It was showed that there was a distinct peptide interaction under different pH values, pH 6.0, 7.0 and 8.0 for each type of lipid membrane with DPPC membrane preventing the peptide self-association even at basic pH, while for DPPG membrane there was a more evident peptide-lipid interaction. FTIR measurements indicate that in the presence of DPPC membrane the peptide was prevented to form beta-sheet aggregates at basic pH, while in the presence of DPPG membranes the self-association behavior of the peptide was more similar to its behavior when in aqueous solution in the absence of lipid membranes. Such results are important for the potential development of novel biomolecular nanostructured materials by the physico-chemical understanding of the peptide-lipid interactions.

Background: It is generally believed that organisms use and accumulate methylamine osmolytes to prevent urea’s damaging effect on protein stability and activity. However, urea-rich cells not only accumulate methylamines but also many other methylated and non-methylated compounds as well. But, so far it is not known whether osmolytes that are not accumulated in urea-rich cells could also confer urea-counteracting properties. Objective: We investigated the behavior of a non-methylamine osmolyte, alanine for its counteracting effect against urea denaturation of a model protein, ribonuclease A (RNase-A). Methods: We have measured structure and thermodynamic parameters (Tm, ΔHm, and ΔGD°) of RNase-A in the presence of alanine, urea and their combination. The results were also compared with the ability of glycine (osmolyte lacking one methyl group when compared with alanine) to counter urea’s effect on protein stability. Results: We observed that alanine but not glycine counteracts urea’s harmful effect on RNase-A stability. Discussion: The results indicated that alanine (in addition to methylamine osmolytes) may serve as an alternate urea-counteractant. Since glycine fails to protect RNase-A from urea’s destabilizing effect, it seems that methylation to glycine might have some evolutionary significance to protect proteins against harmful effects of urea.

The interaction of nickel tetra sulfunated phthalocyanine( NiTSPc) with human serum albumin (HSA), in 20 mM phosphate buffer pH 7.4 was investigated using advanced techniques including fluorescence, synchronous fluorescence, Fourier transform infrared (FT-IR), circular dichroism (CD) spectroscopy and molecular docking. The fluorescence quenching measurements showed a single binding site on HSA for NiTSPc with the binding constant (Kb) value equals to 1.26×106 at 25°C. The results showed that quenching mechanism of HSA by NiTSPc was of dynamic type. The results from FTIR and CD spectroscopies demonstrated that NiTSPc binds to amino acid residues of the main polypeptide chain in protein destroying the hydrogen bonding network. The corresponding thermodynamic parameters were then calculated by analysis of fluorescence data using van’t Hoff plot. These data indicated that driving force for interaction was mainly hydrophobic in nature and the process was entropy driven. The information obtained from CD, FT-IR and synchronous fluorescence spectroscopies revealed that both microenvironment and conformation of HSA was changed. Molecular docking study confirmed the binding mode obtained by experimental data.

Monitoring of multiple sclerosis (MS) requires additional molecular markers. Recently, we used original TCA-precipitation/extraction approach in combination with MALDI TOF/TOF mass-spectrometry and identified earlier unknown 48 kDa form of the unconventional myosin IC isoform b (Myo1C) in blood serum of the MS patients. Further examination of TCA-extracted fraction of blood serum of these patients by means of thin-layer chromatography and HPLC gel-filtration allowed detecting 300-500 Da peptides. MALDI TOF/TOF massspectrometry of these peptides showed that they contain Ser-Pro-Cys amino acid sequence. We discussed potential mechanisms of a release of these peptides that were earlier unknown in blood serum of the MS patients.

In the present study, polyacrylamide gel (PAG) was utilized as bolster material for the immobilization of in-house extracted and partially purified manganese peroxidase (MnP) through an entrapment technique yielding significant MnP immobilization (87.3±3.3 %) and remarkable stability of the enzyme (37.2±2.4 %) after a storage period of two months at 4°C. The immobilization also increased the optimal temperature by 10 °C and provided an alkaline shift of the pH optimum. Moreover, a significant enhancement in the thermo-stability was observed. After an incubation period of 72 h at 50°C, the PAG-entrapped-MnP still exhibited 41.2 % of the initial activity, whereas the free enzyme was completely inactive. Furthermore, PAG-entrapped-MnP showed an excellent recycling efficiency and retained more than 50% of its initial activity after five consecutive reaction cycles. In conclusion, owing to the economic feasibility, carrier-supported MnP may be a promising candidate for various applications in different industrial sectors.

Cell-free translation systems facilitate rapid production of specific proteins and are particularly suited as high-throughput methods for whole-genome protein synthesis. Moreover, these systems do not rely on living cells, thereby allowing the synthesis of unstable or cytotoxic proteins in vitro. In this review, we describe the principles and potential applications of cell-free protein translation systems and the future prospects of proteomics approaches using next-generation sequencing and cell-free expression technologies.

Cell rapidly adapts to the harsh environment under certain conditions such as hypothermia and stress via activity of certain specific cold-shock proteins. Two cold shock proteins, RNA-binding motif protein 3 (RBM3) and coldinducible RNA binding proteins (CIRP), have been unveiled in human cells. RBM3, which is able to regulate their expression at the level of translation by binding to different transcripts, allows the cell to respond rapidly to environmental signals. Additionally, expression of RBM3 is induced under mild to moderate hypothermia, and stress. Stress-response pathways play an essential role in cancer. In different types of cancer, RBM3 is up regulated and correlated with favourable clinic- pathological features. RBM3 plays certain functions such as anti-apoptotic, cell proliferation enhancement, and a proto-oncogene function. Furthermore, Hypothermia-induced neuroprotection up- regulates RBM3 in neuronal cells. In this review, the multifunctional nature of RMB3 is outlined through summarizing the evidences from in vitro and in vivo studies.

Type 2 diabetes mellitus (T2DM) is characterized by abnormalities in carbohydrate, lipoprotein and lipid metabolism, leading to hyperglycemia and several other complications. Insulin is the major hormone regulating these facets by eliciting various biological responses through its receptor. Insulin exerts diverse effects on cells by targeting distinct functions such as gene expression, fatty acid synthesis, glucose transport and receptor translocation. Insulin mediates these effects through signaling pathways utilizing adapter molecules like small Gproteins, lipid and tyrosine kinases. The anomalous cell response in diabetic condition is due to altered expression/function of these molecules. Thiazolidinediones (TZD’s), a class of oral hypoglycemic drugs, have shown to modify these responses, leading to insulin sensitizing effect(s). The TZD’s are not only PPARγ agonists, but substantial insulin sensitizing activity is observed through its direct and indirect targets of the insulin receptor pathway, which contributes to its overall performance. TZD’s alter(s) cell response via downstream players, primarily IRS, Akt/PKB, PKC, GLUT4, MEK, ERK and transcription factor PGC1α. Thus, this review will focus on the alteration(s) of these molecules in various cell types in diabetic condition and their regulation by TZD’s. The physiological changes that occur at the molecular level in T2DM and their modulation by TZD’s will provide insights into the key players involved and the potential drug targets for future drug development. The review further highlights the key markers to be evaluated in screening of any potential anti-diabetic agent, and to standardize therapy for T2DM based upon its modulation of the various signaling pathways.

Scorpions are distributed throughout the world and numerous biological molecules are found in their venom most importantly peptide toxins. These toxins modulate the ion channels either by blocking the pore of the channel or by altering the voltage gating. Molecules which block the pores have been useful in deciphering the structure of the ion channels. Many scorpion toxins have already been used for probing the voltage gated sodium channels and studying their activation and inactivation processes. The specialty of scorpion toxins is to discriminate between vertebrate and invertebrate channels which have led them to applications as pharmacological tools. Most of the scorpion toxin polypeptides were isolated, characterized and were shown to possess vital properties useful in the field of medicine. For instance, they show therapeutic properties such as antimicrobial activity, anticancer activity, used to treat autoimmune diseases and cardiovascular effects. Although the scorpion toxins exhibited good therapeutic effects in vitro and in vivo, no one has reached the market with success up to date. In this mini-review, the scorpion polypeptides, their interactions with ion channels and their uses as therapeutic agents are discussed.