Protein and Peptide Letters - Volume 21, Issue 6, 2014

Cellular protein degradation systems are necessary to avoid the accumulation of misfolded or damaged proteins. Deficiency in these systems might cause to partial degradation of misfolded proteins and generation of amyloidogenic fragments. Protein misfolding is believed to be the primary cause of neurodegenerative disorders such as Alzheimer’s disease (AD). In this study, we investigate effect of two anionic peptide fragments including, an acidic fragment of human Aβ (Aβ1–11) and a phosphorylated fragment of β-Casein (Tetraphosphopeptide), on tau protein aggregation. According to our results, these peptide fragments, induced tau fibrillization in vitro. In sum, we suggest that structural and conformational characters of inducer are as important as charge distribution on anionic inducer molecules however more experiments would be need to exactly confirm this suggestion.

Energy homeostasis is regulated by endocrine factors. The concentration of relaxin-3 in serum is related to body mass index. However, relaxin-3 is found only in the brain and testis. In this study, we examined the expression of relaxin- 3 in adipose tissue and its effects on adipogenesis. The expression of relaxin-3 was determined using RT-PCR, a relaxin- 3 C-peptide-specific radioimmunoassay, specifically in the stromal-vascular fraction (SVF) cells rather than adipocytes. The release of C-peptide was regulated by glucose concentration in the SVF cells. However, the differentiated adipocytes did not express relaxin-3. In glucose perfusion experiments, C-peptide was released in response to high glucose concentrations in the mesenteric perfusate, opposite to insulin release. Additionally, GPCR135 mRNA was expressed in adipocytes. Relaxin-3 increased triglycerides in adipocytes and decreased lipase activity. The present study showed that relaxin-3 is secreted from SVF cells and that it regulates lipid accumulation in adipocytes.

Azoreductase enzymes present in many microorganisms exhibit the ability to reduce azo dyes, an abundant industrial pollutant, to produce carcinogenic metabolites that threaten human health. All biochemically-characterized azoreductases, around 30 to date, have been isolated from aerobic bacteria, except for AzoC, the azoreductase of Clostridium perfringens, which is from a strictly anaerobic bacterium. AzoC is a recently biochemically-characterized azoreductase. The lack of structural information on AzoC hinders the mechanistic understanding of this enzyme. In this paper, we report on the biophysical characterization of the structure and thermal stability of AzoC by using a wide range of biophysical tools: Liquid Chromatography-Mass Spectrometry (LC-MS), Circular Dichroism Spectroscopy, Fouriertransform Infrared (FTIR) Spectroscopy, SDS-PAGE, Size Exclusion Chromatography, MALDI-TOF and UV-visible spectroscopy. We found that the flavin cofactor of AzoC is FAD, while all other structurally-known azoreductases employ FMN as a cofactor. The secondary structure of AzoC has 16% less α-helix structures, 5% more β-sheet structures and 11% more turn and unordered than the average of structurally-known azoreductase that have 10-14% sequence similarities with AzoC. We also found that oxidized AzoC is trimeric, which is unique amongst structurally known azoreductases. In contrast, reduced AzoC is monomeric, despite similarities in catalytic activity and thermal stability of oxidized and reduced AzoC. Our results show that the use of FTIR spectroscopy is crucial for characterization of the β-sheet content in AzoC, illustrating the need for complementary biophysical tools for secondary structural characterization of proteins.

The enzymatic activity of leucine aminopeptidase (EC 3.4.11.1) from the intestinal tract of sugarcane giant borer (Telchin licus licus) was assayed by using a simple and sensitive spectrophotometric assay that uses L-leucyl-2- naphthylamide as substrate. In this assay, L-leucyl-2-naphthylamide is hydrolyzed to produce 2-naphthylamine and Lleucine. The product 2-naphthylamine reacts with Fast Black K and can be monitored using a continuous spectrophotometric measurement at 590 nm. The data on the kinetic parameters indicates that the Km for the L-leucyl-2- naphthylamide at pH 7.0 was found to be lower than those found for other LAP substrates. The Km and Vmax for the LAP were determined to be 84.03 µM and 357.14 enzymatic units mg-1, respectively. A noticeable difference of LAP activity between the two insect orders tested was observed. This method could be used to screen for natural LAP inhibitors.

Antagonists of AT1 receptor are interesting substances to develop drugs that can be used for the treatment of hypertension and other diseases that affect the cardiovascular system. This study investigates the main interactions between various AT1 antagonists and the biological target by applying fragment-based drug design (Hologram QSAR - HQSAR). The proposed HQSAR model yielded significant correlation coefficients (q2 = 0.764 and r2 = 0.914), indicating that the method is rigorous and reliable. All models were externally validated using a test set and the results showed good agreement between the experimental and predicted data (r2 test = 0.740). Therefore, our model can positively contribute to understand the structural features involved in the main interactions between the AT1 antagonists and the residues of the binding site.

TD1, a peptide chaperone consisting of the sequence ACSSSPHKHCG, has been shown to facilitate transdermal delivery for protein molecules via either co-administration or the fusion approach. We previously reported that a single TD1 motif, fused to the N-terminus of human epidermal growth factor (hEGF) can significantly enhance the transdermal efficiency of the recombinant EGF protein. In an effort to further increase the transdermal efficiency, we have created EGF fusion proteins harboring dual TD1 motifs: TD1-hEGF-TD1, containing one TD1 motif at both the N- and the Cterminus, and TD1-TD1-hEGF, containing two tandem TD1 motifs at the N-terminus. Both TD1-hEGF-TD1 and TD1- TD1-hEGF proteins, expressed in Escherichia coli and purified to apparent homogeneity, exhibited biological activity similar to unmodified hEGF, as revealed by their relative abilities to stimulate fibroblast growth, promote fibroblast migration, and activate the MAP kinase signaling cascade. On the other hand, both TD1-hEGF-TD1 and TD1-TD1-hEGF proteins exhibited a transdermal efficiency enhancement. The improvement was >5-fold compared to unmodified hEGF and 3-fold over the hEGF fusion protein with only one TD1 motif attached. These findings provided proof-of-concept for improving transdermal delivery of protein actives through rational protein design.

Due to the vital role in many cell regulatory processes, such as cell cycle control, survival and apoptosis, as well as growth and neurotransmitter signaling, Src homology 2 (SH2) domain-containing phosphatase 2(Shp2) has attracted considerable attention for developing drugs to treat cancers. In this study, by means of the powerful “core hopping” technique, a novel class of inhibitors was discovered based on the compound II-B08. It was observed by molecular dynamics simulations that these novel inhibitors not only possessed the same function as II-B08 did in inhibiting Shp2, but also had stronger binding to the receptor. It was further validated by the outcomes of their ADME (absorption, distribution, metabolism, and excretion) predictions that the new inhibitors hold high potential to become promising drug candidates for developing novel and powerful drugs for anticancer. Subsequently, in vitro evaluation of promising hits revealed a novel and selective inhibitor of Shp2.

E. coli small heat shock proteins IbpA and IbpB (inclusion body binding proteins A and B) are known to act as holding chaperones on denaturing, aggregate-prone proteins. But, there is no clear understanding about which of the IbpA and IbpB has more holdase activity and how the holdase activity of one was influenced by the presence of the other. This study was conducted to resolve the questions, using some uncommon physical techniques like dynamic light scattering, micro-viscometry and atomic force microscopy in addition to the common techniques of spectrophotometry and spectrofluorimetry. The holdase activity was investigated on the heat-denatured L-lactate dehydrogenase (LDH) of rabbit muscle. LDH was found to be deactivated completely without any aggregation at 52°C and with transient aggregation at 60°C; molecular dynamics simulation also revealed that at 52°C, denaturation occurred only at the active site of LDH. When LDH was allowed to be deactivated in the presence of IbpA, IbpB or (IbpA + IbpB), partial inhibition of i) denaturation at 52°C and ii) aggregation at 60°C were observed. The results further demonstrated that the holdase activity of IbpB was higher than that of IbpA and their combined effect was higher than their individual one.

Fatty acid-binding proteins (FABPs) are extensively expressed in animals, involved in the metabolism of fatty acids. FABPs share a much conserved secondary structure though they have 20% ~ 70% identities at the amino acid level. In addition to the role in lipid metabolism, FABPs are closely associated with cytokine production in immune cells and tumor growth and angiogenesis. Increasing studies are broadening our understanding of biological roles of FABPs beyond lipid trafficking and storage.

Iron superoxide dismutase (Fe-SOD) can eliminate superoxide anion radicals and is widely used in pharmaceuticals, cosmetics and foodstuff. It’s significant to determine the factors that influence Fe-SOD thermostability. Previous studies have focused on the relationship between the structural parameters and thermostability of Fe-SOD while the contribution of water molecules was overlooked. In this study, we examined the relationship between hydration waters and Fe-SOD thermostability. The Voronoi polyhedra method was used to explore the distribution of hydration waters around the Fe-SODs and it was interesting to find that the distribution of hydration waters is related to the B-factor of amino acids, i.e., the flexibility of residues can affect the distribution of waters. Protein-water and water-water hydrogen bonds were examined. We found that the hydrogen bond density in thermophilic Fe-SOD was higher than that in mesophilic Fe- SOD. In addition, larger hydrogen bond networks that involve more waters covered the thermophilic Fe-SOD.

Insulin has many actions within cells many of which are dependent on the cell type. For example, insulin stimulates glucose uptake in adipose tissue and skeletal muscle but not in liver. In liver glucose influx will increase as insulin stimulates the phosphorylation of glucose and eventual storage in the form of glycogen. Insulin also increases glucose oxidation, decreases glucose production, decreases lipolysis, increases protein synthesis and inhibits protein degradation in addition to others. Many actions have been related to insulin binding to its receptor and subsequent phosphorylation cascades, but insulin action on protein degradation has been shown to be linked to insulin degradation, specifically insulin degradation by the insulin-degrading enzyme (IDE). This activity has been shown to be due to an interaction of IDE with the proteasome, which is responsible for degradation of ubiquitin-tagged proteins. Smaller fragments of insulin that are produced by the action of IDE that do not bind to the insulin receptor show a small effect on protein degradation and a modest effect on mitogenesis. These small fragments do however inhibit lipolysis in a similar manner to insulin. If fragments are larger and can bind to the receptor they have been shown to increase glucose oxidation. Studies show that fragments of the insulin molecule have cellular activity, and that the varied actions of insulin are not completely controlled by insulin binding to the insulin receptor, even though the mechanisms may not be mutually exclusive.

About twenty years ago, the search for a peptide mimetic of the crucial 928-amino acid human retinoblastoma tumor suppressor protein (RB) has led to the identification of a potential active site in RB spanning 6 amino acids. Subsequent studies revealed that this hexapeptide needs to be coupled to a cellular internalization sequence in order to be biologically active. The prototype molecule resulting therefrom has been the synthetic 22-amino acid peptide MCR-4 that was proven through several investigations to exert both in vitro and in vivo anti-cancer activity both resembling and going beyond the antiproliferative effects of its template RB. This was followed by the elaboration of a distinct series of MCR peptides designed to also interfere with target structures located on the surface of cells and known to be involved in triggering cell proliferation such as the insulin receptor. For this second generation group, the prototype peptide has been another 22-amino acid peptide coined MCR-14 and equally demonstrated to display in vitro and in vivo anti-tumor effects. Finally, a miniaturization of the structure-function relationships intrinsic to the already small MCR-4 peptide has led to the development of the third generation 17-amino acid peptide MCR-15 which in turn was also shown to inhibit in vitro and in vivo malignant cell reproduction. Given more recent conceptual advances, it is warranted to claim that MCR peptides are likely candidate therapeutics not only for the treatment of neoplasias, but also of viral and bacterial infections, type 2 diabetes as well as hypertension.

Cyclic oligopeptides have been introduced into pharmacological use for uses as diverse as selective release of the clotting factor VIII (von Willebrandt factor) by vasopressin, immune modulation by cyclosporin and antibacterial activity by vancomycin. Even now, 60 years after the first isolation of vancomycin (3,4) and the sequencing of oxytocin (48) these compounds have not lost their important role in clinical use. With regard to pharmacological properties oxytocin (as the peptide identic to the human sequence) and vancomycin (as a nonribosomal bacterial peptide) epitomize the swath of cyclic peptide properties.

DNA sequencing has revealed that Gluconobacter oxydans may contain an incomplete phosphoenolpyruvate: carbohydrate phosphotransferase system (PTS), but the function of individual members of the system remains unknown. Here we demonstrated that the predicted histidine protein HPr, an essential component of PTS, can be phosphorylated by a predicted HPr kinase in G. oxydans, where Ser54 in HPr is the site responsible for such a phosphorylation. The discovery implies that G. oxydans may regulate PTS activity in a way similar to that identified in some Gram-positive bacteria with low GC content.