Protein and Peptide Letters - Volume 23, Issue 12, 2016

The endocannabinoid system (ECS) is activated when natural arachidonic acid derivatives (endogenous cannabinoids or endocannabinoids) bind as lipophilic messengers to cannabinoid receptors CB1 and CB2. The ECS comprises many hydrolytic enzymes responsible for the endocannabinoids cleavage. These hydrolases, such as fatty acid amide hydrolase (FAAH) and monoacylglyceride lipase (MAGL), are possible therapeutic targets for the development of new drugs as indirect cannabinoid agonists. Recently, a new family of endocannabinoid modulators was discovered; the lead structure of this family is the nonapeptide hemopressin produced from enzymatic cleavage of the α-chain of hemoglobin and acting as negative allosteric modulator of CB1. Hemopressin shows several physiological effects, e.g., antinociception, hypophagy, and hypotension. However, it is still a matter of debate whether this peptide, isolated from the brain of rats, is a real neuromodulator of the ECS. Recent evidence indicates that hemopressin could be a by-product formed by chemical degradation of a longer peptide RVD-hemopressin during the extraction from the brain homolysate. Indeed, RVD-hemopressin is more active than hemopressin in certain biological tests and may bind to the same subsite as Rimonabant, which is an inverse agonist of CB1 and a μ-opioid receptor antagonist. These findings have stimulated several studies to verify this hypothesis and to evaluate possible therapeutic applications of hemopressin, its peptidic derivatives, and synthetic analogues, opening new perspectives to the development of novel cannabinoid drugs.

For the first time introduced on the Japanese market, bioactive fish hydrolysates are now available all over the world as food supplements, functional food ingredients or nutricosmeceuticals. They are generally produced from low value fish waste, an almost inexhaustible source of raw material, and are sold as high value products, making them economically interesting from a manufacturer’s view point. Most of these products have health or structure/function claims on their packages with different actions like antihypertensive, blood-glucose lowering, anxiolytic, and skin anti-aging activities. Although the different regional legislations all aim to assure consumer safety and prevent misleading of the consumer, the number of legally approved fish hydrolysate containing products drastically differs among different regions. This is because products that have been positively evaluated based on safety and efficacy in one region were found to have not enough evidence for efficacy in another region. These findings call for further international harmonization of the regulation and classification of these products. Moreover, interaction studies of these bioactive products with the normal diet or medicines are generally not performed, keeping the consumer uninformed of the possible risks of combining these products with medicinal products or other food ingredients.

The bacterial protein DnaK promotes folding of newly synthesized polypeptide chains, refolding of misfolded proteins, and protein trafficking. Assisted refolding is especially important under stress conditions induced by antibiotic therapies reducing the desired bactericidal effects. DnaK is supposedly targeted by proline-rich antimicrobial peptides (PrAMPs), but Escherichia coli ΔdnaK mutants and wild type strains are equally susceptible indicating further intracellular targets, such as the 70S ribosome. Crystal structures of PrAMPDnaK- complexes revealed forward and reverse binding modes at the substrate binding domain. Here, we used these ligand-target structures for the first time to rationally optimize peptides using molecular modeling and docking leading to the prediction of four-residue long sequences for improved binding to DnaK. When these sequences were used to replace the original sequence stretch in Onc72, most peptides showed significantly reduced dissociation constants (Kd) determined by fluorescence polarization. In a second approach, the X-ray structures of Api88 and Onc72 bound to DnaK were examined to predict substitutions prone to stronger interactions. Among the 36 peptides obtained from both approaches, six derivatives bound to DnaK with more than 10-fold higher affinities (Kd values in the low micromolar to nanomolar range). Peptides binding stronger to DnaK showed the same minimal inhibitory concentrations against wild type E. coli as the original peptide, but were slightly less active for ΔdnaK mutants. However, one peptide was able to overcome the resistance in an E. coli mutant lacking the SbmA transporter obligatory for the uptake of PrAMPs including Api88 and Onc72. Thus, it´s tempting to speculate that DnaK might be involved in the translocation of PrAMPs into E. coli.

Since camel milk has been attributed with various medicinal properties not found in bovine milk, we are systematically examining the differences between different proteins in bovine and camel milk. The purpose of this study is to investigate the structural differences between the bovine and camel α- lactalbumins. α-Lactalbumin is a highly abundant protein present in the milk of all mammalian species. Here we found several structural differences between bovine and camel α-lactalbumins: camel protein is more stable towards thermal and pHmediated denaturation but less stable towards guanidine hydrochloride-mediated unfolding, aggregates faster and is predicted to be more disordered than bovine α- lactalbumin.

Oncogenes are genes that have the potential to cause cancer. Oncogene research can provide insight into the occurrence and development of cancer, thereby helping to prevent cancer and to design effective treatments. This study proposes a network method called the oncogene prediction method based on shortest path algorithm (OPMSP) for the identification of novel oncogenes in a large protein network built using protein-protein interaction data. Novel putative genes were extracted from the shortest paths connecting any two known oncogenes. Then, they were filtered by a randomization test, and the linkages among them and known oncogenes were measured by protein interaction and sequence data. Thirty-seven new putative oncogenes were identified by this method. The enrichment analysis of the 37 putative oncogenes indicated that they are highly associated with several biological processes related to the initiation, progression and metastasis of tumors. Six of these genes—ESR1, CDK9, SEPT2, HOXA10, LMX1B, and NR2C2—are extensively discussed. Several lines of evidence indicate that they may be novel oncogenes.

Vascular endothelial growth factor receptor 3 (VEGFR3) regulates the growth and differentiation of blood and lymphatic vessels. To determine whether matrix metalloproteinase 14 (MMP14) modulates VEGFR3 expression in the corneal epithelium to influence the avascularity of the cornea, VEGFR3 expression was compared between wild-type and MMP14-deficient (MMP14 Δexon4) corneal epithelial cells. Western blot analysis showed that VEGFR3 protein expression was higher on MMP14 Δexon4 corneal epithelial cells than on wild-type cells, and quantitative RT-PCR analysis showed that VEGFR3 gene expression was highly induced in MMP14 Δexon4 corneal epithelial cells but not in wild-type corneal epithelial cells or wild-type and MMP14 Δexon4 corneal keratocytes. Unlike in epithelial cells, MMP14 Δexon4 keratocytes did not express relatively higher levels of VEGFR3 than wild-type keratocytes. Interestingly, in vitro proteolysis experiments showed that MMP14 does not cleave VEGFR3 in vitro as it does VEGFR1, indicating that other genes may be involved in the modulation of VEGFR3 expression by MMP14. Using proteomic analysis to identify candidate factors, we found that 39 nuclear proteins were differentially expressed between wildtype and MMP14 Δexon4 corneal epithelial cells. These findings suggest that MMP14 may regulate VEGFR3 expression at the transcriptional level on corneal epithelial cells but not on corneal keratocytes.

The biosynthesis of UDP-xylose requires the stepwise oxidation/ decarboxylation of UDP-glucose, which is catalyzed by the enzymes UDPglucuronic acid dehydrogenase (UGD) and UDP-xylose synthase (UXS). UDPxylose biosynthesis is ubiquitous in animals and plants. However, only a few UGD and UXS isoforms of bacterial origin have thus far been biochemically characterized. Sphaerobacter thermophilus DSM 20745 is a bacterium isolated from heated sewage sludge, and therefore can be a valuable source of thermostable enzymes of biotechnological interest. However, no biochemical characterizations of any S. thermophilus enzymes have yet been reported. Herein, we describe the cloning and characterization of putative UGD (StUGD) and UXS (StUXS) isoforms from this organism. HPLC- and plate reader-based activity tests of the recombinantly expressed StUGD and StUXS showed that they are indeed active enzymes. Both StUGD and StUXS showed a temperature optimum of 70°C, and a reasonable thermal stability up to 60°C. No metal ions were required for enzymatic activities. StUGD had a higher pH optimum than StUXS. The simple purification procedures and the thermotolerance of StUGD and StUXS make them valuable biocatalysts for the synthesis of UDP-glucuronic acid and UDP-xylose at elevated temperatures. The biosynthetic potential of StUGD was further exemplified in a coupled enzymatic reaction with an UDP-glucuronosyltransferase, allowing the glucuronylation of the natural model substrate bilirubin.

Acid denaturation of champedak galactose-binding (CGB) lectin was studied in the pH range, 7.0−1.0 using intrinsic fluorescence and ANS fluorescence measurements. The lectin remained stable up to pH 5.0 and showed local disordering in the vicinity of the protein fluorophores within the pH range, 5.0−3.5. Decrease in the pH from pH 3.5 to pH 2.5 led to structural transition, marked by the decrease in the intrinsic fluorescence and increase in the ANS fluorescence signals. This can be ascribed to the dissociation of the tetrameric lectin into monomeric forms. Further decrease in the pH up to pH 1.5 produced another transition, which specified the unfolding of monomers as reflected from the decrease in both intrinsic fluorescence and ANS fluorescence signals. Characterization of the conformational states obtained at pH 7.0, pH 2.5 and pH 1.5 based on intrinsic and ANS fluorescence spectra, gel chromatographic behavior and thermal denaturation confirmed the existence of folded monomeric forms at pH 2.5 and unfolded states at pH 1.5. However, the aciddenatured state of CGB lectin at pH 1.5 retained significant residual structure, as evident from the greater loss of both secondary and tertiary structures in the presence of 6 M guanidine hydrochloride at low pH values. Anion-induced refolding below pH 1.5 was also seen using ANS fluorescence measurements.

Aminotransferases are an important group of enzymes that catalyze the transfer of an amino group of an amino acid into a keto acid. Alanine aminotransferase from Trypanosoma cruzi (TcALAT) was cloned, overexpressed and purified. Far-UV Circular Dichroism (CD), Dynamic Light Scattering (DLS), Analytical Size Exclusion Chromatography (aSEC) and Small Angle X-ray Scattering (SAXS) provide data concerning TcALAT biophysical behavior. CD analysis displayed a typical spectrum of α-β proteins analogously as observed for other alanine aminotransferases. The protein is stable until 40oC and above that temperature starts to denatured. Its temperature of melting is equal to 50oC. DLS, aSEC and SAXS data show that protein is monomeric in solution. All these gather initial information on secondary and quaternary structures of TcALAT.

Cancer cells are characterized by a peculiar pH condition, being the extracellular compartment acidic and the intracellular one neutral or basic, i.e. the opposite of what happens in normal cells. The reversal of the pH contributes to cancer cell proliferation and drug resistance. Among the different enzymes regulating pH gradient, proton transporters Na+/H+ exchangers (NHEs) are considered as suitable targets for drugs that ultimately counteract cancer cell survival. This review will describe the properties of NHEs, focusing on the prototype NHE1 and on the effect of its inhibition on cancer cell metabolism.