Structure and conformation on linear peptides. VI. Structure of D,L-alanyl-L,D-norvaline

The dipeptide, (DL)-alanyl-(DL)-norvaline, crystallizes in the monoclinic space group P2(1)/c, with a = 12.559(2)A, b = 5.265(1), c = 16.003(3), beta = 103.53(2) degrees, Z = 4. The structure was solved by direct methods and refined to an R-value of 0.054 for 871 reflections with I greater than 2 sigma. The molecule exists as a zwitterion in the crystal. The peptide unit is trans and shows significant deviations from planarity (delta omega = 12.4 degrees). The peptide backbone adopts an extended conformation. The unit cell contains D-Ala-L-norval and its enantiomer. The molecular conformation and packing features show a striking resemblance to those for D-Ala-L-Met (1), and leads to the speculation that norvaline might act as an analog of methionine.     

Artifactual staining of proteins on polyacrylamide gels by nitrobluetetrazolium chloride and phenazine methosulfate

Different purified proteins were shown to give purple formazan bands corresponding to the protein stain following electrophoresis on polyacrylamide gels, in the presence of nitrobluetetrazolium (NBT) and phenazine methosulfate (PMS). Both PMS and NBT are needed for formazan production which has a favorable pH at 8.5. Sulfhydryl blockers in the incubation medium inhibited this color development to different extents. While proteins with free SH groups like bovine serum albumin, ovalbumin, and urease showed this pyridine nucleotide independent artifact, nonthiol proteins, viz., bovine pancreatic ribonuclease A, and riboflavin-binding protein from chicken egg white failed to do so. The nonenzymatic formazan formation observed with different proteins could also be shown in an in vitro assay system. It is clear that the “nothing dehydrogenase” phenomenon observed in several cases may be due to the thiol group-mediated artifactual staining of proteins.     

Cancer-selective antiproliferative activity is a general property of some G-rich oligodeoxynucleotides

Oligodeoxynucleotide libraries containing randomly incorporated bases are used to generate DNA aptamers by systematic evolution of ligands by exponential enrichment (SELEX). We predicted that combinatorial libraries with alternative base compositions might have innate properties different from the standard library containing equimolar A + C + G + T bases. In particular, we hypothesized that G-rich libraries would contain a higher proportion of quadruplex-forming sequences, which may impart desirable qualities, such as increased nuclease resistance and enhanced cellular uptake. Here, we report on 11 synthetic oligodeoxynucleotide libraries of various base combinations and lengths, with regard to their circular dichroism, stability in serum-containing medium, cellular uptake, protein binding and antiproliferative activity. Unexpectedly, we found that some G-rich libraries (composed of G + T or G + C nucleotides) strongly inhibited cancer cell growth while sparing non-malignant cells. These libraries had spectral features consistent with G-quadruplex formation, were significantly more stable in serum than inactive libraries and showed enhanced cellular uptake. Active libraries generally had strong protein binding, while the pattern of protein binding suggested that G/T and G/C libraries have distinct mechanisms of action. In conclusion, cancer-selective antiproliferative activity may be a general feature of certain G-rich oligodeoxynucleotides and is associated with quadruplex formation, nuclease resistance, efficient cellular uptake and protein binding.     

Antimicrobial activity of metal and non-metallic nanoparticles from Cyperus rotundus root extract on infectious disease causing pathogens

In the present study, gold nanoparticles (CRnp) has been prepared using aqueous extract of Cyperus rotundus root at room temperature, sunlight, sonication, microwave oven heating and hot air oven method. Effect of concentration variation was studied using microwave-assisted synthesis. Grayish pink colour gold nanoparticles were formed within 5 s in microwave-assisted synthesis. Preliminary phytochemical screening showed the presence of alkaloids, protein and phenolic groups. These metabolites may be the responsible for the formation of gold nanoparticles. Reduced graphene oxide (CRrGO) was prepared using refluxing method and nano composite (CRNC) was prepared using equal ratio (1:1) of CRnp and CRrGO under homogenization method. The prepared CRnp, CRrGO and CRNC were characterized by spectroscopic techniques such as UV–visible spectroscopy, FTIR, XRD, Raman spectroscopy and FESEM. Thermal stability analysis of the CRrGO was carried out using TGA. FESEM results revealed the synthesized CRnp to be spherical in nature with average diameter 15 nm. CRrGO showed flake-like structures with few layers which was further confirmed by FESEM and Raman spectroscopy. The FESEM image of CRNC clearly portrays CRnp to be strongly bound to the surface of CRrGO. Anti-bacterial activity of the synthesized CRnp, CRrGO, CRNC and CRa synthesized nanoparticles to be active against gram negative and gram positive bacteria.     

Retention of functional characteristics of glutathione-S-transferase and lactate dehydrogenase-A in fusion protein

A paradigm shift toward fusion proteins to render multiple functionalities and applications on a single platform has been incurred in enzyme based diagnosis. Herein, we report development and systematic characterizations of glutathione-S-transferase (GST) and human lactate dehydrogenase A (hLDHA) in a fusion protein (GST–hLDHA) to achieve functional activities of GST and hLDHA simultaneously. The GST-pGEX-4T-2 vector system was used for cloning and purification of hLDHA, utilizing the affinity based interaction between GST and GSH in column chromatography. Bacterially purified protein was subjected to the Western blot analysis and structural analysis by circular dichroism spectroscopy, which revealed intact structural framework of the fusion construct. Kinetic characterization of the fusion GST–hLDHA protein toward GSH and NADH, suggested retention of functional activities of GST and hLDHA in fused protein as indicated by the kinetic parameters k_m and k_cat/k_m. Further analysis of effect of temperature and pH on GST–hLDHA activity revealed maximum activity around human physiological conditions (37°C and pH 8). Preservation of the structural and functional characteristics of the fusion enzyme paves the way for potential application for the detection of NADH and GSH in conjunction as biomarkers for cancer diagnosis.     

Structure and conformation of linear peptides. I. Structure of L-tyrosyl-L-tyrosine

L-tyrosyl-L-tyrosine crystallizes as a dihydrate in the orthorhombic system, space group C222(1), with a = 12.105(2), b = 12.789(2), c = 24.492(3) A, Z = 8. The structure was solved by direct methods and refined to a final R-value of 0.059 for 1740 observed reflections. The molecule exists as a zwitterion, the peptide unit is trans planar, and the backbone torsion angles correspond to an extended conformation, with psi 1 = 149.4 degrees, phi 2 = -161.2 degrees, psi 2 = 158.3 degrees. The values of the side-chain torsion angles (chi 1, chi 2) are (-58.8 degrees, -63.1 degrees) for the first tyrosine and (-171.7 degrees, -116.5 degrees) for the second. The planes of the aromatic rings are nearly parallel (dihedral angle of 6.1 degrees), and their centers are separated by 10.9 A. The carboxyl plane forms a dihedral angle of 23.8 degrees with the plane of the peptide bond.     

Selenium-mediated biochemical changes in Japanese quails

The effect of selenium (Se) on collagen characteristics and glutathione peroxidase (GSH-Px) activity in the skin of Japanese quailsCoturnix coturnix japonica fed a formulated, semipurified, low-Se diet (basal) (0.05 ppm) was investigated. The quails exhibited severe Se-deficiency symptoms and significant reduction in skin GSH-Px activity at the end of 30 d. Selenium supplementation at a 2-ppm level restored the normal skin conditions and enhanced skin GSH-Px activity significantly. But a dietary Se level of 0.1 ppm was found to be inadequate in restoring the general skin conditions and GSH-Px activity. A markedly low total collagen content of about 23% was observed in the skin of quails fed the basal diet, compared to 39% of total collagen content in the skin of the 2-ppm Se-supplemented group. Molecular organization of skin collagen of quails on the basal and 0.1-ppm Se diet showed an abundance of monomeric forms with less crosslinks, compared to the presence of polymeric forms with more crosslinks, indicating enhanced stability in the skin collagen of quails on the 2-ppm diet. The delay in the in vitro fibril formation of collagen from the basal and 0.1-ppm Se groups, compared to a relatively faster rate in the case of the 2-ppm Se group, indicates a disturbance in the aggregation phenomenon of collagen. The increase in skin GSH-Px activity and concurrent increase in polymeric collagen on increasing the dietary Se level suggest a possible role for Se in collagen metabolism.