Protein model discrimination attempts using mutational sensitivity,predicted secondary structure,and model quality information

Structure prediction methods often generate a large number of models for a target sequence. Even if the correct fold for the target sequence is sampled in this dataset, it is difficult to distinguish it from other decoy structures. An attempt to solve this problem using experimental mutational sensitivity data for the CcdB protein was described previously by exploiting the correlation of residue depth with mutational sensitivity (r ~ 0.6). We now show that such a correlation extends to four other proteins with localized active sites, and for which saturation mutagenesis datasets exist. We also examine whether incorporation of predicted secondary structure information and the DOPE model quality assessment score, in addition to mutational sensitivity, improves the accuracy of model discrimination using a decoy dataset of 163 targets from CASP. Although most CASP models would have been subjected to model quality assessment prior to submission, we find that the DOPE score makes a substantial contribution to the observed improvement. We therefore also applied the approach to CcdB and four other proteins for which reliable experimental mutational data exist and observe that inclusion of experimental mutational data results in a small qualitative improvement in model discrimination relative to that seen with just the DOPE score. This is largely because of our limited ability to quantitatively predict effects of point mutations on in vivo protein activity. Further improvements in the methodology are required to facilitate improved utilization of single mutant data.     

Studies on rat ovarian receptors for lutropin (luteinizing hormone). Applicability of radioimmunoassay to measure lutropin bound to receptors.

Measurement of receptor-bound unlabelled physiologically active lutropin (luteinizing hormone, LH) was possible by a modified radioimmunoassay. The conventional radioimmunoassay conducted at 4 degrees C was inadequate, whereas the modified assay performed at 37 degrees C could measure receptor-bound lutropin. The radioimmunoassay at 37 degrees C takes only 36h for completion compared with 5-7 days at 4 degreesC. The sensitivity and range of dose-response curves are, however, unaltered. The validity of the technique was established by a number of criteria.     

Value based products from human placenta

Human placenta is a rich source of many biological products. It is an economical source as it is easily available as a hospital waste. The products obtained from human placenta include enzymes, genetic material, cellular proteins and antibodies. Some classes of enzymes which are not available after parturition or which cannot be obtained from the human body can be obtained from placenta. This article reviews various placental products including their extraction and purification.     

The Role of the Mammalian DNA End-processing Enzyme Polynucleotide Kinase 3’-Phosphatase in Spinocerebellar Ataxia Type 3 Pathogenesis

DNA strand-breaks (SBs) with non-ligatable ends are generated by ionizing radiation, oxidative stress, various chemotherapeutic agents, and also as base excision repair (BER) intermediates. Several neurological diseases have already been identified as being due to a deficiency in DNA end-processing activities. Two common dirty ends, 3’-P and 5’-OH, are processed by mammalian polynucleotide kinase 3’-phosphatase (PNKP), a bifunctional enzyme with 3’-phosphatase and 5’-kinase activities. We have made the unexpected observation that PNKP stably associates with Ataxin-3 (ATXN3), a polyglutamine repeat-containing protein mutated in spinocerebellar ataxia type 3 (SCA3), also known as Machado-Joseph Disease (MJD). This disease is one of the most common dominantly inherited ataxias worldwide; the defect in SCA3 is due to CAG repeat expansion (from the normal 14–41 to 55–82 repeats) in the ATXN3 coding region. However, how the expanded form gains its toxic function is still not clearly understood. Here we report that purified wild-type (WT) ATXN3 stimulates, and by contrast the mutant form specifically inhibits, PNKP’s 3’ phosphatase activity in vitro. ATXN3-deficient cells also show decreased PNKP activity. Furthermore, transgenic mice conditionally expressing the pathological form of human ATXN3 also showed decreased 3’-phosphatase activity of PNKP, mostly in the deep cerebellar nuclei, one of the most affected regions in MJD patients’ brain. Finally, long amplicon quantitative PCR analysis of human MJD patients’ brain samples showed a significant accumulation of DNA strand breaks. Our results thus indicate that the accumulation of DNA strand breaks due to functional deficiency of PNKP is etiologically linked to the pathogenesis of SCA3/MJD.     

The shear mechanical properties of diabetic and non-diabetic plantar soft tissue

Changes in the plantar soft tissue shear properties may contribute to ulceration in diabetic patients, however, little is known about these shear parameters. This study examines the elastic and viscoelastic shear behavior of both diabetic and non-diabetic plantar tissue. Previously compression tested plantar tissue specimens (n=54) at six relevant plantar locations (hallux, first, third, and fifth metatarsal heads, lateral midfoot, and calcaneus) from four cadaveric diabetic feet and five non-diabetic feet were utilized. Per in vivo data (i.e., combined deformation patterns of compression followed by shear), an initial static compressive strain (36-38%) was applied to the tissue followed by target shear strains of 50% and 85% of initial thickness. Triangle waves were used to quantify elastic parameters at both strain levels and a stress relaxation test (0.25 s ramp and 300 s hold) was used to quantify the viscoelastic parameters at the upper strain level. Several differences were found between test groups including a 52-62% increase in peak shear stress, a 63% increase in toe shear modulus, a 47% increase in final shear modulus, and a 67% increase in middle slope magnitude (sharper drop in relaxation) in the diabetic tissue. Beyond a 54% greater peak compressive stress in the third metatarsal compared to the lateral midfoot, there were no differences in shear properties between plantar locations. Notably, this study demonstrates that plantar soft tissue with diabetes is stiffer than healthy tissue, thereby compromising its ability to dissipate shear stresses borne by the foot that may increase ulceration risk.     

Structural properties of EGCG-induced, nontoxic Alzheimer's disease Aβ oligomers

The green tea compound epigallocatechin-3-gallate (EGCG) inhibits Alzheimer's disease β-amyloid peptide (Aβ) neurotoxicity. Solution-state NMR allows probing initial EGCG-Aβ interactions. We show that EGCG-induced Aβ oligomers adopt a well-defined structure and are amenable for magic angle spinning solid-state NMR investigations. We find that EGCG interferes with the aromatic hydrophobic core of Aβ. The C-terminal part of the Aβ peptide (residues 22-39) adopts a β-sheet conformation, whereas the N-terminus (residues 1-20) is unstructured. The characteristic salt bridge involving residues D23 and K28 is present in the structure of these oligomeric Aβ aggregates as well. The structural analysis of small-molecule-induced amyloid aggregates will open new perspectives for Alzheimer's disease drug development.     

Activation of ras signaling pathway by 8-oxoguanine DNA glycosylase bound to its excision product, 8-oxoguanine

8-Oxo-7,8-dihydroguanine (8-oxoG), arguably the most abundant base lesion induced in mammalian genomes by reactive oxygen species, is repaired via the base excision repair pathway that is initiated with the excision of 8-oxoG by OGG1. Here we show that OGG1 binds the 8-oxoG base with high affinity and that the complex then interacts with canonical Ras family GTPases to catalyze replacement of GDP with GTP, thus serving as a guanine nuclear exchange factor. OGG1-mediated activation of Ras leads to phosphorylation of the mitogen-activated kinases MEK1,2/ERK1,2 and increasing downstream gene expression. These studies document for the first time that in addition to its role in repairing oxidized purines, OGG1 has an independent guanine nuclear exchange factor activity when bound to 8-oxoG.     

Bioprospecting Micromonospora from Kaziranga National Park of India and their anti-infective potential

Large number of strains was isolated from soils of Kaziranga National Park of North-East India using selective isolation procedure. They were assigned to the genus Micromonospora on the basis of their typical colonial and pigmentation features. The taxonomic identities of the isolates were confirmed on the basis of their molecular characters (16SrDNA). A total of one hundred Micromonospora strains were isolated during the present investigation. The diagnostic cell wall sugar and amino acids were determined from these Micromonospora strains. After preliminary screening most of the isolates exhibited excellent anti-infective activity against human bacterial pathogens Staphylococcus aureas, Bacillus subtilis, Proteus vulgaris, Echerichia coli, Pseudomonas aeroginosa and fungal pathogens Aspergillus niger, Fusarium oxysporum and Candida albicans. Among these isolates one strain designated as HK-10 showed promising activity against human pathogens S. aureas, B. subtilis, P. vulgaris and P. aeroginosa.     

Downregulation of NF-κB and PCNA in the regulatory pathways of apoptosis by cyclooxygenase-2 inhibitors in experimental lung cancer

Non-steroidal anti-inflammatory drugs (NSAIDs) are emerging as novel chemopreventive agents against a variety of cancers owing to their capability in blocking the tumor development by cellular proliferation, angiogenesis and by promoting apoptosis. The present study further explored the comparative role of a traditional NSAID, indomethacin and a newly developed coxib, etoricoxib against 9,10-dimethylbenz(a)anthracene (DMBA)-induced lung carcinogenesis in rats. Morphological and histological analysis revealed the occurrence of tumors and lesions along with constricted alveolar spaces in the DMBA treated animals which were largely corrected both by indomethacin and etoricoxib. COX-1 was found to be uniformly expressed in all the groups while COX-2 levels were raised prominently in the DMBA treated animals. Proliferation, as studied by PCNA expression was found to be markedly increased in the DMBA group as compared to the others. Increased NF-κB expression in the DMBA group was found to correct with the co-administration of NSAIDs. Also, fluorescent co-staining of the isolated lung cells revealed a significantly decreased apoptosis and altered mitochondrial membrane potential. In conclusion, these parameters indicate to the chemopreventive action of the two NSAIDs studied in lung cancer and as their mechanism of action suggests, can be achievable both by COX-dependent and COX-independent pathways.