Dimensionality reduction in computational demarcation of protein tertiary structures

Predictive classification of major structural families and fold types of proteins is investigated deploying logistic regression. Only five to seven dimensional quantitative feature vector representations of tertiary structures are found adequate. Results for benchmark sample of non-homologous proteins from SCOP database are presented. Importance of this work as compared to homology modeling and best-known quantitative approaches is highlighted.     

Unc45b forms a cytosolic complex with Hsp90 and targets the unfolded myosin motor domain

Myosin folding and assembly in striated muscle is mediated by the general chaperones Hsc70 and Hsp90 and a myosin specific co-chaperone, UNC45. Two UNC45 genes are found in vertebrates, including a striated muscle specific form, Unc45b. We have investigated the role of Unc45b in myosin folding. Epitope tagged murine Unc45b (Unc45b(Flag)) was expressed in muscle and non-muscle cells and bacteria, isolated and characterized. The protein is a soluble monomer in solution with a compact folded rod-shaped structure of approximately 19 nm length by electron microscopy. When over-expressed in striated muscle cells, Unc45b(Flag) fractionates as a cytosolic protein and isolates as a stable complex with Hsp90. Purified Unc45b(Flag) re-binds Hsp90 and forms a stable complex in solution. The endogenous Unc45b in muscle cell lysates is also found associated with Hsp90. The Unc45b(Flag)/Hsp90 complex binds the partially folded myosin motor domain when incubated with myosin subfragments synthesized in a reticulocyte lysate. This binding is independent of the myosin rod or light chains. Unc45b(Flag) does not bind native myosin subfragments consistent with a chaperone function. More importantly, Unc45b(Flag) enhances myosin motor domain folding during de novo motor domain synthesis indicating that it has a direct role in myosin maturation. Thus, mammalian Unc45b is a cytosolic protein that forms a stable complex with Hsp90, selectively binds the unfolded conformation of the myosin motor domain, and promotes motor domain folding.     

Review in vitro-induced flowering in bamboos

Summary The majority of bamboos (Graminae) are arborescent and perennial. The erect stems (culms) of woody bamboos are useful for a wide variety of purposes. Most bamboos flower only once at the end of very long vegetative growth phases and die afterwards. Flowering in bamboos is thought to be under genetic control, occurring somewhat like an alarm clock, going off at a preset time. The nature of this genetic clock and any interaction between the ‘internal clock’ and the environment are not yet known. Because of this ‘peculiar’ flowering behavior, bamboo seeds are available only at very long intervals. Obtaining concurrent flowering in two or more species (or varieties) in space and time is difficult, making perennial seed propagation and genetic improvement by breeding nearly impossible. Besides, this peculiar flowering behavior of bamboos is also believed to have brought the giant pandas to the verge of extinction. One of the spectacular developments in the area of bamboo genetic improvement has been the precocious in vitro induction of flowering. By this method it has been possible to rapidly accelerate the reproductive development (within 3–6 mo. versus 30–60 yr in nature). This has opened the possibility of perennial seed propagation and hybridization. In vitro induction of flowering can be obtained by diverse methods which show some similarities and differences. Induction of flowering is possible in cultures derived from both juvenile and mature explants. The proportion of seedlings induced to flower is possibly influenced by genotypic variation, though the role of methods used cannot be ruled out. A cytokinin or a shift in the auxin-cytokinin equilibrium is believed to bring about in vitro induction of flowering. The pH of the media also has an influence. Induction of flowering and rhizogenesis is considered to be an antagonistic phenomenon in vitro. A comparison between in vitro and in vivo flowering in Bambusa arundinacea has shown that though smaller, in vitro-induced florets are comparable to normal florets. There is reduced pollen fertility and some impairment in pollen wall development. Biochemical studies on the in vitro-induced flowering in bamboos have shown (1) selective expression of esterase and peroxidase isozymes during transition of nonembryogenic calluses to embryogenic calluses, somatic embryo development, germination and subsequent flowering of somatic embryo derived shoots, and (2) minimal peroxidase activity before rhizogenesis and induction of flowering in vitro. There are reports of published and comparable methods having failed to induce flowering in vitro.     

Multiple shoot regeneration and tissue culture studies on Bacopa monnieri (L.) Pennell

 Adventitious shoot buds were induced from leaf and stem explants of Bacopa monnieri on Murashige and Skoog medium supplemented with benzyladenine or kinetin. The source of the explants as well as different gelling agents in the medium were found to influence shoot induction and eventual shoot growth. The best response was obtained in leaf explants taken from shoot cultures grown in medium supplemented with 2 μM benzyladenine and gelled with 0.2% gelrite. A transverse section of the leaf explant incubated in this medium showed several shoot primordia emerging from the leaf surface. This system exhibited a potential for repeated harvesting of the shoots from the original leaf explant as the latter continued to expand and regenerate new shoots, upon repeated periodical subculturing onto fresh medium. However, the callusing response of the plant was very low. Qualitative TLC studies of the regenerated shoots revealed a phytochemical profile similar to that of the field grown-plants. Received: 20 March 1998 / Revision received: 1 December 1998 / Accepted: 12 December 1998     

Synthesis and Biological Evaluation of Novel Multi-target-Directed Benzazepines Against Excitotoxicity

Excitotoxicty, a key pathogenic event is characteristic of the onset and development of neurodegeneration. The glutamatergic neurotransmission mediated through different glutamate receptor subtypes plays a pivotal role in the onset of excitotoxicity. The role of NMDA receptor (NMDAR), a glutamate receptor subtype, has been well established in the excitotoxicity pathogenesis. NMDAR overactivation triggers excessive calcium influx resulting in excitotoxic neuronal cell death. In the present study, a series of benzazepine derivatives, with the core structure of 3-methyltetrahydro-3H-benzazepin-2-one, were synthesised in our laboratory and their NMDAR antagonist activity was determined against NMDA-induced excitotoxicity using SH-SY5Y cells. In order to assess the multi-target-directed potential of the synthesised compounds, Aβ_1–42 aggregation inhibitory activity of the most potent benzazepines was evaluated using thioflavin T (ThT) and Congo red (CR) binding assays as Aβ also imparts toxicity, at least in part, through NMDAR overactivation. Furthermore, neuroprotective, free radical scavenging, anti-oxidant and anti-apoptotic activities of the two potential test compounds (7 and 14) were evaluated using primary rat hippocampal neuronal culture against Aβ_1–42-induced toxicity. Finally, in vivo neuroprotective potential of 7 and 14 was assessed using intracerebroventricular (ICV) rat model of Aβ_1–42-induced toxicity. All of the synthesised benzazepines have shown significant neuroprotection against NMDA-induced excitotoxicity. The most potent compound (14) showed relatively higher affinity for the glycine binding site as compared with the glutamate binding site of NMDAR in the molecular docking studies. 7 and 14 have been shown experimentally to abrogate Aβ_1–42 aggregation efficiently. Additionally, 7 and 14 showed significant neuroprotective, free radical scavenging, anti-oxidant and anti-apoptotic properties in different in vitro and in vivo experimental models. Finally, 7 and 14 attenuated Aβ_1–42-induced tau phosphorylation by abrogating activation of tau kinases, i.e. MAPK and GSK-3β. Thus, the results revealed multi-target-directed potential of some of the synthesised novel benzazepines against excitotoxicity.     

Effect of bis[curcumino]oxovanadium complex on non-diabetic and streptozotocin-induced diabetic rats

The effect of the vanadium complex bis[curcumino]oxovanadium (BCOV) on blood glucose level, serum lipid levels, blood pressure and vascular reactivity were studied in non-diabetic and streptozotocin-induced diabetic (STZ-diabetic) rats and compared to that of vanadyl sulfate. Blood glucose level, serum lipid levels, and blood pressure were significantly increased in STZ-diabetic rats. Vascular reactivity to various agonists such as noradrenaline and acetylcholine were significantly increased in STZ-diabetic rats. Blood glucose and serum lipid levels were restored to normal in STZ-diabetic animals treated with vanadyl sulfate at a concentration of 0.5 mmol/kg/day (p.o.). However, vanadyl sulfate at a concentration of 0.2 mmol/kg/day (p.o.) did not produce any significant change in blood glucose and lipid levels. There was no significant effect of vanadyl sulfate (0.2 or 0.5 mmol/kg/day) treatment on blood pressure and vascular reactivity in STZ-diabetic rats. Vanadyl sulfate significantly reduced the body weight of non-diabetic and STZ-diabetic rats. Moreover, it also caused severe diarrhea in both groups of animals. Treatment with BCOV (0.05, 0.1 and 0.2mmol/kg/day, p.o.) significantly decreased blood glucose level and serum lipids in STZ-diabetic rats. Furthermore, administration of BCOV to STZ-diabetic rats restored the blood pressure and vascular reactivity to agonists to normal. There was no significant change in the body weight of BCOV treated non-diabetic and STZ-diabetic rats. Diarrhea was not observed in both BCOV treated groups. In conclusion, the present study shows that the vanadium complex BCOV has antidiabetic and hypolipedimic effects. In addition, it improves the cardiovascular complications associated with diabetes.     

Peptidomimetic 2-cyanopyrrolidines as potent selective cathepsin L inhibitors

Cathepsins have been found to have important physiological roles. The implication of cathepsin L in various types of cancers is well established. In a search for selective cathepsin L inhibitors as anticancer agents, a series of 2-cyanoprrolidine peptidomimetics, carrying a nitrile group as warhead, were designed. Two series of compounds, one with a benzyl moiety and a second with an isobutyl moiety at P(2) position of the enzyme were synthesized. The synthesized compounds were evaluated for inhibitory activity against human cathepsin L and cathepsin B. Although, none of the compounds showed promising inhibitory activity, (E)N-{(S)1-[(S)2-cyano-1-pyrrolidinecarbonyl]-3-methylbutyl}-2,3-diphenylacrylamide (24) with an isobutyl moiety at P(2) was found to show selectivity as a cathepsin L inhibitor (Ki 5.3 microM for cathepsin L and Ki > 100 microM for cathepsin B). This compound could act as a new lead for the further development of improved inhibitors within this inhibitor type.     

Fluorescence studies on the interaction of choline-binding domain B of the major bovine seminal plasma protein,PDC-109 with phospholipid membranes

The microenvironment and accessibility of the tryptophan residues in domain B of PDC-109 (PDC-109/B) in the native state and upon ligand binding have been investigated by fluorescence quenching, time-resolved fluorescence and red-edge excitation shift (REES) studies. The increase in the intrinsic fluorescence emission intensity of PDC-109/B upon binding to lysophosphatidylcholine (Lyso-PC) micelles and dimyristoylphosphatidylcholine (DMPC) membranes was considerably less as compared to that observed with the whole PDC-109 protein. The degree of quenching achieved by different quenchers with PDC-109/B bound to Lyso-PC and DMPC membranes was significantly higher as compared to the full PDC-109 protein, indicating that membrane binding afforded considerably lesser protection to the tryptophan residues of domain B as compared to those in the full PDC-109 protein. Finally, changes in red-edge excitation shift (REES) seen with PDC-109/B upon binding to DMPC membranes and Lyso-PC micelles were smaller that the corresponding changes in the REES values observed for the full PDC-109. These results, taken together suggest that intact PDC-109 penetrates deeper into the hydrophobic parts of the membrane as compared to domain B alone, which could be the reason for the inability of PDC-109/B to induce cholesterol efflux, despite its ability to recognize choline phospholipids at the membrane surface.