Crystal structure of a tripeptide containing aminocyclododecane carboxylic acid: a supramolecular twisted parallel β‐sheet in crystals

The crystal structure of a tripeptide Boc‐Leu‐Val‐Ac₁₂c‐OMe ( 1 ) is determined, which incorporates a bulky 1‐aminocyclododecane‐1‐carboxylic acid (Ac₁₂c) side chain. The peptide adopts a semi‐extended backbone conformation for Leu and Val residues, while the backbone torsion angles of the C^α,α‐dialkylated residue Ac₁₂c are in the helical region of the Ramachandran map. The molecular packing of 1 revealed a unique supramolecular twisted parallel β‐sheet coiling into a helical architecture in crystals, with the bulky hydrophobic Ac₁₂c side chains projecting outward the helical column. This arrangement resembles the packing of peptide helices in crystal structures. Although short oligopeptides often assemble as parallel or anti‐parallel β‐sheet in crystals, twisted or helical β‐sheet formation has been observed in a few examples of dipeptide crystal structures. Peptide 1 presents the first example of a tripeptide showing twisted β‐sheet assembly in crystals. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.     

Investigating proline puckering states in diproline segments in proteins

In the current study, the puckering states of the Proline ring occurring in diproline segments (^LPro‐^LPro) in proteins has been investigated with a segregation made on the basis of cis and trans states for the Pro‐Pro peptide bond and the conformational states for the diproline segment to investigate the effects of conformation of the diproline segment on the corresponding puckering state of the Proline ring in the segment if any. The value of the endocyclic ring torsional angles of the pyrrolidine ring has been used for calculating and visualizing various puckering states using a proposed new sign convention (+/?) nomenclature. The results have been compared to that obtained in a previous study on peptides from this group. In this study, quite interestingly, the Planar (G) conformation that was present in 14.3% of the cases in peptides, appears to be nearly a rare conformation in the case of proteins (1.9%). The present study indicates that the (C^γ‐exo/C^γ‐exo), (C^γ‐exo/Twisted C^γ‐exo‐C^β‐endo) and (Twisted C^γ‐endo‐C^β‐exo/Twisted C^γ‐endo‐C^β‐exo) categories are the most preferred combinations. For Proline rings in proteins, the states C^γ‐exo, Twisted C^γ‐exo‐C^β‐endo and Twisted C^γ‐endo‐C^β‐exo are the most preferred states. Within diproline segments, the pyrrolidine ring conformations do not show a strong co‐relation to the backbone conformation in which they are observed. It is likely that five‐membered rings have a considerable plasticity of structure and are readily deformed to accommodate a variety of energetically preferred backbone conformations. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 605–610, 2013.     

A novel single amino acid change in small subunit ribosomal protein S5 has profound effects on translational fidelity

S5 is a small subunit ribosomal protein (r-protein) linked to the functional center of the 30S ribosomal subunit. In this study we have identified a unique amino acid mutation in Escherichia coli S5 that produces spectinomycin-resistance and cold sensitivity. This mutation significantly alters cell growth, folding of 16S ribosomal RNA, and translational fidelity. While translation initiation is not affected, both +1 and -1 frameshifting and nonsense suppression are greatly enhanced in the mutant strain. Interestingly, this S5 ribosome ambiguity-like mutation is spatially remote from previously identified S5 ribosome ambiguity (ram) mutations. This suggests that the mechanism responsible for ram phenotypes in the novel mutant strain is possibly distinct from those proposed for other known S5 (and S4) ram mutants. This study highlights the importance of S5 in ribosome function and cell physiology, and suggests that translational fidelity can be regulated in multiple ways.     

Differentiation ex ovulo of Embryos and Plantlets in Stem Tissue Cultures of Tylophora indica

Tylophora indica callus tissue repeatedly subcultured every month on a series of different nutrient media in sequence regenerated roots, shoots and typical, bipolar embryos in vitro from unorganized callus parenchyma. The embryo-like structures developed from somatic cells grew into normal plantlets when isolated and cultured on appropriate milieu of nutrients and hormones bypassing the normal sexual method of reproduction. Likewise, free cells in suspension also passed through embryonic stages reminiscent of development from fertilized egg.     

Loss of Urokinase Receptor Sensitizes Cells to DNA Damage and Delays DNA Repair

DNA damage induced by numerous exogenous or endogenous factors may have irreversible consequences on the cell leading to cell cycle arrest, senescence and cell death. The DNA damage response (DDR) is powerful signaling machinery triggered in response to DNA damage, to provide DNA damage recognition, signaling and repair. Most anticancer drugs induce DNA damage, and DNA repair in turn attenuates therapeutic efficiency of those drugs. Approaches delaying DNA repair are often used to increase efficiency of treatment. Recent data show that ubiquitin-proteasome system is essential for signaling and repair of DNA damage. However, mechanisms providing regulation of proteasome intracellular localization, activity, and recruitment to DNA damage sites are elusive. Even less investigated are the roles of extranuclear signaling proteins in these processes. In this study, we report the involvement of the serine protease urokinase-type plasminogen activator receptor (uPAR) in DDR-associated regulation of proteasome. We show that in vascular smooth muscle cells (VSMC) uPAR activates DNA single strand break repair signaling pathway. We provide evidence that uPAR is essential for functional assembly of the 26S proteasome. We further demonstrate that uPAR mediates DNA damage-induced phosphorylation, nuclear import, and recruitment of the regulatory subunit PSMD6 to proteasome. We found that deficiency of uPAR and PSMD6 delays DNA repair and leads to decreased cell survival. These data may offer new therapeutic approaches for diseases such as cancer, cardiovascular and neurodegenerative disorders.     

Macrobenthic biomass relations in the Faroe-Shetland Channel: an Arctic-Atlantic boundary environment

The Faroe-Shetland Channel, located in the NE Atlantic, ranges in depth from 0-1700 m and is an unusual deep-sea environment because of its complex and dynamic hydrographic regime, as well as having numerous different seafloor habitats. Macrofaunal samples have been collected on a 0.5 mm mesh sieve from over 300 stations in a wide area survey and on nested 0.5 and 0.25 mm mesh sieves along a specific depth transect. Contrary to general expectation, macrofauanl biomass in the Channel did not decline with increasing depth. When examined at phylum level, two main biomass patterns with depth were apparent: (a) polychaetes showed little change in biomass on the upper slope then increased markedly below 500 m to a depth of 1100 m before declining; and (b) other phyla showed enhanced biomass between 300-500 m. The polychaete response may be linked with a seafloor environment change to relatively quiescent hydrodynamic conditions and an increasing sediment mud content that occurs at c. 500 m. In contrast, the mid-slope enhancement of other phyla biomass may reflect the hydrodynamically active interface between the warm and cold water masses present in the Channel at c. 300-500 m. Again contrary to expectation, mean macrofaunal body size did not decline with depth, and the relative contribution of smaller (>0.25 mm<0.5 mm) to total (>0.25 mm) macrobenthos did not increase with depth. Overall our total biomass and average individual biomass estimates appear to be greater than those predicted from global analyses. It is clear that global models of benthic biomass distribution may mask significant variations at the local and regional scale.     

Diversity and ecology of lianas in tropical dry evergreen forests on the Coromandel Coast of India under various disturbance regimes

In this study we attempted to explore patterns of diversity, abundance, climbing and dispersal mode of lianas in relation to disturbance in 40 Indian subtropical dry forests. The sites were selected to represent four disturbance categories: relatively undisturbed, moderately disturbed, much disturbed and heavily disturbed. All lianas ≥1 cm dbh were counted, which resulted in a total amount of 5689 individuals of lianas, representing 77 species in 62 genera and 32 families. Liana species richness and abundance increased with forest disturbance, but the liana basal area values showed an opposite trend, with high scores in undisturbed sites. Twining was the main climbing mechanism (61.3%) and zoochory (59.6%) was the main dispersal mode in all the four forest categories. Application of Bray–Curtis cluster analysis produced three distinct clusters in which the much disturbed category was more distant from the others. High abundance of large lianas in undisturbed sites and that of the invasive Lantana camara in heavily disturbed site signals the conservation significance of the less disturbed study sites. The predominance of zoochorous dispersal indicates the faunal dependence of lianas, besides of host trees, thus underlining the need for a holistic approach in biodiversity conservation of this and similar tropical forests.     

Hepatitis C virus internal ribosome entry site-mediated translation is stimulated by specific interaction of independent regions of human La autoantigen

The human La autoantigen has been shown to interact with the internal ribosome entry site (IRES) of hepatitis C virus (HCV) in vitro. Using a yeast three-hybrid system, we demonstrated that, in addition to full-length La protein, both N- and C-terminal halves were able to interact with HCV IRES in vivo. The exogenous addition of purified full-length and truncated La proteins in rabbit reticulocyte lysate showed dose-dependent stimulation of HCV IRES-mediated translation. However, an additive effect was achieved adding the terminal halves together in the reaction, suggesting that both might play critical roles in achieving full stimulatory activity of the full-length La protein. Using computational analysis, three-dimensional structures of the RNA recognition motifs (RRM) of the La protein were independently modeled. Of the three putative RRMs, RRM2 was predicted to have a good binding pocket for the interaction with the HCV IRES around the GCAC motif near the initiator AUG and RRM3 binds perhaps in a different location. This observation was further investigated by the filter-binding and toe-printing assays. The results presented here strongly suggest that both the N- and C-terminal halves can interact independently with the HCV IRES and are involved in stimulating internal initiation of translation.     

Synthesis of aryl-2-deoxy-D-lyxo/arabino-hexopyranosides from 2-deoxy-1-thioglycosides

The synthesis of either anomers of aryl 2-deoxy-D-glycopyranosides from 2-deoxy-1-thioglycosides is reported. The alpha-anomers form as the major product when thioglycosides react with differently substituted phenols and naphthols, in the presence of N-iodosuccinimide/triflic acid. On the other hand, reaction of the thioglycosides with bromine initially, followed by reaction with aryloxy anions lead to aryl 2-deoxy-beta-D-glycosides with high specificities.     

Ac2PIM-responsive miR-150 and miR-143 Target Receptor-interacting Protein Kinase 2 and Transforming Growth Factor Beta-activated Kinase 1 to Suppress NOD2-induced Immunomodulators

Specific and coordinated regulation of innate immune receptor-driven signaling networks often determines the net outcome of the immune responses. Here, we investigated the cross-regulation of toll-like receptor (TLR)2 and nucleotide-binding oligomerization domain (NOD)2 pathways mediated by Ac₂PIM, a tetra-acylated form of mycobacterial cell wall component and muramyl dipeptide (MDP), a peptidoglycan derivative respectively. While Ac₂PIM treatment of macrophages compromised their ability to induce NOD2-dependent immunomodulators like cyclooxygenase (COX)-2, suppressor of cytokine signaling (SOCS)-3, and matrix metalloproteinase (MMP)-9, no change in the NOD2-responsive NO, TNF-α, VEGF-A, and IL-12 levels was observed. Further, genome-wide microRNA expression profiling identified Ac₂PIM-responsive miR-150 and miR-143 to target NOD2 signaling adaptors, RIP2 and TAK1, respectively. Interestingly, Ac₂PIM was found to activate the SRC-FAK-PYK2-CREB cascade via TLR2 to recruit CBP/P300 at the promoters of miR-150 and miR-143 and epigenetically induce their expression. Loss-of-function studies utilizing specific miRNA inhibitors establish that Ac₂PIM, via the miRNAs, abrogate NOD2-induced PI3K-PKCδ-MAPK pathway to suppress β-catenin-mediated expression of COX-2, SOCS-3, and MMP-9. Our investigation has thus underscored the negative regulatory role of Ac₂PIM-TLR2 signaling on NOD2 pathway which could broaden our understanding on vaccine potential or adjuvant utilities of Ac₂PIM and/or MDP.