Axial ranking of residues in collagen in relation to edge association and fibril formation

In our earlier analysis of intermolecular interactions between collagen molecules, a major concern with the program employed is that it compared numbers of interactions between residues located on edges of defined, identical width and thus would not necessarily compare the same number of residues in each edge. This would be particularly true of some values of θ where well-defined vertical ranking of residues occurs. We have examined ranking of residues in relation to intermolecular edge association between bovine skin [α1(I)]₃ model collagen molecules by utilizing two different methods of counting intermolecular interactions between residues. The interaction peaks at θ = 27.69° and 36.00° are absent or relatively less intense in the plots obtained by utilizing radial distances between interacting residues instead of vertical bands of defined width. These studies suggest caution in accepting recently reported analyses of superhelix coiling of the collagen molecule which point to values of 27.69° or 36.00° for the twist of the superhelix. Although intramolecular interactions clearly point to interaction of collagen molecules at D intervals, they are insufficiently restricted in distribution to provide a reliable estimate of the superhelix angle by procedures so far employed.     

Exploration of highly selective fluorogenic ‘on–off' chemosensor for H2PO4− ions: ICT‐based sensing and ATPase activity profiling

Abstract In this study, the recognition contour of Chemosensor 1 was investigated using semiaqueous methanol (X_H, mole fraction = 0.31) for a range of anions and bioactive species. Host–receptor signalling based on the internal charge transfer mechanism for Chemosensor 1 was explored and reported. Structure of Chemosensor 1 and its plausible anion coordination based on hydrogen bonding is complemented with density functional theory. Consequently, we investigated the applicability of the synthesized probe in blood plasma, urine, tap water samples, and for monitoring of ATP in lysosomes by apyrase enzyme.     

Studies on Bleomycin-DNA and Bleomycin-Iron Interactions

Abstract

The bleomycins, a group of antitumor antibiotics (Figure 1), cause the degradation of DNA by a process requiring iron(II) and dioxygen (1,2). DNA degradation appears to involve two steps: association of the drug with the nucleic acid and degradation of the DNA. As part of studies directed toward achieving an understanding of how the bleomycins degrade DNA, we have examined various properties of the drug using a variety of chemical and physico- chemical techniques, including NMR and Mössbauer spectroscopy. We have studied both the interaction of the antibiotic with its target (DNA) as well as its association with its metal ion cofactor. This work has been performed on the intact drug and its derivatives as well as on synthetic models of the parent drug. This paper reviews and updates the recent work from this laboratory on the bleomycins.     

Indole acetic acid mimics the effect of salt stress in relation to enzymes of carbohydrate metabolism in chickpea seedlings

The effect of addition of indole acetic acid (3 M) andNaCl (75 mM) on growth and enzymes of carbohydrate metabolism inchickpea seedlings was compared. In comparison with control seedlings, theseedlings growing in the presence of indole acetic acid (IAA) had reducedamylase activity in cotyledons and enhanced sucrose synthase (SS) and sucrosephosphate synthase (SPS) activities in cotyledons and shoots at all days ofseedling growth. Compared with control seedlings, sucrose content was higher incotyledons, shoots and roots and reducing sugar content was lower in shoots ofIAA treated seedlings. A low invertase (acid and alkaline) activity in shoots ofIAA treated seedlings could lead to reduced sink strength and hence decreasedgrowth of seedlings. Effects of NaCl stress on growth and activities of amylase,SS and SPS in cotyledons and invertase, SS and SPS in shoots were similar tothose observed with addition of IAA.     

Phytic acid and raffinose series oligosaccharides metabolism in developing chickpea seeds

Phytic acid and raffinose series oligosaccharides (RFOs) have anti-nutritional properties where phytic acid chelates minerals and reduces their bioavailability to humans and other animals, and RFOs cause flatulence. Both phytic acid and RFOs cannot be digested by monogastric animals and are released as pollutant-wastes. Efforts are being made to reduce the contents of these factors without affecting the viability of seeds. This will require a thorough understanding of their metabolism in different crops. Biosynthetic pathways of both metabolites though are interlinked but not well described. This study was made on metabolism of these two contents in developing chickpea (Cicer arietinum L cv GL 769) seeds. In this study, deposition of RFOs was found to occur before deposition of phytic acid. A decline in inorganic phosphorus and increase in phospholipid phosphorus and phytic acid was observed in seeds during development. Acid phosphatase was the major phosphatase in seed as well as podwall and its activity was highest at early stage of development, thereafter it decreased. Partitioning of ¹⁴ C label from ¹⁴ C-glucose and ¹⁴ C-sucrose into RFOs and phytic acid was studied in seeds in presence of inositol, galactose and iositol and galactose, which favored the view that galactinol synthase is not the key enzyme in RFOs synthesis.     

The meaning of interaction parameters in two-state protein complexes

The theory of interaction parameters has thus far been based on the free-energy relationships in the formation of ternary complexes formed between a pair of ligands and a protein molecule. The concept has been formulted in terms of a thermodynamic square comprised of the free protein, the two binary complexes, and the ternary complex. However, an increasing number of proteins have been found to exist as equilibrium mixtures of two macrostates. The equilibrium constants for such two-state transitions vary quite considerably between the various binary and ternary complexes of a given protein. We show here that the interpretations of interaction parameters in such two-state systems, requiring the use of a thermodynamic cube, are much more complex than those based on the classic thermodynamic square commonly employed. We demonstrate the use of enthalpies of interaction and heat capacities of interaction to analyze the source of observed free enerigies of interaction in such systems. Specifically, we find that measured negative interaction parameters may arise simply from the inability of a system to achieve all of the positive component effects anticipated by the conventional formulation.     

Intact memory for irrelevant information impairs perception in amnesia

Memory and perception have long been considered separate cognitive processes, and amnesia resulting from medial temporal lobe (MTL) damage is thought to reflect damage to a dedicated memory system. Recent work has questioned these views, suggesting that amnesia can result from impoverished perceptual representations in the MTL, causing an increased susceptibility to interference. Using a perceptual matching task for which fMRI implicated a specific MTL structure, the perirhinal cortex, we show that amnesics with MTL damage including the perirhinal cortex, but not those with damage limited to the hippocampus, were vulnerable to object-based perceptual interference. Importantly, when we controlled such interference, their performance recovered to normal levels. These findings challenge prevailing conceptions of amnesia, suggesting that effects of damage to specific MTL regions are better understood not in terms of damage to a dedicated declarative memory system, but in terms of impoverished representations of the stimuli those regions maintain.     

Metabolic pathway promiscuity in the archaeon Sulfolobus solfataricus revealed by studies on glucose dehydrogenase and 2-keto-3-deoxygluconate aldolase

The hyperthermophilic Archaeon Sulfolobus solfataricus metabolizes glucose by a non-phosphorylative variant of the Entner-Doudoroff pathway. In this pathway glucose dehydrogenase and gluconate dehydratase catalyze the oxidation of glucose to gluconate and the subsequent dehydration of gluconate to 2-keto-3-deoxygluconate. 2-Keto-3-deoxygluconate (KDG) aldolase then catalyzes the cleavage of 2-keto-3-deoxygluconate to glyceraldehyde and pyruvate. The gene encoding glucose dehydrogenase has been cloned and expressed in Escherichia coli to give a fully active enzyme, with properties indistinguishable from the enzyme purified from S. solfataricus cells. Kinetic analysis revealed the enzyme to have a high catalytic efficiency for both glucose and galactose. KDG aldolase from S. solfataricus has previously been cloned and expressed in E. coli. In the current work its stereoselectivity was investigated by aldol condensation reactions between D-glyceraldehyde and pyruvate; this revealed the enzyme to have an unexpected lack of facial selectivity, yielding approximately equal quantities of 2-keto-3-deoxygluconate and 2-keto-3-deoxygalactonate. The KDG aldolase-catalyzed cleavage reaction was also investigated, and a comparable catalytic efficiency was observed with both compounds. Our evidence suggests that the same enzymes are responsible for the catabolism of both glucose and galactose in this Archaeon. The physiological and evolutionary implications of this observation are discussed in terms of catalytic and metabolic promiscuity.     

Competent dendritic cells derived from CD34+ progenitors express CMRF-44 antigen early in the differentiation pathway

Differentiation of CD34(+) haematopoietic stem cells into functional dendritic cells (DC) was investigated using the mAb CMRF-44 and other mAb against DC-associated markers. GM-CSF mobilized peripheral blood stem cells were obtained from healthy donors by leukapheresis. CD34(+) cells were purified using CD34(+)-positive selection,and subsequent immunomagnetic depletion of CD14 and CD2 cells. CD34(+) cells were cultured in medium supplemented with one or more of GM-CSF,TNF-alpha, IL-4 or IL-6. CMRF-44 Ag expression was monitored by flow cytometry, and DC function by allogeneic MLR and tetanus toxoid(TT) presentation assays. CD34(+) cells quickly acquired the CMRF-44 Ag when cultured in the presence of TNF-alpha.By day 3, more than 50% of the cells were double-positive for CD34 and CMRF-44. CD34 expression was gradually lost, so that by day 9, the majority of the cells were CD34(-)/CMRF-44(+).GM-CSF and TNF-alpha also induced CD40 expression, and up-regulation of CD54 and MHC class II on CD34(+) cells; their expression was correlated to the CMRF-44 Ag. Day 3 CD34(+)/CMRF-44(+) cells,but not CD34(+)/CMRF-44(-) cells, become potent APC when cultured further with GM-CSF plus TNF-alpha. These CMRF-44(+) cells were potent inducers of Th1-type immune response in the primary allogeneic MLR and present TT to autologous CD4(+) T cells. TNF-alpha alone is sufficient to induce CMRF-44 expression on CD34(+) cells, but in combination with GM-CSF expands the CMRF-44(+) population. CMRF-44 expression correlates with DC function and may be a useful early marker for commitment of CD34(+) cells to the DC differentiation pathway.     

Differences in the Activation State of Ribulose-1,5-bisphosphate Carboxylase/Oxygenase in Barley,Pea, and Wheat at Two Altitudes

Activation state of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPCO) is an important parameter determining the rate of net photosynthesis (P _N) in situ for which no information is available with reference to altitude. We analyzed activation state along with P _N in three plant species and their cultivars grown at low (LA, 1 300 m) and high (HA, 4 200 m) altitudes. No significant change in P _N and the initial activity of RuBPCO was obtained with reference to altitude. However, activation state of RuBPCO was reduced significantly in the HA plants as compared to the LA ones. Hence low partial pressure of CO₂ prevailing at HA might be responsible for the lower activation state of RuBPCO.