Conserved water-mediated H-bonding dynamics of catalytic Asn 175 in plant thiol protease

The role of invariant water molecules in the activity of plant cysteine protease is ubiquitous in nature. On analysing the 11 different Protein DataBank (PDB) structures of plant thiol proteases, the two invariant water molecules W1 and W2 (W220 and W222 in the template 1PPN structure) were observed to form H-bonds with the O_b atom of Asn 175. Extensive energy minimization and molecular dynamics simulation studies up to 2 ns on all the PDB and solvated structures clearly revealed the involvement of the H-bonding association of the two water molecules in fixing the orientation of the asparagine residue of the catalytic triad. From this study, it is suggested that H-bonding of the water molecule at the W1 invariant site better stabilizes the Asn residue at the active site of the catalytic triad.     

Heparin binds to Leishmania donovani promastigotes and inhibits protein phosphorylation.

We show that promastigotes of Leishmania donovani, the causative agent of visceral leishmaniasis (kala-azar), possess heparin receptors on their surface. From a linear Scatchard plot of the binding data obtained using [3H]heparin and viable promastigotes, one derives a binding constant of 4.7 x 10(-7) M and an estimate of 860,000 receptors per parasite. The [3H]heparin bound to parasites could not be displaced by hyaluronic acid or by three other glycosaminoglycans (dermatan sulphate, chondroitin 4-sulphate and chondroitin 6-sulphate). It was demonstrated that exponential phase promastigotes growing in medium 199 supplemented with fetal bovine serum incorporate 35SO4 into a cell-associated macromolecule that has the properties of heparin proteoglycan. Heparin inhibits the activity of the cell-surface histone-protein kinase; incubation of viable promastigotes with [gamma-32P]ATP and MgCl2 (10 mM) in the absence and presence of heparin (0.01-0.5 mg/ml) for 10 min, followed by analysis by SDS/polyacrylamide-gel electrophoresis and autoradiography, revealed that the phosphorylation of 12 or 13 parasite proteins was inhibited by the glycosaminoglycan. These data suggest that heparin may play a role in the host-parasite relationship.     

Standardization of parameters for the mycobacillin synthetase activity

An effective method of preparation involving sonication was developed for cell-free mycobacillin synthetase fromBacillus subtilis. The enzyme showed optimum activity at a buffer concentration of 50 mM (Tris-HCl) and pH 7.5. ATP and Mg²⁺ which were essential for synthesis showed an optimum requirement at a ratio of 1∶1. The synthetase was markedly inhibited by ADP whereas AMP was without any effect. ATP or ATP-generating system could not be replaced by GTP, UTP or CTP. Co²⁺ and Mn²⁺ could to some extent substitute Mg²⁺. Mercapto reagents inhibited the antibiotic synthesis. Exogenous addition of pantothenic acid had no effect.     

Role of ATP and enzyme-bound nascent peptides in the control of elongation for mycobacillin synthesis.

The presence of a Zn2+-dependent acid p-nitrophenyl phosphatase (EC 3.1.3.2) in bovine liver was described. The enzyme was purified to apparent homogeneity and migrates as a single band during electrophoresis on polyacrylamide gel. The enzyme requires Zn2+ ions for catalytic activity, other bivalent cations have little or no effect. The enzyme, of Mr 118,000, optimum pH 6-6.2 and pI 7.4-7.5, was inhibited by EDTA, tartrate, adenine and ATP, but not by fluoride. The common phosphate esters are poor substrates for the enzyme, which hydrolyses preferentially p-nitrophenyl phosphate and o-carboxyphenyl phosphate. The Zn2+-dependent acid p-nitrophenyl phosphatase of bovine liver was different from the high-Mr acid phosphatases previously detected in mammalian tissues.     

Regulation of fibrinogen assembly. Transfection of Hep G2 cells with B beta cDNA specifically enhances synthesis of the three component chains of fibrinogen

Previous studies indicated that synthesis of B beta chain may be a rate-limiting factor in the production of human fibrinogen since Hep G2 cells contain surplus pools of A alpha and gamma but not of B beta chains, and fibrinogen assembly commences by the addition of preformed A alpha and gamma chains to nascent B beta chains attached to polysomes. To test whether B beta chain synthesis is rate limiting Hep G2 cells were transfected with B beta cDNA, and its effect on fibrinogen synthesis and secretion was measured. Two sets of stable B beta cDNA-transfected Hep G2 cells were prepared, and both cell lines synthesized 3-fold more B beta chains than control cells. The B beta-transfected cells also synthesized and secreted increased amounts of fibrinogen. Transfection with B beta cDNA not only increased the synthesis of B beta chain but also increased the rate of synthesis of the other two component chains of fibrinogen and maintained surplus intracellular pools of A alpha and gamma chains. Transfection with B beta cDNA did not affect the synthesis of albumin, transferrin, or anti-chymotrypsin and had a small inhibitory effect on the synthesis of C-reactive protein. Taken together these studies demonstrate that increased B beta chain synthesis specifically causes increased production of the other two component chains of fibrinogen and that unequal and surplus amounts of A alpha and gamma chains are maintained intracellularly.     

Effect of temperature on the spectral properties of coenzyme F420 and related compounds.

The uv-visible spectra of 7,8-didemethyl-8-hydroxy-5-deazaflavin-5'-phosphoryllactyl glutamate (coenzyme F420), a naturally occurring 5-deazaflavin derivative, in three different buffers changed with a rise in temperature; the effect on the extinction coefficient at 420 nm (epsilon 420) was as follows: In phosphate-buffered solutions at pH less than 7.5, the epsilon 420 increased (at pH 5.0 for a temperature shift from 15 to 60 degrees C, delta epsilon 420 was +87%), but between pH 7.5 and 8, epsilon 420 changed very little. At pH greater than 8.0 in phosphate- or borate-buffered solutions, epsilon 420 decreased slightly. In morpholineethanesulfonic acid (Mes)-buffered F420 solutions at pH 5 and 5.5, epsilon 420 changed very little, whereas at pH 6-8, the epsilon 420 decreased. Absorbance of F420 at 401 nm in phosphate buffer at pH 5 to 9 was not significantly affected by temperature. Changes in epsilon 420 due to temperature change corresponded to changes in the pKa of 8-OH of the deazaflavin molecule; studies with adenylated F420 showed that the 8-OH of F420 was responsible for these changes.(ABSTRACT TRUNCATED AT 250 WORDS)     

Molecular dynamics simulation of oligosaccharides containing N-acetyl neuraminic acid

αD -N-acetyl neuraminic acid (Neu5Ac, sialic acid) is a commonly occurring carbohydrate residue in various cell surface glycolipids and glycoproteins. This residue is linked terminally or internally to Gal residues via an α(2 → 3) or α(2 → 6) linkage. In the cell surface receptor, sialyl-Lewis^X, a terminal α(2 → 3) linkage is present. Previous studies from our laboratory have shown that in solution Lewis^X adopts a relatively rigid structure. In order to model the Neu5Ac residue, vacuum molecular dynamics of this monosaccharide were compared with simulations that explicitly include solvent water. The dynamical average of the monosaccharide conformation obtained from the two simulations was similar. Vacuum calculations for the disaccharide Neu5Ac α(2 → 3) Gal β-O-methyl show that a number of low energy minima are accessible to this disaccharide. Molecular dynamics simulations starting from the low energy minima show conformational transitions with a time scale of 10–50 ps among several of the minima while large barriers between other minima prevent transitions on the time scale studied. Simulations of this disaccharide in the presence of solvent show fewer conformational transitions, illustrating a dampening effect of the solvent that has been observed in some other studies. Our results are most consistent with an equilibrium among multiple conformations for the Neu5Ac α(2 → 3) Gal β linkage. © 1994 John Wiley & Sons, Inc.     

Cellular affinity is the only deciding factor for microcarrier selection for the cultivation of anchorage dependent cells

Summary Vero and BHK-21 cells are not attached and spreaded equally on the same microcarrier. BHK-21 cells require a microenvironment similar to the mammalian tissue for attachment and spreading. Cellular affinity, which control adhesion to the surface, varied with the growth phase, membrane integrity and the type of microcarrier.     

Biodegradation of rice stumps by soil mycoflora

Summary Cellulose and lignin contents in left-overs of rice stump decreased due to decay caused by soil mycoflora. The loss of cellulose and lignin was considerable in presence of Curvularia and Fusarium respectively. Other tested mycoflora could also destroy cellulose and lignin to some extent. The amount of loss of cellulose and lignin increased with time of incubation of the tested mycoflora.     

Insulin-activated protein kinases phosphorylate a pseudosubstrate synthetic peptide inhibitor of the p70 S6 kinase

p70 S6 kinase, a major insulin-mitogen-activated ribosomal S6 protein kinase in mammalian cells, is activated by phosphorylation of multiple Ser/Thr residues on the enzyme polypeptide. A synthetic peptide, corresponding to a 37-residue segment from the carboxyl-terminal tail of the kinase which resembles the sequence phosphorylated in S6, acts as a competitive inhibitor of p70 S6 kinase without itself being phosphorylated by the enzyme. This synthetic peptide is phosphorylated by an array of protein kinases which are rapidly activated by insulin. Thus, these sequences of p70 S6 kinase constitute a potential autoinhibitory pseudosubstrate site, whose phosphorylation is catalyzed by candidate upstream-activating protein kinases.