CLIX: a search algorithm for finding novel ligands capable of binding proteins of known three-dimensional structure.

A computer algorithm, CLIX, capable of searching a crystallographic data-base of small molecules for candidates which have both steric and chemical likelihood of binding a protein of known three-dimensional structure is presented. The algorithm is a significant advance over previous strategies which consider solely steric or chemical requirements for binding. The algorithm is shown to be capable of predicting the correct binding geometry of sialic acid to a mutant influenza-virus hemagglutinin and of proposing a number of potential new ligands to this protein.     

Cultivar and Rhizobium strain effect on nitrogen fixation and transport inPhaseolus vulgaris L.

The effects of Rhizobium strain and its interaction with plant cultivar were examined in glasshouse-grownPhaseolus vulgaris in two experiments where the physiological attributes defining the symbiotic efficiency were determined. Strains of Rhizobium significantly affected nodulation, rates of N accumulation, partitioning of N within the mature shoot and remobilizaton of the N stored in the vegetative organs to the seeds. The most efficient symbiosis (strain CO5 with Negro Argel), in comparison with the least efficient symbiosis (strain 127 K-17 with Venezuela-350) showed higher rates of C₂H₂ reduction from flowering to mid pod fill stage, evolved less hydrogen from nodules and showed higher rates of N transport as well as higher percentages of ureide-N in the xylem sap. At maturity, the best cultivar/strain association exceeded the total N accumulated in the seed and the harvest index of the poorest symbiosis in 88% and 20%, respectively. The other symbiotic combinations were intermediate in all characteristics. Nitrogen accumulation in plant shoot showed highly significant correlation with acetylene reduction rates, nodule relative efficiency, total N transport in the xylem sap and percentage of N transported as ureides.     

The influence of the culture medium on the competitive abilities ofBradyrhizobium japonicum strains

Growth on culture media results in changes in Rhizobium competitivity:Bradyrhizobium japonicum strain G2, when mixed with the strain GMB 1 in the same ratio, formed 85% of the total nodule numbers when the strains were cultured on the YEM medium, whereas, it formed only 55% of the nodules when they were cultured on the MSY medium.     

Native root-nodule bacteria of traditional soybean-growing areas of northern Thailand

Over 1500 root-nodule bacteria were isolated from a range of uninoculated soybeans, and one cowpea, trap-hosts, sown in 1985 into traditional soybean-growing areas of soybean-growing areas of northern Thailand. Most isolates were slow-growing Bradyrhizobium japonicum. Using a modified bottle-jar technique, 586 of the isolates were tested with a range of soybean hosts and one cowpea host. The results indicated:

Structural, motional, and kinetic features of the Cu(II)-(L-His)2 complex in aqueous solution

A careful analysis by 1H and 13C FT-NMR on the Cu(II) (L-histidine)2 complex was carried out which allows delineation of structure and dynamics in solution. A mixture of complexes was shown such that 24% of the Cu(II) (L-histidine)2 complex contains both histidines bound in the histaminelike way, while the remaining 76% contains one L-His molecule bound in the histaminelike way and the other L-His molecule bound in the glycinelike way. The motional correlation time and relevant features of the exchange process were also delineated.     

Vasoactive intestinal peptide effects on GH3 pituitary tumor cells: high affinity binding, affinity labeling, and adenylate cyclase stimulation. Comparison with peptide histidine isoleucine and growth hormone-releasing factor

The vasoactive intestinal polypeptide (VIP) receptor was characterized on the GH3 rat pituitary tumor cell line using competitive binding studies with peptides having sequence homology with VIP. Further studies investigated receptor coupling to the adenylate cyclase complex by measurement of cAMP levels. Finally, the molecular weight of the receptor was estimated by affinity labeling techniques. Studies using 125I-VIP and unlabeled competing peptides revealed a single class of high affinity binding sites with a dissociation constant (KD) of 17 +/- 2 nM (mean +/- S.E.M.) for VIP, 275 +/- 46 nM for peptide histidine isoleucine (PHI), and 1380 +/- 800 nM for human pancreatic growth hormone releasing factor (GHRF). VIP and PHI each stimulated intracellular cAMP accumulation in a dose-dependent manner; both peptides demonstrated synergism with forskolin. In contrast, GHRF neither stimulated accumulation of cAMP nor demonstrated synergism with forskolin. VIP plus PHI (1 microM each) caused no significant increase in cAMP over either VIP or PHI alone, implying that the two peptides act through the same receptor. Covalent crosslinking of 125I-VIP to its binding site using either disuccinimidyl suberate (DSS) or ethylene glycol bis(succinimidyl succinate) (EGS) was followed by SDS-PAGE and autoradiography. The result is consistent with an Mr 47 000 VIP-binding subunit comprising or being associated with the VIP receptor of GH3 pituitary tumor cells.     

Liposome-mediated labeling of adrenocorticotropin fragments parallels their biological activity

To test our hypothesis that specific interactions of ACTH peptides with model lipid membranes reflect the biological importance of similar interactions on target cells, we investigated the liposome-mediated labeling of ACTH fragments with the extremely hydrophobic photolabel, 3-trifluoromethyl-3-(m-[125I]iodophenyl)diazirine. Correlations were found between the labeling rates and the agonistic and antagonistic potencies of the peptides for in vitro steroidogenesis and inhibition of a synaptosomal protein kinase. A model for the cross-reactivity between ACTH and opioid peptides is discussed.     

Evaluation of H2O activity in the free or phosphorylated catalytic site of Ca2+-ATPase

The sarcoplasmic reticulum Ca2+-ATPase catalyses a reversible calcium transport coupled to phosphate transfer between ATP and water. It has been proposed [Biochemistry (1980) 19, 4252-4261] that the reactivity of the acyl-phosphate bond is dependent on the water activity within the catalytic site. We have tested this hypothesis and found that the polarity in the free catalytic site is lower than that of water, a further and large decrease is observed when the enzyme is phosphorylated by Pi. Phosphorylation by ATP indicates that this polarity change is specifically associated with the formation of the ADP-insensitive phosphoenzyme.     

Proton magnetic resonance studies of 7 Fe ferredoxins: Lower potential of the [4 Fe–4 S] redox center than the [3 Fe–3 S] cluster

Two types of iron-sulfur clusters, [3 Fe–3 S] and [4 Fe–4 S], were identified by ¹H-NMR in ferredoxins from Thermus thermophilus, Mycobacterium smegmatis and Pseudomonas ovalis. The [4 Fe–4 S] clusters always showed the redox couples which had potentials lower than that of the [3 Fe–3 S] clusters.