Participation of alkaline phosphatase in the active transport of phosphates in brush border membrane vesicles

This paper reports the separation and preliminary characterization of the products formed by the reaction of the antitumor compound cis-Pt(NH₃)₂Cl₂ with DNA. Electrophoresis of the acid hydrolysed platinum-DNA complex gave a profile of platinum concentration which contained 5 peaks whose relative intensities varied with the amount of cis-Pt(NH₃)₂Cl₂ fixed on the DNA. Similar analysis of the products formed between DNA and trans-Pt(NH₃)₂Cl₂ or [Pt(dien)Cl]Cl, which are not active antitumor agents, indicated that these compounds bound to DNA in a different manner than cis-Pt(NH₃)₂Cl₂. DNA isolated from Escherichia coli which had been treated with cis-Pt(NH₃)₂Cl₂ or [Pt(dien)Cl]Cl did not give the same electrophoresis profiles as the corresponding platinum-DNA complexes formed in vitro.     

A ganglioside receptor on lymphocytes mediates recognition of self

Lymphocytes from mouse spleen and thymus form spontaneous rosettes with autologous erythrocytes. Certain gangliosides are described here as potent inhibitors of this cell contact formation. A comparison of several gangliosides shows that lymphocytes from thymus and spleen differ significantly in their reactivity towards GM1, GM3, GD1a, GD1b and GT1b. Differences are also seen between inbred mouse strains.     

A branch and bound algorithm for the protein folding problem in the HP lattice model

A branch and bound algorithm is proposed for the two-dimensional protein folding problem in the HP lattice model. In this algorithm, the benefit of each possible location of hydrophobic monomers is evaluated and only promising nodes are kept for further branching at each level. The proposed algorithm is compared with other well-known methods for 10 benchmark sequences with lengths ranging from 20 to 100 monomers. The results indicate that our method is a very efficient and promising tool for the protein folding problem.     

Liganded hemoglobin structural perturbations by the allosteric effector L35

Effector binding to liganded hemoglobin (Hb) provides a new understanding of structural determinants of Hb function. L35, a bezafibrate-related compound, is one of the more potent synthetic regulators of Hb oxygen (O(2)) affinity. In the presence of inositol hexaphosphate and bezafibrate (or derivatives), liganded Hb at low pH (pH approximately 6.5) exhibits extremely low O(2) affinity and very low cooperativity. In this study, the nature of L35 binding to COHbA at pH 6.35, an altered R-state, is presented. Solution-active site-specific spectroscopic probings by front-face fluorescence and circular dichroism reveal that L35 induces a global heterogeneous conformation in COHbA at pH 6.35 that includes: a T-like structural feature at the alpha1beta2 interface; an R-like structural feature within the heme environment; and an intermediate-like state at the central cavity. These long-range structural perturbations appear to stem from L35 binding to two classes of binding sites: the central cavity (primarily at the alphaalpha cleft) and the surface. These results indicate that L35 induces an allosteric transition species, characterized by domain-specific tertiary and quaternary-like conformation within a global R-quaternary structure.     

Effect of calcium on subcellular distribution of peroxidases

About 40% of the peroxidase activity extracted from hypocotyl hooks of etiolated Cucurbita pepo was pelletable at 20000 g. The activity in the pellet was partially solubilized by the addition of 5 mM EGTA. This effect of EGTA was reversed by Ca²⁺, but not by Mg²⁺. Reassociation of EGTA-solubilized peroxidases to 4 cellular fractions obtained by centrifugation on discontinuous sucrose gradients was assayed. It appeared that the enzymes could be linked to ribosomes or RNP particles through Ca²⁺. Two fractions, identified as smooth and rough endoplasmic reticulum, also bound peroxidases and, in this case, the Ca²⁺-mediated binding involved a loss of the enzyme activity. The fraction containing mitochondria and plasmalemma exhibited a slight binding capacity. Isoelectric focusing in thin layer polyacrylamide gel showed that only 5 out of the 10 isoperoxidases present in hypocotyl hooks had their pelletability level changed by Ca²⁺.     

Backbone nuclear relaxation characteristics and calorimetric investigation of the human Grb7-SH2/erbB2 peptide complex

Grb7 is a member of the Grb7 family of proteins, which also includes Grb10 and Grb14. All three proteins have been found to be overexpressed in certain cancers and cancer cell lines. In particular, Grb7 (along with the receptor tyrosine kinase erbB2) is overexpressed in 20%–30% of breast cancers. Grb7 binds to erbB2 and may be involved in cell signaling pathways that promote the formation of metastases and inflammatory responses. In a prior study, we reported the solution structure of the Grb7-SH2/erbB2 peptide complex. In this study, T₁, T₂, and steady-state NOE measurements were performed on the Grb7-SH2 domain, and the backbone relaxation behavior of the domain is discussed with respect to the potential function of an insert region present in all three members of this protein family. Isothermal titration calorimetry (ITC) studies were completed measuring the thermodynamic parameters of the binding of a 10-residue phosphorylated peptide representative of erbB2 to the SH2 domain. These measurements are compared to calorimetric studies performed on other SH2 domain/phosphorylated peptide complexes available in the literature.     

Flexibility of metal binding sites in proteins on a database scale

Protein metal binding sites in the pre-bound (apo) state, and their rearrangements upon metal binding were not analyzed previously at a database scale. Such a study may provide valuable information for metal binding site prediction and design. A high resolution, nonredundant dataset of 210 metal binding sites was created, containing all available representatives of apo-holo pairs for the most populated metals in the PDB. More than 40% of the sites underwent rearrangements upon metal binding. In 30 cases rearrangements involved the backbone. The tendency for side-chain rearrangement inversely correlates with the number of first-shell residues. Analysis of side-chain reorientations as a result of metal binding showed that in 95% of the rigid-backbone binding sites at most one side chain moved. Thus, in general, part of the first coordination shell is already in place in the pre-bound form. The frequencies of side-chain reorientation directly correlated with metal ligand flexibility and solvent accessibility in the apo state.     

Biosynthesis of UDP-xylose: characterization of membrane-bound At<Emphasis Type="Italic">Uxs2</Emphasis>

UDP-xylose (UDP-Xyl) is a sugar donor for the synthesis of glycoproteins, polysaccharides, various metabolites, and oligosaccharides in plants, vertebrates, and fungi. In plants, the biosynthesis of UDP-Xyl from UDP-glucuronic acid (UDP-GlcA) appears to be catalyzed by numerous UDP-glucuronic acid decarboxylase (Uxs) isoforms. For example, six Uxs isoforms in Arabidopsis thaliana (L.) and four in rice have been identified. However, the reason/s for the existence of several isoforms that are necessary for the synthesis of UDP-Xyl remains unknown. Here, we describe a Uxs isoform in Arabidopsis, AtUXS2, encoding an integral membrane protein that appears to be localized to the Golgi apparatus. The enzyme is a dimer and has distinct properties. Unlike the UXS3 isoform, which is shown here to be a soluble protein, the UXS2 isoform is membrane bound. The characteristics of the membrane-bound AtUxs2 and cytosolic AtUxs3 support the hypothesis that unique UDP-GlcA-DCs possessing distinct sub-cellular localizations can spatially regulate specific xylosylation events in plant cells.     

Variation in Chromatin Structure of the rDNA Transcribed Region in Human Peripheral Blood Lymphocytes

The rDNA transcribed region (TR) was tested for its accessibility for RsaI recognizing 15 TR sites, DNase I, and photoinducible arylazide (N-(4-azido-2-hydroxybenzoyl)-N,N"-diaminoheptane acetate) in isolated nuclei, and for the arylazide in intact cells. Arylazide readily entered the cells and did not appreciably affect the chromatin structure. Its photolysis products efficiently modified DNA in accessible sites. Single-strand breaks made by DNase I were not transformed into two-strand ones in rDNA TR, suggesting the necessity of denaturing electrophoresis for such an analysis. About 70% of all rDNA copies proved poorly accessible for endonucleases and arylazide, the accessibility being higher in their 18S and 5.8S rRNA gene regions than in the regions of the external transcribed spacers (ETSs) and the 28S rRNA gene. Proteinase K disrupted this structure, and the corresponding copies were extracted from nuclei. This explained whyin situ hybridization occasionally fails to reveal rDNA in the nucleolar fibrillar center (FC) on electron microscopic preparations. In other rDNA copies, TR (excluding 5"-ETS) was accessible for nucleases and arylazide. These copies were not extracted from nuclei treated with proteinase K. Some of their RsaI sites were protected by tightly bound proteins. Seven such regions were identified in TR. Possible association of the molecular structure, nucleolar location, and functional state of rDNA is discussed.