Prediction of the packing arrangement of strands in β-sheets of globular proteins

A method is proposed for predicting the adjacency order in which strands pack in a -sheet in a protein, on the basis of its amino acid sequence alone. The method is based on the construction of a predicted contact map for the protein, in which the probability that various residue pairs are close to each other is computed from statistically determined average distances of residue pairs in globular proteins of known structure. Compact regions, i.e., portions of the sequence with many interresidue contacts, are determined on the map by using an objective search procedure. The proximity of strands in a -sheet is predicted from the density of contacts in compact regions associated with each pair of strands. The most probable -sheet structures are those with the highest density of contacts. The method has been tested by computing the probable strand arrangements in a five-strand -sheet in five proteins or protein domains, containing 62–138 residues. Of the theoretically possible 60 strand arrangements, the method selects two to eight arrangements as most probable; i.e., it leads to a large reduction in the number of possibilities. The native strand arrangement is among those predicted for three of the five proteins. For the other two, it would be included in the prediction by a slight relaxation of the cutoff criteria used to analyze the density of contacts.     

Complete nucleotide sequence of the mitochondrial DNA from a liverwort,Marchantia polymorpha

Libraries of cosmid and plasmid clones covering the entire region of mtDNA from the liverwortMarchantia polymorpha were constructed. These clones were used for the determination of the complete nucleotide sequence of the liverwort mtDNA totally 186,608 bp (GenBank no. M68929) and including genes for 3 species of ribosomal RNAs, 29 genes for 27 species of transfer RNAs, and 30 genes for functionally known proteins (16 ribosomal proteins, 3 subunits of cytochromec oxidase, apocytochromeb protein, 3 subunits of H⁺-ATPase, and 7 subunits of NADH ubiquinone oxidoreductase). The genome also contains 32 unidentified open reading frames. Thus the complete nucleotide sequences from both chloroplast and mitochondrial genomes have been determined in the same organism. Plasmid clones are available upon the request. Gene names are represented according to Lonsdale and Leaver (1988) with modifications recommended by Lonsdale (personal communication).     

NAD+ Glycohydrolase of the Plasma Membrane Prepared from Glial and Neuronal Cells

NAD+ glycohydrolase (EC 3.2.2.5) activity was detected in the plasma membrane prepared from the primary culture of rat astrocytes. The enzyme has a broad optimum pH range. From the kinetic analysis, a Michaelis constant of 91.2 microM and a maximum velocity of 0.785 mumol/min/mg protein were obtained. ADPribose exhibited a competitive inhibition with respect to NAD. The inhibition by nicotinamide was shown to be of a non-competitive type. ATP and GTP were found to be competitive inhibitors. NAD+ glycohydrolase activity was not detected in the plasma membrane prepared from the primary culture of neuronal cells of chick embryos.     

A New Myelin-Deficient Mutant Hamster: Biochemical and Morphological Studies

Biochemical and morphological studies were done on a new trembling mutant hamster CBB. The yield of myelin from the mutant was 30 and 40% of the control at 46 and 140 days of age, respectively, but myelin composition and 2',3'-cyclic nucleotide-3'-phosphohydrolase (CNPase) activity were normal. Morphologically, about 18% of the axons were myelinated in the mutant optic nerve at 46 days of age, in which the myelinated fibers were those with larger diameters (more than 0.6 micron), while the control had a peak at 0.4 micron in diameter. The ultrastructure and thickness of compact myelin lamellae in the mutant were normal. Myelination and the structure of peripheral nerve myelin appeared normal. The results indicate that the essential defect is the delay and arrest of myelination in the CNS, which is probably caused by either a decreased rate of synthesis of myelin components in oligodendrocytes or a defect in the oligodendrocyte-axon recognition in smaller axons.     

Manganese-histidine cluster as the functional center of the water oxidation complex in photosynthesis

The recent model of Kambara and Govindjee for water oxidation [Kambara T. and Govindjee (1985) Proc. Natl. Acad. Sci. U.S.A., 82:6119–6123] has been extended in this paper by examining all the data in order to identify the most likely candidate for the redox-active ligand (RAL), suggested to operate between the water oxidizing complex (WOC) and Z, the electron donor to the reaction center P680. We have concluded that a very suitable candidate for RAL is the imidazole moiety of a histidine residue. The electrochemical data available on imidazole derivatives play heavily in this identification of RAL. Thus, we suggest that histidine might play the role of an electron mediator between the WOC and Z. A model of S-states in terms of their plausible chemical identity is presented here.Abbreviations J electronic spin of ion - P680 reaction center chlorophyll - RAL Redox active ligand - S_n state of the oxygen-evolving system - WOC water oxidation complex - Z electron donor to P680 Dedicated to Prof. L.N.M. Duysens on the occasion of his retirement     

Flavonoids in the leaves of twenty-eight polygonaceous plants

Flavonoids in the leaves of twenty-eight species belonging to the Polygonaceae were studied. Thirty-three kinds of flavonoids were isolated, and eighteen kinds were obtained as crystals. Quercetin glycosides were commonly found in the family. In the quercetin glycosides, 3-O-rhamnoside was most frequently found: 3-O-glucuronide is also distributed widely. Myricetin glycosides were rare. Methylated flavonols were found in some species of the sectionsEchinocaulon andPersicaria. Eleven kinds ofC-glycosylflavones were found in the present survey, andC-glycosylflavones were distributed in all species of the genusRheum and in almost all species of the section Tiniaria.Rumex Acetosella andPolygonum suffultum are exceptional, the former contains flavone glycoside and the latterC-glycosylflavones only, as main components.     

Mutants of Group D1Salmonella Carrying the Somatic Antigen of Group A Organisms: Isolation and Serological Characterization

O antigen mutants were obtained from Salmonella durban, a group D(1) organism, by treatment with N-methyl-N'-nitro-N-nitrosoguanidine. Serological studies demonstrated that the mutants lost the O-9 antigen factor of the parent organism but acquired the O-2 factor specific to group A Salmonella. Lipopolysaccharides of the mutant strains contained paratose which determines the specificity of O-2 factor. Tyvelose, present in the wild-type lipopolysaccharide, was not found in the mutants. H antigens and other biological characteristics of the mutant strains were the same as those of the wild-type organism. The present finding implies that group A Salmonella species might be derived from group D(1) organisms.