Application of three-dimensional molecular hydrophobicity potential to the analysis of spatial organization of membrane domains in proteins: I. Hydrophobic properties of transmembrane segments of Na+, K+-ATPase

A new computer-aided molecular modeling approach based on the concept of three-dimensional (3D) molecular hydrophobicity potential has been developed to calculate the spatial organization of intramembrane domains in proteins. The method has been tested by calculating the arrangement of membrane-spanning segments in the photoreaction center ofRhodopseudomonas viridis and comparing the results obtained with those derived from the X-ray data. We have applied this computational procedure to the analysis of interhelical packing in membrane moiety of Na⁺, K⁺-ATPase. The work consists of three parts. In Part I, 3D distributions of electrostatic and molecular hydrophobicity potentials on the surfaces of transmembrane helical peptides were computed and visualized. The hydrophobic and electrostatic properties of helices are discussed from the point of view of their possible arrangement within the protein molecule. Interlocation of helical segments connected with short extramembrane loops found by means of optimization of their hydrophobic/hydrophilic contacts is considered in Part II. The most probable 3D model of packing of helical peptides in the membrane domain of Na⁺, K⁺-ATPase is discussed in the final part of the work.     

A non-alphoid repetitive DNA sequence from human chromosome 21

Summary A non-alphoid repetitive DNA from human chromosome 22, consisting of a 48-bp motif, shows homology to both G-group chromosomes in the gorilla, thus indicating the presence of additional repeat family members on further human chromosomes. Therefore, we screened a chromosome-21-specific cosmid library using this repetitive sequence from chromosome 22 (D22Z3). Some 40–50 cosmid clones were positive in tests for hybridization. One of the clones giving the strongest signals was digested with EcoRI/PstI, which we knew to cut frequently within the repeats; this resulted in fragments containing repeat units only. The fragments were subcloned into plasmid vector pTZ 19. Sequence-analysis of a 500-bp insert showed ten copies of a 48-bp repeat similar to D22Z3, with about 15% sequence deviation from the chromosome 22 consensus sequence. In situ hybridization of the newly isolated recombinant established its chromosome 21 specifity at high stringency. Physical mapping by pulsed field gel electrophoresis placed this new repeat in close vicinity to the chromosome 21 alphoid repeat. No cross-hybridization with other mammalian genomes except for those of apes was observed. The locus has been designated D21Z2 by the Genome Data Base. A gel mobility shift assay indicated that this repetitive motif has protein-binding properties.     

N-terminal amino-acid sequence of pig kidney dipeptidyl peptidase IV solubilized by autolysis.

The N-terminal amino-acid sequence of the intrinsic membrane protein dipeptidyl peptidase IV (DP IV) was determined. The protein was isolated from pig kidney and solubilized by autolysis at pH 3.8. The first 34 amino acids were sequenced and indicated approximately 78% identity to the N-terminal sequence of rat liver DP IV.     

Immunoelectron microscopic studies on the localization of peptidoglycan peptide subunit pentapeptides in bacterial cell walls

The peptide subunit pentapeptide H-L-Ala-D-Glu(L-Lys-D-Ala-D-Ala-OH)-NH₂ of peptidoglycan was localized in the cell walls of several Gram-positive bacteria employing the indirect immunoferritin technique. Specific antibodies to the D-alanyl-D-alanine moiety of non-crosslinked peptide subunit pentapeptide were raised in rabbits by immunization with synthetic immunogen albumin-(CH₂CO-Gly-L-Ala-L-Ala-D-Ala-D-Ala-OH)₃₉. Specificity of these antibodies for the peptide subunit pentapeptide and not for the peptide subunit tetrapeptide was corroborated in a Farr-type radio-active hapten binding assay. Specificity of labelling with ferritin was established by immunoelectron microscopic controls, and by the excellent correlation between specific labelling of cells with ferritin and the particular peptidoglycan primary structure of bacterial strains investigated. Cells of Lactobacillus gasseri, Streptococcus pyogenes and Staphylococcus aureus revealing non-crosslinked peptide subunit pentapeptides in their peptidoglycans could specifically be labelled. Lactobacillus acidophilus and Bacillus subtilis, on the contrary, missing such pentapeptides, failed in labelling.The implication of this method to possibly localize the points of attack of penicillin or cycloserine is discussed.Abbreviations used meso-A₂pm meso-diaminopimelic acid - DSM Deutsche Sammlung für Mikroorganismen, Göttingen, FRG This paper is dedicated to Professor Gerhart Drews on the occasion of his 60th birthday     

A domain-specific marker for the hepatocyte plasma membrane. II. Ultrastructural localization of leucine aminopeptidase to the bile canalicular domain of isolated rat liver plasma membranes

Leucine aminopeptidase (LAP) is an integral membrane glycoprotein localized to the apical membrane domain of intestinal and kidney epithelial cells. By indirect immunofluorescence, we have shown that antibodies raised against rat intestinal LAP recognized a similar protein concentrated in the bile canalicular (BC) domain of the hepatocyte in situ (Roman, L.M., and A.L. Hubbard, 1983, J. Cell Biol., 96:1548-1558). We have extended this localization to the ultrastructural level. When a saponin-permeabilized, agarose-embedded plasma membrane (PM) fraction was incubated with affinity-purified anti-LAP, 85% of the protein A-gold particles associated with the three recognizable PM domains were present in the BC. The levels of labeling on the other two domains (sinusoidal and lateral) did not exceed that observed with nonimmune controls. The concentration of LAP in the BC domain in isolated PM sheets prompted us to use this antigen for the affinity isolation of BC membrane (Roman, L.M., and A.L. Hubbard, 1984, J. Cell Biol., 98:1497-1504, companion paper).     

Chemical composition and structure of cell wall teichoic acids of staphylococci

The cell wall teichoic acid structures of 22 staphylococci including 13 type strains were determined. Most of the strains contain a poly(polyolphosphate) teichoic acid with glycerol and/or ribitol as polyol component. The polyolphosphate backbone is partially substituted with various combinations of sugars and/or amino sugars. Most of the substituents occur in a monomeric form but some strains also contain dimers of N-acetylglucosamine as substituents. Staphylococcus hyicus subsp. hyicus NCTC 10350 and S. sciuri DSM 20352 revealed rather complex cell wall teichoic acids. They consist of repeating sequences of phosphate-glycerol-phosphate-N-acetylglucosamine. The amino sugar component is present in this case as a monomer or an oligomer (n less than or equal to 3). Moreover, the glycerol residues are partially substituted with N-acetylglucosamine. The cell wall teichoic acid of S. auricularis is a poly(N-acetylglucosaminyl-phosphate) polymer similar to that found in S. caseolyticus ATCC29750. The cell wall teichoic acid structures for type strains of S. auricularis, S. capitis, S. cohnii, S. haemolyticus, S. hominis, S. hyicus subsp. hyicus, S. sciuri, S. xylosus and S. warneri were determined for the first time in detail. The structures of some of the previously described teichoic acids had to be revised (S. epidermidis, S. simulans, S. aureus phage type 187).     

ACTIVITY OF MARGINAL AND PLATE MERISTEMS DURING LEAF DEVELOPMENT OF XANTHIUM PENNSYLVANICUM

The mitotic and biosynthetic activities of the marginal and plate meristems were studied during the entire course of leaf development of Xanthium pennsylvanicum. In contrast to statements in the literature, marginal meristem activity is long in duration, as assayed by the mitotic counts and H³-thymidine incorporation. This me istem is active 23 days. The plate meristem is active for an additional 3 days after cessation of cell division in the marginal meristem, but the total duration of its mitotic activity is also approximately 23 days. Numerous periclinal cell divisions of the plate meristem form additional cell layers and contribute to the growth of the lamina in thickness. Incorporation of H³-thymidine increased during the course of leaf development. Cells between plastochronic ages 0 and 2.0 incorporated more of the radioisotopic precursor than those of younger leaf primordia. The uptake and incorporation of H³-thymidine into nuclear DNA was more sluggish during the early stages of development than in the more expanded leaves. No DNA synthesis was demonstrated after cessation of cell division in the leaf lamina. Metabolic or endomitotic DNA synthesis after leaf plastochron index (LPI) 3.0 seems improbable. No significant differences in the incorporation of H³-thymidine could be demonstrated between the marginal and plate meristems. This would indicate no distinct biosynthetic differences between the two meristems. The definitions of the marginal and plate meristems of Xanthium leaves were formulated in view of the above findings.