Physicochemical basis of the recognition process in nucleic acid interactions, IV. Costacking as the cause of mispairing and intercalation in nucleic acid interactions.
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Benzopyrenes↗
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The influence of short-range interactions on protein conformation. I. Side chain-backbone interactions within a single peptide unit.
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Alanine↗
Theoretical studies of metal-phosphate interactions: interaction of Li+, Na+, K+, Be++, Mg++, and Ca++ with H2PO4- and (CH3O)2PO2-: implications for nucleic acid solvation.
Model phosphate-metal solvation complexes have been studied by ab-initio self-consistent-field techniques. The complexes studied include (RO)2PO2-(R = H or CH3) with Li+, Na+, K+, Be++, Mg++, Ca++, H2O, and Cl-. The geometries of the complexes were chosen to approximate reasonable model solvation complexes for phosphate groups in a nucleic acid environment. Calculated energies of formation vary as Be++ greater than Mg++ greater than Ca++ greater than Li+ greater than Na+ greater than K+ for all isostructural complexes, consistent with experimental binding trends. These results suggest that site binding of this type can successfully account for the relative specificities of ion binding in polynucleotides and other phosphate-containing molecules.
Beryllium↗
Regulatory interactions between mitochondrial genes: interactions between two mosaic genes.
We have studied the mitochondrial DNA and the phenotypes of strains of Saccharomyces cerevisiae with specific intervening sequences in two mosaic genes: cob (the gene for apocytochrome b) and oxi3 (the gene for subunit I of cytochrome oxidase). The results suggest the following. (i) The presence of an intervening sequence downstream encompassing the intron box7 is sufficient for the regulation of oxi3 by cob (BOX phenotype); two sequences (containing intron loci box3 and box10) upstream in cob and two in oxi3 are dispensable. (ii) Strains without the two sequences upstream still contain the downstream sequence and the competence to specify a functional trans-acting element. Mutational lesions in this segment are phenotypically indistinguishable from box7 mutants, including the accumulation of polypeptides with homologous amino acid sequences. (iii) A catabolite-sensitive BOX phenotype, characteristic of mutants in the first exon, requires the simultaneous presence of an adjacent intervening sequence. A model is presented in which a hypothetical product specified by an intron (locus box7) of the cob gene controls the expression of a second mosaic gene (oxi3).
DNA Restriction Enzymes↗
Interaction between pseudorabies virus and heparin/heparan sulfate. Pseudorabies virus mutants differ in their interaction with heparin/heparan sulfate when altered for specific glycoprotein C heparin-binding domain.
Cell surface heparan sulfate serves as an initial receptor for a number of herpesviruses including pseudorabies virus (PrV). It has been demonstrated that the heparan sulfate-binding domain of PrV glycoprotein C is composed of three discrete clusters of basic residues corresponding to amino acids 76-RRKPPR-81, 96-HGRKR-100, and 133-RFYRRGRFR-141, respectively, and that these clusters are functionally redundant, i.e. each of them could independently support PrV attachment to cells (Flynn, S. J., and Ryan, P. (1996) J. Virol. 70, 1355-1364). To evaluate the functional significance of each of these clusters we have used PrV mutants in which, owing to specific alterations in glycoprotein C, the heparan sulfate-binding site is dominated by a single specific cluster. These mutants exhibited different patterns of susceptibility to selectively N-, 2-O-, and 6-O-desulfated heparin preparations in virus attachment/infectivity assay. Moreover PrV mutants differed as regard to efficiency of their attachment to and infection of cells pretreated with relatively low amounts of heparan sulfate-degrading enzymes. Furthermore glycoprotein C species, purified from respective mutants, bound heparin oligosaccharide fragments of different minimum size. These differences suggest that specific clusters of basic amino acids of the heparan sulfate-binding domain of glycoprotein C may support PrV binding to different structural features/stretches within the heparan sulfate chain.
Amino Acid Sequence↗
Arginine/serine-rich protein interaction domain-dependent modulation of a tau exon 10 splicing enhancer: altered interactions and mechanisms for functionally antagonistic FTDP-17 mutations Delta280K AND N279K.
Tau exon 10 splicing is altered by autosomal dominant mutations that cause frontotemporal dementia with parkinsonism chromosome 17-type and by unknown mechanisms in other related neurodegenerative disorders. Identifying cis- and trans-regulators of tau exon 10 splicing is therefore crucial for understanding disease mechanisms. We previously identified several splicing enhancers and silencers within exon 10 and intron 10. Here, we show that splicing factors SF2/ASF, Tra2beta, and a 50-kDa nuclear protein bind in vitro to the polypurine enhancer at the 5' end of exon 10. Disease splicing mutations N279K and Delta280K disrupt the enhancer and alter associations with these factors. N279K targets robustly bind Tra2beta compared with the normal enhancer, which may explain why N279K enhances exon 10 splicing in vivo. In contrast, factor associations with Delta280K targets are nearly undetectable, explaining why Delta280K almost abolishes exon 10 splicing in vivo. Small interfering RNA-mediated suppression of endogenous SF2/ASF and Tra2beta significantly reduces exon 10 splicing. Exogenous SF2/ASF dramatically enhances normal exon 10 splicing and efficiently rescues the Delta280K splicing defect. Domain deletion analyses show that the C-terminal RS domains of SF2/ASF and Tra2beta are required for normal exon 10 splicing in vivo. In contrast to Tra2beta, the SF2/ASF RS domain remains essential in the presence of a strengthened enhancer or when either weak splice site is strengthened. The data suggest that SF2/ASF has both essential and regulatory roles, whereas Tra2beta has a supporting role in exon 10 splicing.
Alternative Splicing↗
Interaction and insight in group psychotherapy: the case for interaction.
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Female↗
The histocompatibility restrictions on macrophage T-helper cell interaction determine the histocompatibility restrictions on T-helper cell B-cell interaction.
To study the histocompatibility restriction between macrophages and helper T cells, carrier primed guinea pig T cells were positively selected in vitro with antigenpulsed macrophages for 7 days and the selected T cells were then mixed with hapten-primed B cells and stimulated with antigen in a modified Mishell-Dutton system. Helper T cells could only be selected with syngeneic, but not allogeneic, antigen-pulsed macrophages and would then collaborate only with syngeneic, but not allogeneic, hapten-primed spleen cells. When F1 T cells were selected with antigen-pulsed parental macrophages they would only collaborate with B cells of the same parental strain as the macrophages used in the selection culture. These results are strongly in support of the view that the primed T cell is activated by carrier determinants of the nominal antigen in association with Ia antigens on macrophages and the helper T cell, in turn, activates B cells which bear the same Ia antigens and determinants of the nominal antigen bound to immunoglobulin receptors on their surface. In addition, in experiments with antigens the response to which is controlled by I-linked genes, we demonstrated that primed (responder X nonresponder)F1 T cells would only collaborate with B cells of the responder parent. The defect appeared to be at the level of the B cell in that the addition to the cultures of antigen-presenting cells of the responder type did not restore the ability of F1 T cells to collaborate with non-responder B cells.
Animals↗
Core-sigma interaction: probing the interaction of the bacteriophage T4 gene 55 promoter recognition protein with E.coli RNA polymerase core.
The bacterial RNA polymerase sigma subunits are key participants in the early steps of RNA synthesis, conferring specificity of promoter recognition, facilitating promoter opening and promoter clearance, and responding to diverse transcriptional regulators. The T4 gene 55 protein (gp55), the sigma protein of the bacteriophage T4 late genes, is one of the smallest and most divergent members of this family. Protein footprinting was used to identify segments of gp55 that become buried upon binding to RNA polymerase core, and are therefore likely to constitute its interface with the core enzyme. Site-directed mutagenesis in two parts of this contact surface generated gene 55 proteins that are defective in polymerase-binding to different degrees. Alignment with the sequences of the sigma proteins and with a recently determined structure of a large segment of sigma70 suggests that the gp55 counterpart of sigma70 regions 2.1 and 2.2 is involved in RNA polymerase core binding, and that sigma70 and gp55 may be structurally similar in this region. The diverse phenotypes of the mutants implicate this region of gp55 in multiple aspects of sigma function.
Bacteriophage T4↗
Social interaction and perceived adequacy of interaction of the rural aged.
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Aged↗
Interaction of aminoglycosides and cephalosporins against Pseudomonas aeruginosa. Correlation between interaction index and killing curve.
Three multiresistant clinical isolates of Pseudomonas aeruginosa were evaluated, by the chequerboard and the killing curve methods, for in-vitro synergy between cephalosporins and aminoglycosides. The killing-curve method was standardized to give results comparable with those obtained with the chequerboard test (FIC index). This was achieved with combinations showing synergy by chequerboard (FIC less than or equal to 0.75) by using in the killing curves subinhibitory concentrations: half the MIC in single antibiotic assay and one eighth the MIC in the combinations. For combinations that showed indifference by chequerboard (FIC = 1) half the MIC was used for antibiotics alone and in combination. For the antagonistic combinations by chequerboard (FIC greater than 2) concentrations equal to the MIC were used with single antibiotics and combinations in the killing curve experiments. Prediction of killing curve results could then be obtained with the FIC index. The killing curve results could not be explained by pH changes or inactivation of the antibiotics.
Amikacin↗
Global aspects of C/N interactions determining plant-environment interactions.
The atomic C:N ratio in photolithotrophs is a function of their content of nucleic acids, proteins, lipids, polysaccharides, and other organic materials, and varies from about 5 in some protein-rich microalgae to much higher values in macroalgae and in higher plants with relatively more structural and energy storage materials. These differences in C:N ratios among organisms means that there is more N assimilation by photosynthetic organisms in the oceans than on land despite the near equality of global photosynthetic C assimilation rates in the two environments. Aquatic organisms obtain inorganic C and inorganic N from the surrounding water. Terrestrial photolithotrophs obtain inorganic C, dinitrogen (by diazotrophy) and some combined N from the atmosphere, with the remaining combined N coming from the soil. The nitrogen cost of growth (biomass production rate per unit plant N) varies with the C:N ratio and specific growth rate of the organism. The C:N ratio of plants can be increased with no, or minimal, decrease in growth rate by switching from N-containing to N-free solutes involved in, for example, UV-B screening or by reducing the content of particular proteins. The water cost of growth (water lost per unit biomass gain) in terrestrial plants is a function of N supply and of C supply; water cost is lower with higher N and C availability. Water supply is also important in determining denitrification rates on land and on N (and C) fluxes from terrestrial to aquatic systems.
Carbon↗
Interaction of tyrosyl, histidyl, and tryptophanyl peptides with DNA: specificity and mechanism of the interaction.
In the Tyr-(Gly)(1-4)-Tyr series maximal thermal stabilization of calf thymus DNA (deltaT(m)=10 degrees ) occurred with the Tyr-(Gly)(2)-Tyr peptide, where three base pairs could separate the two tyrosyl residues. Tyr-Gly-Tyr-Gly-Tyr stabilized the DNA by 6 degrees . The alternating Trp-Gly-Trp-Gly-Trp and His-Gly-His-Gly-His peptides were equally as effective as the Tyr-Gly-Tyr-Gly-Tyr peptide in stabilizing calf thymus DNA against thermal denaturation. But the alternating Phe-Gly-Phe-Gly-Phe peptide afforded little stabilization, suggesting that a sidechain possessing both a conjugated pi-electron system and an electron donor atom is necessary for DNA stabilization. Introduction of electron withdrawing iodo or nitro group into the tyrosyl sidechains almost completely abolished the stabilizing effect. Although the tyrosyl peptides seem to be specific for GC-base pairs, no correlation was found in natural DNA between% GC and% thermal stabilization. Eukaryotic DNAs showed twice the stabilization of prokaryotic DNAs with the same GC content.
Amino Acid Sequence↗
Direct interaction rescue, a novel filamentous phage technique to study protein-protein interactions.
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Base Sequence↗
Histone Hl-DNA interaction. Influence of phosphorylation on the interaction of histone Hl with linear fragmented DNA.
By measuring the fluorescence polarization of fluorescent histone H1 derivatives complexed with DNA, binding of the histone to DNA was studied as a function of ionic strength in the solution prior to and after the H1 phosphorylation on Ser-37 residue. Fluorescent labels were covalently linked either specifically to Tyr-72 residues or unspecifically to lysine residues in the H1 polypeptide chain. The values of the corresponding rotational relaxation times showed that at low ionic strength all the segments of the H1 molecule were immobilized on binding to DNA. The gradual increasing NaC1 concentration in the solution of H1-DNA complex was accompanied at first by additional retardation of the histone mobility in the complex, and then by progressive release of histone H1 from from the complex which was completed at 0.5-0.6 M NaC1 irrespective of phosphorylation. tat the same time the phosphorylation of histone H1 led to removal of the central and, presumably, N-terminal regions of H1 from DNA.
DNA↗
Polynucleotide-protein interactions in the translation system. Identification of proteins interacting with tRNA in the A- and P-sites of E. coli ribosomes.
Ultraviolet irradiation (lambda = 254 nm) of ternary complexes of E. coli 70 S ribosomes with poly(U) and either Phe-tRNAPhe (in the A-site) or NAcPhe-tRNAPhe (in the P-site) effectively induces covalent linking of tRNA with a limited number of ribosomal proteins. The data obtained indicate that in both sites tRNA is in contact with proteins of both 30 S and 50 S subunits (S5, S7, S9, S10, L2, L6 and L16 proteins in the A-site and S7, S9, S11, L2, L4, L7/L12 and L27 proteins in the P-site). Similar sets of proteins are in contact with total aminoacyl-tRNA and N-acetylaminoacyl-tRNA. However, here no contacts of tRNA in the P-site with the S7 and L25/S17 proteins were revealed, whereas in the A-site total aminoacyl-tRNA contacts L7/L12. Proteins S9, L2 and, probably, S7 and L7/L12 are common to both sites.
Binding Sites↗
Proteins of small subunits of rat liver ribosomes that interact with poly(U). I. Effects of preincubation of poly(U) with 40 S subunits on the interactions of 40 S subunit proteins with aurintricarboxylic acid and with N,N'-p-phenylenedimaleimide.
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Animals↗
Interaction of myosin subfragment-1 with actin. III. Effect of cleavage of the subfragment-1 heavy chain on its interaction with actin.
To determine the reason why the Mg2+-ATPase activity of subfragment-1 prepared with chymotrypsin was activated more by actin than that of subfragment-1 prepared with trypsin was and the reason why the former could enhance the polymerization of actin and the latter could not, we digested subfragment-1, prepared with chymotrypsin, with trypsin and examined the actin activated Mg2+-ATPase activity and the ability to polymerize actin. It was found that cleavage of the heavy chain decreased the actin activated Mg2+-ATPase activity of subfragment-1 prepared with chymotrypsin but did not affect its ability to polymerize actin. Trypsin attacked the subfragment-1 heavy chain at two sites and produced 26 K, 50 K, and 21 K fragments. From the comparison of the time course of tryptic digestion with that of the decrease in actin activation, it was deduced that cleavage of the 50 K-21 K junction was mainly responsible for the decrease in actin activation. We also measured the length and the amount of F-actin polymerized by the addition of different amounts of subfragment-1. It was found that the amount of F-actin increased with the increase in the amount of subfragment-1 added and that the length of F-actin also increased though slightly. We concluded from the results that subfragment-1 enhanced the polymerization not only by facilitating the nucleus formation but also by strengthening the bond between actin monomers in forming F-actin.
Actins↗