Selective recognition of tandemly repeated DNA sequences by homo- and heterodimers of short peptides

The non-covalent and specific protein-protein interaction is critical to the specificity and the cooperativity of the DNA-binding by protein dimers. We have designed and synthesized three sets of peptide dimers with covalent- or noncovalent artificial dimerization modules to elucidate the structural and thermodynamic aspects for the sequence-specific DNA-binding by protein dimers. We have investigated the DNA binding of covalent dimer, noncovalent homodimer and noncovalent heterodimer with specific or nonspecific DNA sequences by gel mobility shift assay. Although the amino acid sequence of DNA-binding region of these peptide dimers are the same, the selectivity and the cooperativity of DNA binding by these peptide dimers were found to be different.     

RecQ helicase, in concert with RecA and SSB proteins, initiates and disrupts DNA recombination

RecQ helicase is important to homologous recombination and DNA repair in Escherichia coli. We demonstrate that RecQ helicase, in conjunction with RecA and SSB proteins, can initiate recombination events in vitro. In addition, RecQ protein is capable of unwinding a wide variety of DNA substrates, including joint molecules formed by RecA protein. These data are consistent with RecQ helicase assuming two roles in the cell; it can be (1) an initiator of homologous recombination, or (2) a disrupter of joint molecules formed by aberrant recombination. These findings also shed light on the function of the eukaryotic homologs of RecQ helicase, the Sgs1, Blm, and Wrn helicases.     

Cytochrome c and dATP-dependent formation of Apaf-1/caspase-9 complex initiates an apoptotic protease cascade

We report here the purification of the third protein factor, Apaf-3, that participates in caspase-3 activation in vitro. Apaf-3 was identified as a member of the caspase family, caspase-9. Caspase-9 and Apaf-1 bind to each other via their respective NH2-terminal CED-3 homologous domains in the presence of cytochrome c and dATP, an event that leads to caspase-9 activation. Activated caspase-9 in turn cleaves and activates caspase-3. Depletion of caspase-9 from S-100 extracts diminished caspase-3 activation. Mutation of the active site of caspase-9 attenuated the activation of caspase-3 and cellular apoptotic response in vivo, indicating that caspase-9 is the most upstream member of the apoptotic protease cascade that is triggered by cytochrome c and dATP.     

Members of the USF family of helix-loop-helix proteins bind DNA as homo- as well as heterodimers

Free-living haematophagous insects risk death through host grooming responses or through increased susceptibility to predation whenever they take a bloodmeal. In this paper we investigate the effects of these risks on the feeding strategy of tsetse. A model is presented that allows for death of tsetse by starvation if they do not succeed in feeding within a fixed time (set at 6 days in the first instance) and for mortality specifically associated with feeding. In addition there is background mortality that applies to all flies at all times. The model is used to compute the individual life-time fertility (number of female puparia per female) as a function of the probability of obtaining a meal (indicated by field data to be very high, usually > 0.85 per day) and the day on which flies start to search for a meal. We suggest that the feeding strategy that would be selected for is that which allows the maximum reproductive output. The model shows that this strategy involves making no attempts to feed for 3-4 days after the previous meal and then attempting to feed with the greatest possible probability until a meal is obtained. The predicted feeding interval, obtained independently of any trapping data, agrees closely with all previous estimates from field studies using a variety of methods. Preliminary results from a laboratory experiment reveal an increased risk of predation of recently fed as compared with hungry tsetse. The lower the actual feeding mortality the more frequently will flies be able to feed should conditions so demand. It is adaptive, however, for tsetse to delay attempting to feed for as long as they can, which is made possible by the near certainty of locating and feeding on a host within 1 day, using their sophisticated sensory systems.     

The formation of modulated structures in Ni-V alloys

The precipitation of the ordered Ni₃V phase in binary Ni-V alloys has been studied by employing transmission electron microscopy, X-ray analysis, electrical resistivity and mechanical property measurements. The reaction consists of two stages, the first of which involves the formation of domain wave composition modulations manifested by a tweed microstructure and an accompanying strain field. The second stage is an amplification of the long-range order waves and is manifested by the formation of the ordered Ni₃V phase. The strain fields produced by the domain waves interact with the strain field of the Ni₃V nuclei leading to the formation of a single variant of tetragonal Ni₃V in a given region of the matrix. The strength of the continuously ordered alloys is controlled by the strain in the lattice in agreement with the Mott and Nabarro theory of strengthening.     

Cleavage of type I procollagen by human mast cell chymase initiates collagen fibril formation and generates a unique carboxyl-terminal propeptide

The ability of human mast cell chymase and tryptase to process procollagen was examined. Purified human intestinal smooth muscle cell procollagen was incubated with human mast cell tryptase or human mast cell chymase. Purified chymase, but not tryptase, exhibited procollagen proteinase activity in the presence of EDTA. Addition of purified porcine heparin over a range of 0.1-100 microg/ml did not affect either the rate or the products of procollagen chymase cleavage. The cleavage site of chymase on the pro-alpha1(I) collagen carboxyl terminus was found to be in the propeptide region at Leu-1248-Ser-1249. Cleavage at this site suggested that the collagen products would form fibrils and confirmed the production of a unique carboxyl-terminal propeptide. Turbidometric fibril formation assay demonstrated de novo formation of chymase-generated collagen fibrils with characteristic lag, growth, and plateau phases. When observed by dark field microscopy, these fibrils were similar to fibrils formed by the action of procollagen proteinases. Thus, mast cell chymase, but not tryptase, exhibits procollagen peptidase-like activity as evidenced by its ability to process procollagen to fibril-forming collagen with concurrent formation of a unique carboxyl-terminal propeptide. These data demonstrate that mast cell chymase has a potential role in the regulation of collagen biosynthesis and in the pathogenesis of fibrosis.     

Calretinin immunoreactive structures in the human hippocampal formation

The calcium-binding protein calretinin is present in an intrinsic GABAergic and an extrinsic non-GABAergic system in the rat and monkey hippocampal formation. Important species differences have been noted in hippocampal cell types immunostained for calretinin and the termination pattern of calretinin containing hypothalamic afferents in the hippocampus. In the present study, calretinin-containing neurons were visualized using immunocytochemistry in the human hippocampal formation of individuals which showed no significant neuropathological alterations. Calretinin-immunoreactivity was present exclusively in non-granule cells of the dentate gyrus and in non-pyramidal cells of Ammon's horn. Calretinin-positive neurons were found most frequently in the hilus of the fascia dentata and in strata radiatum and lacunosum-moleculare of CA1, whereas neurons in CA2 and CA3 were rarely immunostained. The majority of calretinin-immunoreactive neurons were small, bipolar or fusiform neurons. The dendritic trees of the calretinin-positive neurons were, for the most part, parallel to the dendrites of the principal cells. In the hilus, however, we observed cells with dendrites restricted to the hilar area. These dendrites were parallel to the granule cell layer. In the stratum lacunosum-moleculare, neurons with dendrites oriented parallel to the hippocampal fissure were frequently detected. In general, dendrites were smooth or sparsely spiny, displaying small conventional spines. The axons usually emerged from the proximal dendrite and could be followed over long distances. Axons were thin, had small varicosities and displayed only few collaterals which branched relatively far away from the cell body. Distinct bands of darkly stained calretinin-positive fibers occupied the innermost portion of the dentate molecular layer and the pyramidal cell layer of CA2. This distribution of calretinin-immunoreactive structures in the human hippocampus is similar to that observed in other primates but differs from that described in lower mammals, i.e., the rat. Our findings suggest that primates may share a common hippocampal calretinin-containing system, presumably both the intrinsic GABAergic and the extrinsic hypothalamic non-GABAergic components.     

The formation of cell structures in fatigued iron crystals

Single crystals of α-Fe have been fatigued in constant stress amplitude reversed plane bending. TheS-N curve, the plastic strain amplitude variation, and the dislocation substructures developed in the crystals during fatigue have been studied. The formation of a cell structure was found to occur once a critical dislocation density had accumulated, the nature of which was influenced by the crystallography of the specimen and underwent changes with continued testing. The evolution of a continuous cell structure with testing coincided with a large decline in the level of plastic strain amplitude, and it appears that it is these substructures which account for fatigue hardening. From the observations of crack formation and the mode of dislocation movement during saturation, a mechanism for crack initiation is suggested.     

Multilamellar structures of DNA complexes with cationic liposomes

Studies of DNA complexes with cationic liposomes are prompted by the search for nonviral DNA carriers for gene therapy. Recent experiments have identified a stable multilamellar phase in which ordered smectic layers of DNA alternate with cationic bilayers. In this paper we identify the forces governing DNA adsorption on cationic lamellae, including a membrane-induced attraction between the adsorbed DNA. Calculating the DNA interhelical spacing as a function of system composition, the model successfully explains recent surprising observations.     

The formation of adjacent triplex-duplex domainsin DNA

The ability of single-stranded DNA oligomers to form adjacent triplex and duplex domains with two DNA structural motifs was examined. Helix-coil transition curves and a gel mobility shift assay were used to characterize the interaction of single-stranded oligomers 12-20 nt in length with a DNA hairpin and with a DNA duplex that has a dangling end. The 12 nt on the 5'-ends of the oligomers could form a triplex structure with the 12 bp stem of the hairpin or the duplex portion of the DNA with a dangling end. The 3'-ends of the 17-20 nt strands could form Watson-Crick pairs to the five base loop of the hairpin or the dangling end of the duplex. Complexes of the hairpin DNA with the single-stranded oligomers showed two step transitions consistent with unwinding of the triplex strand followed by hairpin denaturation. Melting curve and gel competition results indicated that the complex of the hairpin and the 12 nt oligomer was more stable than the complexes involving the extended single strands. In contrast, results indicated that the extended single-stranded oligomers formed Watson-Crick base pairs with the dangling end of the duplex DNA and enhanced the stability of the adjacent triplex region.     

A comparative morphological study of homo- and heterotopic neural transplants

A comparative study of the development of neocortex embryonal anlage was carried out using light and electron microscopy in 15 days Wistar-line rat embryo after its transplantation into the brain and disturbed sciatic nerve of mature rats. Homotopic transplants contained twice more neurons than heterotopic ones 30 days later. Unlike to intracerebral transplants, in grafts developing in the nerve, there forms a multilayer lining from ependymocytes on the border with recipient tissue. Microenvironment was suggested to influence the realization of the transferred cells precursors histoblastic properties.     

Geometrical criteria for formation of coiled-coil structures of polypeptide chains

Crick's general formulas describing a coiled coil are expressed in a different form to combine the parameters of a coiled coil with the backbone dihedral angles of a polypeptide chain, assuming that the bond lengths and bond angles of the chain are fixed. While the existence of a low-energy coiled-coil conformation depends on energetic considerations, these formulas, which pertain to single-stranded structures and, by application of symmetry operations, to multistranded structures, provide the geometrical criteria for the existence of coiled coils. The concept of "the averaged structure of the minor helix", introduced here, makes it possible to relate the shape of the major helix to that of the minor helix. It is shown, in the analysis of a simple model of a single-stranded coiled-coil beta structure, that strong geometrical restrictions exist for the formation of coiled-coil structures from a given minor helix conformation of a polypeptide chain; these restrictions are expressed in a general form that is applicable to any coiled-coil of any number of residues in a repeat unit. As an application, the possible existence of a two-stranded coiled-coil antiparallel beta structure is considered, both geometrically and energetically, and discussed in relation to the observed twisted beta structures in globular proteins. The proposed coiled-coil models of alpha-helical proteins are also examined briefly.     

DNA damage, micronucleus formation, and cell death from 125I decays in DNA

CHO cells were pulse-labeled with 125I-iododeoxyuridine, harvested 30 min or 5 h after labeling, and stored at -196 degrees C for accumulation of 125I decays. The 30- min groups yielded low-LET survival curves (large shoulder, D0 136 decays/cell); 5-h groups showed a high-LET pattern of cell killing (no shoulder, D0 45 decay/cell). Surprisingly, the shift in 125I action was abolished in cells exposed to HAT medium; both 30-min and 5-h cell groups exhibited high-LET-type killing (no shoulder, D0 52 decays/cell). The striking difference in cell death was not accompanied by any change in induction or repair of DNA DSBs, but the pattern of micronucleus formation (and by implication chromosome damage) did parallel 125I-induced cell death. These findings suggest that cell killing may not be directly linked to the absolute number of DNA DSBs and that damage to higher-order genome structures may be an important factor in radiation-induced cell death.     

MutY DNA glycosylase: base release and intermediate complex formation

MutY protein, a DNA glycosylase found in Escherichia coli, recognizes dA:dG, dA:8-oxodG, and dA:dC mismatches in duplex DNA, excising the adenine moiety. We have investigated the mechanism of action of MutY, addressing several points of disagreement raised by previous studies of this enzyme. MutY forms a covalent intermediate with its DNA substrate but does not catalyze strand cleavage. The covalent intermediate has a half-life of approximately 2.6 h, 2 orders of magnitude greater than the half-life of Schiff bases formed when E. coli formamidopyrimidine-DNA glycosylase (Fpg) and endonuclease III react with their respective substrates. The covalent complex between MutY and its DNA substrate involves Lys-142; however, the position of this residue in the presumptive active site differs from that of catalytic residues involved in Schiff base formation associated with endonuclease III and related DNA glycosylases/AP lyases. MutY converts DNA duplexes containing the dA:8-oxodG mispair to a product containing an abasic site; heat-induced cleavage of this product may account for the several reports in the literature that ascribe AP lyase activity to MutY. The MutY-DNA intermediate complex is highly stable and hinders access by Fpg to DNA, thereby avoiding a double-strand break. Cross-linking of MutY to DNA may play an important role in the regulation of base excision repair.