DNA binding site of the helix destabilizing protein gp32 from bacteriophage T4.

A helix destabilizing protein, the product of gene 32 (gp32) of bacteriophage T4, was subjected to limited proteolysis to produce three types of products with differing affinities for DNA. Previous work has suggested that the 18 amino acids at the N-terminus are required for tight binding to single-stranded DNA (Hosoda &; Moise, 1978). This paper reports the sequence of the N-terminal region and predicts the amino acid residues responsible for DNA binding.     

Comparison of the state of deoxyhemoglobin S molecules in solution and in fibers by hydrogen exchange kinetics

Hydrogen exchange kinetics of deoxyhemoglobin S gel and deoxyhemoglobin A solution were compared at 4.8 mM tetramer concentration, 25 degrees C, and in sodium phosphate buffer at pH 7.0 with gamma/2 = 0.2 by means of microdialysis using tritium as a trace label. Cyanomethemoglobin A in solution and as crosslinked crystals were compared under the same conditions. The exchange values from 15 to 10(4) min were fitted to a power law, and the distribution function of exchange rates was calculated. There was no significant difference in the distribution for deoxyhemoglobin S gel and deoxyhemoglobin A. Exchange from crosslinked cyanomethemoglobin crystals was less in the early time region than for the solution state, but after 600 min the exchange curves were the same. This resulted in a larger area for the distribution function, although the predominate rates were nearly the same. The effect of polymerization on conformational fluctuations was very small, smaller than the effect of crosslinking hemoglobin crystals.     

Regeneration of the segment boundary in Oncopeltus

The segment boundary of Oncopeltus is a compartment border. It is also an element in the pattern of the abdomen, being marked by a groove in the surface of the cuticle and an abrupt change in the pigmentation of the cells. If the segment boundary is either burnt or extirpated, the surviving cells of the two neighbouring segments migrate into the wounded area and form a new segment boundary where they confront each other. Grafting experiments with genetically marked cells demonstrate that a boundary is regenerated wherever cells from remote locations in the anteroposterior axis of any segment are apposed; thus anterior and posterior cells from the same segment form an ectopic boundary when brought together, while cells from equivalent positions in two segments heal together without forming a boundary. We consider the segment boundary to be an element in a pattern which reiterates down the longitudinal axis of the body—whenever cells from different positions in this pattern are brought together intercalation occurs. The intercalation can either be within a segment (no boundary forms) or between segments (a boundary forms). The route of intercalation appears to be the shortest available, so that when the apposed cells are more than half a segment length apart a new boundary forms.     

Conformational stability of type I collagen triple helix: evidence for temporary and local relaxation of the protein conformation using a proteolytic probe

Native collagen polypeptides exist in a unique triple helical conformation resistant to most proteinases. In this study, the stability of type I collagen triple helix, employing a mixture of trypsin and alpha-chymotrypsin as a proteolytic probe, was examined. The degradation of type I [3H]collagen was monitored as 3H-labeled peptides soluble in trichloroacetic acid (TCA) or by sodium dodecyl sulfate (SDS)-polyacrylamide slab gel electrophoresis. In one set of experiments, collagen substrates were preincubated at various temperatures for up to 8 h, followed by a 15-min proteolytic treatment at the same temperature. At 43 degrees C, most of the collagen was degraded, while the fraction of the substrate degraded at 40, 38, and 35 degrees C was 53, 41 and 19%, respectively. This fraction was independent of the preincubation time which varied from 10 to 480 min. Thus, at any given temperature, a constant fraction of the collagen substrate was susceptible to proteolysis. Measurement of the midpoint temperature (Tm) of the helix to coil transformation for type I collagen, at neutral pH employing an increasing temperature gradient and brief proteolysis at the individual temperatures, indicated a value of 38.8 degrees C. However, determination of the Tm by employing proteolytic digestions at a constant temperature (30 degrees C) using conditions under which the nonhelical peptides are readily digested to TCA-soluble peptides while native collagen resists such proteolysis, indicated a value of 42.7 degrees C. In further studies, collagen was subjected to continuous proteolysis for up to 24 h. A large fraction of collagen was digested at 30 or 34 degrees C, temperatures well below the Tm of the helix to coil transformation. SDS-polyacrylamide gel electrophoresis of the degradation products obtained at these temperatures revealed multiple cleavage fragments. Finally, temperature double-jump experiments indicated that the destabilization of the triple helix is reversible provided that the Tm of the substrate is not exceeded. The results provide evidence for reversible and local relaxation of the collagen triple helix.     

Identification of a protein linked to the ends of adenovirus DNA.

A DNA-protein complex from human adenoviruses has been further characterized by electron microscopy, radiochemical labeling and analytical ultracentrifugation. Preparations of the complex contain a large percentage of forms of DNA which are either circular or oligomeric and are readily distinguishable from preparations of pronase-treated adenovirus DNA by analytical ultracentrifugation in cesium chloride gradients containing 4 M guanidinium chloride. The protein component has been iodinated in vitro with ¹²⁵I using Bolton and Hunter reagent, and SDS-polyacrylamide gel analysis of the labeled protein indicates that it has an apparent molecular weight of 55,000 daltons. DNAase I digestion of the DNA-protein complex labeled with ³²PO₄ results in release of a ³²PO₄-labeled protein which remains labeled even after boiling in 1% SDS and 1% mercaptoethanol. Subsequent digestion of this entity with snake venom phosphodiesterase leads to release of ³²P₄-labeled 5′-phosphate deoxynucleotides. Digestion of the DNA-protein complex with Eco R1 and analysis of the isolated restriction fragments indicates that the protein is present on each terminal fragment. We conclude that there is a protein of 55,000 daltons directly attached to each 5′ end of molecule probably via a covalent linkage. We propose that the protein functions during DNA replication by facilitating priming of the progeny strands, thus allowing the 5′ ends of the DNA to be replicated.     

A time lag in the onset of ATP-Pi exchange catalyzed by purified ATP-synthase (CF0-CF1) proteoliposomes and by chloroplasts

The time course of ATP-Pi exchange which is catalyzed by the isolated chloroplast ATP synthase in phospholipid vesicles was studied. The following observations were made. (i) The onset of 32Pi incorporation into ATP lags behind ATP hydrolysis. The lag lasts for about 2 min at 37 degrees C and is followed by a steady-state rate which is constant for more than 30 min. Under the same experimental conditions, ATP hydrolysis shows an initial burst followed by a constant, slower rate. (ii) The initial lag is independent of Mg-ATP concentration in the range 0.2-5 mM and of the presence of ADP. In contrast, the steady-state rate of ATP-Pi exchange has an apparent Km of 0.3 mM for Mg-ATP and is stimulated by ADP. (iii) Increasing the temperature from 30 to 45 degrees C decreases the lag from 6 min to zero. The steady-state rate of ATP-Pi exchange is affected to a much smaller extent by the temperature in this range. (iv) The lag is insensitive to valinomycin or tetraphenylboron, while the steady-state rate is partially inhibited. Nigericin and protonophores affect both the lag and steady-state rate. (v) ATP-induced membrane potential formation, as followed by oxonol VI, does not correlate with the lag in its kinetics and temperature dependence. ATP-induced pH gradient formation could not be detected in the proteoliposome system. (vi) Light-triggered ATP-Pi exchange in chloroplasts shows essentially the same time course as the proteoliposome system, but the lag lasts for only about 20 s at room temperature and is unaffected by a preexisting proton gradient. These results suggest that the initial lag in ATP-Pi exchange does not reflect the time required for the buildup of a protomotive force (delta - mu H+) nor the time required to produce ADP. It is suggested, therefore, that the lag reflects an internal autocatalytic conformational change in the ATP-synthase complex which is initiated by ATP hydrolysis and which converts the enzyme from an "exclusive ATPase state" to a "reversible ATP-synthase state". This slow transition is not directly coupled to a trans-membrane pH or potential gradient.     

A simple procedure for large-scale preparation of pure plasmid DNA free from chromosomal DNA from bacteria

A very simple, inexpensive procedure for preparing pure plasmid DNA from bacteria is described. In this method, lysozyme-induced spheroplasts are made in presence of 833 micrograms/ml of ethidium bromide which are then lysed by a mixture of Brij 58 and sodium deoxycholate, and the lysate is centrifuged at 48,000 g for 25 min whereby about 99.9% of total chromosomal DNA is pelleted. From the supernatant containing plasmid DNA, the proteins are removed by phenol extraction and the major part of RNA by CaCl2 precipitation, and finally the small amount of residual RNA is removed by RNase treatment. The average yield of pBR322 DNA from 1 liter of amplified culture by this procedure is 2 to 2.5 mg and the preparation is highly pure, containing only about 0.005% of total yield as chromosomal DNA contaminant. Moreover, the substrate activity and the transforming ability of the plasmid DNA prepared by this method remain unaffected.     

A fluorometric-HPLC assay for quantitating the binding of benzo[a]pyrene metabolites to DNA

A nonradiometric method is presented for quantitating low levels of benzo[a]pyrene (BP) derivatives that are covalently bound to the DNA of BP-treated mice. This method consists of hydrolyzing the DNA with acid to liberate the BP-adducts in the form of the isomeric tetrols of BP. These tetrols have fluorescence quantum yields of ～0.7 in deoxygenated solution at 298 K. Hence they are easily quantitated, following HPLC separation, by means of fluorescence detection. The sensitivity of the method is such that one bound BP residue per 10⁷ bases can be detected in 100 μg of DNA.     

A developmental study of the cuticular hydrocarbons of Sarcophaga bullata.

The accumulation of cuticular hydrocarbon was measured throughout the life of Sarcophaga bullata. Less than 5 μg hydrocarbon per insect are present until the third larval instar when synthesis increases the quantity present to 10 to 20 μg by pupariation. The rate of synthesis increases at this time to 5 to 8 μg/day and continues until 40 to 45 μg are present per insect. This amount remains constant until several days before the pupal-adult ecdysis when synthesis again occurs. The rate of synthesis by these pharate adults is >20 μg/day. When the adult emerges it contains between 90 and 100 μg which increases slightly during the adult stadium. Two periods of rapid accumulation of cuticular hydrocarbon are observed: (1) during pupariation and the 3 day period following pupariation, and (2) during the 4 day period preceding the pupal-adult ecdysis. When pupariation is inhibited by contact with water, the rate of hydrocarbon biosynthesis also fails to increase.     

Preliminary characterization of a xylose acceptor prepared by hydrogen fluoride treatment of proteoglycan core protein

Polysaccharide was removed from rat chondrosarcoma chondroitin sulfate proteoglycan by hyaluronidase digestion followed by treatment with 70% polyhydrogen fluoride (HF) in pyridine or by the Smith procedure. Both methods were greater than 95% effective in removing carbohydrate. However, the nearly complete removal of carbohydrate by either method resulted in a 50-fold decrease in immunoreactivity as determined by a quantitative radioimmune inhibition assay, suggesting that some structural alteration may have occurred. In contrast, core protein deglycosylated by the HF procedure was a better xylosyltransferase acceptor than that prepared by the Smith procedure. HF-treated core protein exhibited a higher acceptor capacity (V_max approximately 2.5-fold that for the Smith-treated core protein) although the K_m values were similar.     

The role of the environment around the catalytic triad in β-trypsin: A molecular orbital study

In the enzymatic reaction of β-trypsin the role of environment around the catalytic triad is studied by means of ab initio molecular orbital calculations. The triple ion form of the catalytic triad (Asp 102(?)-His 57(+)-Ser 195(?)) is considerably more stable than the double proton-transferred form (Asp 102(neutral)-His 57(neutral)-Ser 195(?)), due to the environment around it, rather than its nature. The “electrostatic mechanism” is more favorable than the “charge relay mechanism” owing to the nature of the enzyme as a biopolymer.     

First DNA sequence of a chloroplast mutation: A missense alteration in the ribulosebisphosphate car☐ylase large subunit gene

Sequence comparison of the chloroplast genes of the large subunit of ribulosebisphosphate car☐ylase from wild-type and from a uniparental mutant of the green unicellular algaChlamydomonas reinhardii has revealed a single nucleotide change. The corresponding Gly to Asp amino acid substitution would introduce a negative charge into the presumptive substrate binding region of the enzyme and would explain the inactivity of the mutant protein. This is the first chloroplast mutation whose DNA sequence is known. Our results establish the first exact point of correlation between the physical map of the chloroplast genome ofC. reinhardii and a specific genetic locus.     

Calorimetric study of carbohydrate binding to Concanavalin A

Flow microcalorimetry has been used to examine the ΔH of binding of two types of saccharides, a series of simple monosaccharides and a series of α-(1 → 4)-linked glucosides, to the lectin Concanavalin A. It has been found that the ΔH decreases with any change in the stereochemistry of a hydroxyl group relative to methyl α-d-mannopyranoside. The data have allowed the calculation of the relative contribution of two of the hydroxyl groups. The ΔH's of binding for the α-(1 → 4)-linked glucosides are approximately 31 kJ/mol, and the apparent association constants vary insignificantly with increasing length. This result indicates that only one glucose residue binds to concanavalin A by hydrogen bonds, and that the additional glucose residues have no interaction either by hydrogen bonds or by nonspecific hydrophobic interactions. This result confirms the absence of an extended binding site for α-(1 → 4)-linked glucopyranosides, in contrast to that proposed for α-(1 → 2)-linked mannopyranosides which show an increase in apparent association constants with increasing length.     

Comparative study of kinetoplast DNA in culture, blood and intracellular forms of Trypanosoma cruzi.

A comparative study has been made on the kinetoplast DNA (kDNA) from I in culture epimastigote, blood trypomastigote and intracellular amastigote stages of Trypanosoma cruzi. The basic properties of the kDNA in all 3 forms were identical. Thus the DNA was in the form of networks of density 1.698-9 g/cm3 and with sedimentation coefficients (S20w) of approximately 5500, the networks being composed of large complexes of minicircular and apparently linear molecules, the former having contour lengths of 0.45 MICROMETer. Several differences were noted. The ultrastructural arrangement of the kDNA in the kinetoplast of the blood stage consisted of three to four double rows of DNA as compared to one double layered row in the other two stages. There was proportionately more kDNA in the blood stages, suggesting that, since the networks have apparently the same size (see above), more than one is present. DNA loops situated at the periphery of the kDNA networks were observed in higher proportion in blood and intracellular forms. Dimeric and oligomeric circles were present in the kDNA of the blood and intracellular stages in much greater proportion than in culture epimastigote stages. Few large circular molecules, heterogeneous in size, were also observed in intracellular blood stages. There were some differences, mainly quantitative, in the gel electrophoresis patterns after endonuclease digestion.