A particulate DNA polymerase activity in adult rat brain

A particulate fraction of adult rat brain (sucrose buoyant density 1.24 gm/ml) catalyzed the incorporation of [³H]dTTP into an acid-insoluble product in an endogenously templated reaction sensitive to ribonuclease pretreatment. Upon fractionation, this activity was identified in the cerebellum, pons, frontal lobes and base. The DNA polymerase present in these brain fractions exhibited a strong preference for the synthetic template dT_12–18·poly rA rather than dT_12–18·poly dA; dT₁₀ was completely inactive. Purification and equilibrium Cs₂SO₄ gradient centrifugation of the [³H]DNA product-endogenous template complex suggested that RNA was serving as primer for endogenous DNA synthesis.     

Immunoglobulin M possesses two binding sites for complement subcomponent C1q, and soluble 1:1 and 2:1 complexes are formed in solution at reduced ionic strength

Soluble complexes were formed between C1q, a subunit of the first component of human complement, and four different Waldenstr?m IgM proteins at reduced ionic strengths. The equilibria between these complexes and the free proteins were studied in the ultracentrifuge. Complex formation was found to be a very sensitive function of the salt concentration, and at physiological ionic strength complex formation was negligible. The complexes were cross-linked with a water-soluble carbodiimide and separated by sucrose gradient centrifugation. Both 22 S 1:1 and 26 S 2:1 C1q X IgM complexes were formed; stoichiometry was established by cross-linking 125I-C1q with 131I-IgM and determining the ratios of the specific activities of the gradient-purified materials. The association process was studied as a function of protein concentration and was analyzed by Scatchard and Hill plots to yield stoichiometry, association constant, and degree of cooperativity. The results indicated that IgM has two identical and independent binding sites for C1q. The intrinsic association constant was found to vary between 10(6) M-1 at 0.084 M ionic strength to 10(4) M-1 at physiological ionic strength; the slope of the log-log plot gave a value of -6.0. The cross-linked complexes were examined by electron microscopy, and the C1q appeared to be attached to the IgM through the C1q heads, implying that the biologically significant binding sites were involved in this interaction. For the 2:1 complexes, the two C1q appeared to attach to opposite surfaces of the IgM, suggesting the presence of a pseudo-2-fold axis lying in the plane of the IgM disk.     

Immunoglobulin G antibody bound to the C1q subcomponent of human complement exhibits segmental flexibility

The rotational dynamics of rabbit immunoglobulin G (IgG) anti-dansyl antibodies bound to the C1q subcomponent of human complement were studied by nanosecond fluorescence spectroscopy. Deconvoluted anisotropy decays of IgG-C1q mixtures were fitted to a two-exponential expression and were corrected for the effects of unbound IgG, which was determined with an analytical ultracentrifuge. Compared with the anisotropy parameters for free IgG, the pre-exponential weighting factors and the short correlation time of the C1q-bound antibody were nearly unchanged, and the long correlation time increased by only about 45 nanoseconds. These results, together with rotational diffusion calculations, indicate that the Fab arms of the C1q-bound antibody exhibited considerable flexibility. This finding may have biological relevance because it suggests that C1q can bind to the Fc segments of IgG molecules anchored in an immune complex, even though the angles between the two Fab arms of the different antibodies may vary. The results of this study also support our earlier interpretation that both the short and long correlation times of IgG principally represent flexible motions of the Fab segments.     

Charge effects in the sedimentation of polyelectrolytes

The theory for sedimentation of macromolecular polyelectrolytes in solutions of low-ionic strength has been modified for the case of a supporting low molecular weight electrolyte possessing a partial specific volume close to unity. The final equations simplify greatly, allowing sedimentation data to be plotted in a linear fashion. These data then may be readily extrapolated to infinite dilution, yielding a value, S^o, simply related to size and shape. From the initial slope of such plots, the net charge on the macro-molecular polyelectrolyte may be determined. It is suggested that tetramethyl-ammonium chloride may prove to be a satisfactory supporting electrolyte for such studies.     

Anomalies in sedimentation. II. Testing the entanglement hypothesis

Zones of T2 DNA were sedimented through uniform solutions of T7 DNA to determine if the smaller DNA molecules would become entangled in the larger. No entanglement could be demonstrated even at high DNA concentrations. It is suggested that molecular entanglement is not responsible for the sudden loss of DNA from solution which occurs in high centrifugal fields. This communication also includes observations on the effects of rotor speed on the sedimentation behavior of DNA in high centrifugal fields, distortion of zone shape at high concentrations, and hydrodynamic interactions between DNA and MS2 bacteriophage particles.     

Zone Centrifugation in a Cesium Chloride Density Gradient Caused by Temperature Change

In this communication is described a new technique for the determination of sedimentation coefficients of macromolecules banded in equilibrium density gradients. Initially, the macromolecules are banded in the analytical ultracentrifuge at a low temperature of about 5°C. After equilibrium has been obtained, the temperature is increased to 25°C. The equilibrium band will now sediment to a new equilibrium position in the ultracentrifuge cell: (a) By following the position of the migrating band as a function of time, sedimentation coefficients may be determined. (b) If several species having different sedimentation coefficients are present in the original band, then during the course of the migration the band may split into several new bands which eventually reunite at the final equilibrium position. (c) If different chemical species of macromolecules such as nucleic acids and carbohydrates are present, in general they will exhibit different temperature density relationships, and can move different distances and directions in response to temperature change.     

Conformation of apolipoprotein B after lipid extraction of low density lipoproteins attached to an electron microscope grid

We have examined the shape of apolipoprotein B (apoB) from low density lipoproteins (LDL) using a new method to prepare the electron microscope grids. After adsorption of the lipoproteins to a carbon-coated copper grid, lipids were extracted with ethanol-ether 4:1; an aqueous negative stain was then applied. When the LDL residue was examined after this treatment, apoB, together with residual lipid, appeared as an elongated flexible structure about 600-700 A in length consisting of multiple domains of variable width from 20-70 A. Occasionally, the elongated apoB formed an irregular ring-shaped structure, but most of the rings were open. When LDL were pretreated with glutaraldehyde, then adsorbed, extracted, and stained, most of the images were closed rings with an average contour length of 700 A, again consisting of multiple domains of variable sizes. These results are consistent with apoB being composed of multiple domains arranged in an elongated structure on the surface of the LDL, and with distant domains possessing a mutual affinity that favors their cross-linking.     

The lepidopteran mitochondrial control region: structure and evolution

For several species of lepidoptera, most of the approximately 350-bp mitochondrial control-region sequences were determined. Six of these species are in one genus, Jalmenus; are closely related; and are believed to have undergone recent rapid speciation. Recent speciation was supported by the observation of low interspecific sequence divergence. Thus, no useful phylogeny could be constructed for the genus. Despite a surprising conservation of control-region length, there was little conservation of primary sequences either among the three lepidopteran genera or between lepidoptera and Drosophila. Analysis of secondary structure indicated only one possible feature in common--inferred stem loops with higher-than-random folding energies-- although the positions of the structures in different species were unrelated to regions of primary sequence similarity. We suggest that the conserved, short length of control regions is related to the observed lack of heteroplasmy in lepidopteran mitochondrial genomes. In addition, determination of flanking sequences for one Jalmenus species indicated (i) only weak support for the available model of insect 12S rRNA structure and (ii) that tRNA translocation is a frequent event in the evolution of insect mitochondrial genomes.      

Glutamine repeats and inherited neurodegenerative diseases: molecular aspects

Several dominantly inherited, late onset, neurodegenerative diseases are due to expansion of CAG repeats, leading to expansion of glutamine repeats in the affected proteins. These proteins are of very different sizes and, with one exception, show no sequence homology to known proteins or to each other; their functions are unknown. In some, the glutamine repeat starts near the N-terminus, in another near the middle and in another near the C-terminus, but regardless of these differences, no disease has been observed in individuals with fewer than 37 repeats, and absence of disease has never been found in those with more than 41 repeats. Protein constructs with more than 41 repeats are toxic to E. coli and to CHO cells in culture, and they elicit ataxia in transgenic mice. These observations argue in favour of a distinct change of structure associated with elongation beyond 37–41 glutamine repeats. The review describes experiments designed to find out what these structures might be and how they could influence the properties of the proteins of which they form part. Poly- -glutamines form pleated sheets of β-strands held together by hydrogen bonds between their amides. Incorporation of glutamine repeats into a small protein of known structure made it associate irreversibly into oligomers. That association took place during the folding of the protein molecules and led to their becoming firmly interlocked by either strand- or domain-swapping. Thermodynamic considerations suggest that elongation of glutamine repeats beyond a certain length may lead to a phase change from random coils to hydrogen-bonded hairpins. Possible mechanisms of expansion of CAG repeats are discussed in the light of looped DNA model structures.