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R T Simpson

Publications and source records attributed to R T Simpson.

At least 73 records · Page 4Linked to original sources
PubMed1979

Conformation of DNA in chromatin core particles containing poly(dAdT)-poly(dAdT) studied by 31 P NMR spectroscopy.

We have prepared semi-synthetic chromatin core particles from a complex of chicken erythrocyte inner histones (H2A, H2B, H3 and H4) with double-stranded poly(dAdT).poly(dAdT) and studied the conformation of the phosphodiester backbone using 31P NMR at 109.3 MHz. At 20 degrees C, the core particle spectrum is fit well by a single Lorenzian distribution with a line width of 110 Hz. This signal is significantly broader than that for the 145 base pair poly(dAdT).poly(dAdT) alone; the latter consists of two resonances, approximately equal in intensity, with average line width 41 Hz. Major changes in the spectrum ensue on heating the core particle preparation. In conjunction with other results (1) these data suggest four states for the core particle at increasing temperatures. Additionally, analysis of the spectrum of the unmelted core particle and its differences from protein-free DNA of the same length suggests that the conformation of the phosphodiester backbone and/or its interactions with histones along the length of the core particle DNA segment may not be uniform.

Animals↗
PubMed1979

An alternating conformation characterizes the phosphodiester backbone of poly(dA-dT) in solution.

A highly homogeneous 145-base-pair fragment of double helical poly(dA-dT) . poly(dA-dT) was obtained by micrococcal nuclease digestion of a semisynthetic chromatin prepared from the nucleosome core histones (H2A, H2B, H3, H4) and the synthetic polydeoxyribonucleotide. In contrast to higher molecular weight alternating copolymers, this fragment displayed two resolved 31P NMR signals, separated by 24 Hz at 10.93 MHz. The two signals were of equal intensity at all temperatures less than the Tm for the fragment. Analyses of the possible origins for the two reasonances leads to the conclusion that the phosphodiester backbone of this DNA contains two distinct phosphorus environments, probably in an alternating array. We suggest that this may indicate the presence of sequence-dependent local variation in the helical structure of DNA in general.

DNA↗
PubMed1979

Cromatin and core particles formed from the inner histones and synthetic polydeoxyribonucleotides of defined sequence.

Chicken erythrocyte inner histones (H2A, H2B, H3 and H4) were associated with the two complementary homopolymeric polydeoxyribonucleotides and the two alternating copolymeric polydeoxyribonucleotides. No evidence for formation of chromatin-like structures was obtained for the complexes with poly(dG) . poly(dC) or poly(dA) . poly(dT). Both poly (dGdC) . poly(dGdC) and poly(dAdT) . poly(dAdT) could be folded by histones to yield material digested by DNAase I to multiples of about 10 and by staphylococcal nuclease to 146 bp core particles. Due to the lack of sequence heterogeniety in the complex of histones with poly(dAdT) . poly(dAdT), core particles with remarkable fine structural detail are obtained. The internal organization of DNA in the AT-containing and GC-containing core particles appears not to be identical.

Animals↗
PubMed1978

Structure of chromatin containing extensively acetylated H3 and H4.

I have grown HeLa cells in 5 mM sodium n-butyrate leading to extensive in vivo histone acetylation, and have characterized the structure of chromatin containing the modified histones. Nuclear DNA in butyrate-treated cells is digested 5-10 fold more rapidly by DNAase I than the DNA of control cells. Staphylococcal nuclease degrades the two nuclear samples to acid-soluble material with identical rates; this nuclease, however, does excise nucleosomes with extensively acetylated histones from the nucleoprotein chain preferentially. The physical properties of unsheared chromatin and isolated core particles from control and butyrate-treated cells are closely similar, as are the rates of digestion of core particles from the two cell preparations by DNAase I. Determination of the relative susceptibilities of cleavage sites for DNAase I demonstrates that the site 60 bases from the ends of the DNA resistant in control cells, becomes susceptible to the nuclease in core particles containing acetylated histones. Similarly, the 5' terminal phosphate at the end of DNA in core prticles is removed by staphylococcal nuclease 2-3 fold faster in particles containing acetylated histones than in particles from control cells.

Acetylation↗
PubMed1978

Protein kinase in HeLA nucleosomes: a reevaluation of the interactions of histomes with the ends of core particle DNA.

HeLa chromatin core particles contain a protein kinase which transfers phosphate from ATP to both nonhistone proteins and histones. The enzyme preferentially modifies H3 among the histones; about 7% of the H3 molecules in the nucleoprotein are modified at saturation. Activity of this kinase likely contributed to earlier results using crosslinking methodology to study which histones interact with the ends of core particle DNA. When the kinase is largely removed by sedimentation of core particles through sucrose gradients containing 0.45 M NaCl, crosslinking of the 5'-terminal label on DNA is observed only to histone H3. The overall efficiency of the crosslinking reaction is about 15%. The origin of the 5'-terminal 32P previously assigned as crosslinked to H4 is not explained by the current experiments.

Adenosine Triphosphate↗
PubMed1977

Molecular homogeneity of the histone content of HeLa chromatin subunits.

Interaction of affinity chromatographically purified antihistone H3 and antihistone H4 with isolated HeLa core particles, followed by separation of unreacted and reacted particles by sedimentation, demonstrates that every core particle contains these histones. Taken together with our previous data indicating the presence of H2B in every nucleosome (Simpson, R. T., and Bustin, M. (1976), Biochemistry 15, 4305), these data lead to the conclusion that each core particle contains two each of the four smaller histones. In contrast to the lack of interference in binding of more than one molecule of antibody to a single species of histone to the core particle, steric hindrance exists when attempts are made to bind both anti-H3 and anti-H4 to core particles.

Antibodies↗
PubMed1977

Localization of the sites along nucleosome DNA which interact with NH2-terminal histone regions.

Trypsin digestion of HeLa nucleosomes produces the same series of discrete histone breakdown products observed previously by others during digestion of chromatin; thus, trypsin excises the NH2-terminal ends of the histones from the chromatin core particle. The resulting nucleoprotein complex sediments at 9 S, has an increased molecular ellipticity at 280 nm, and has DNase I-susceptible sites at 10 nucleotide intervals. Nucleosomes containing a 32P label at the 5'-DNA termini were digested sequentially with trypsin and DNase I. Following trypsin digestion, the segments of nucleosome DNA 20 to 35 and 60 to 80 nucleotides from the 5' end became more susceptible to DNase I, suggesting that these segments interact with the trypsin-sensitive regions of the histones.

Binding Sites↗
PubMed1977

Characterization of chromatin modified with ethyl acetimidate.

Thymus chromatin was extensively modified with ethyl acetimidate, substituting up to 90% of the lysyl residues of the histones while retaining the positive charge of the basic amino acid. Physiochemical and immunochemical characterization of this derivative chromatin indicates a high degree of retention of the native structure of the nucleoprotein even after extensive modification. The alterations which are detected are most simply interpreted as resulting from a weakening of the interactions of histone H1 with DNA in the modified chromatin. The near-native character of amidinated chromatin contrasts with the more extensive structural alterations observed in acetylated chromatin. Our data demonstrate the suitability of this reagent for mapping available lysyl residues in this and other nucleoproteins and suggest that the related bisimido esters may be reagents of choice for cross-linking of chromatin histones.

Animals↗
PubMed1977

DNase-sensitive sites in nucleosomes. Their relative suspectibilities depend on nuclease used.

We have used three endonucleases having different catalytic and physicochemical properties to digest HeLa nucleosomes (chromatin core particles) which had been labeled with 32P at their 5'-DNA termini. Each endonuclease nicks nucleosome DNA at the identical sites, supporting the idea that the conformation of the DNA within a nucleosome is the major factor influencing its nuclease susceptibility and indicating that nucleases can indeed yield important information as to nucleoprotein structure. On the other hand, the relaative susceptibility of a given site can differ for each nuclease, indicating that enzyme-substrate interactions unique for each enzyme influence the course of the reaction; this limits the structural information which can be obtained by using a single nuclease to study nucleoprotein structure.

Aspergillus↗
PubMed1977

Partial dissociation and renaturation of embryonic chick delta-crystallin. Characterization by ultracentrifugation and circular dichroism.

1. delta-Crystallin from 15-day-old embryonic chick lenses was characterized by circular dichrosim (CD) spectroscopy. Examination by CD spectroscopy in the far ultraviolet (190-250 nm) demonstrated that the secondary structure of delta-crystallin has at least 75% alpha-helix; the delta-crystallin subunits dissociated in sodium dodecyl sulfate retain their alpha-helical content. This appreciable alpha-helical content of delta-crystallin contrasts with the absence of alpha-helix in other lens crystallins. 2. As judged by CD spectroscopy in the near ultraviolet (250-320 nm) the tertiary structure of embryonic delta-crystallin is not readily disrupted by environmental changes, such as NaCl, KSCN or the non-ionic detergent Emulphogene BC 720, and is stable to temperature fluctuation between 2 and 56 degrees C. 3. Experiments were directed towards deaggregation and renaturation of the four subunits of embryonic delta-crystallin by treatment with urea or guanidine hydrochloride. The native tertiary structure of delta-crystallin was lost above 4 M urea or 2 M guanidine hydrochloride, as judged by CD spectroscopy in the near ultraviolet. Ultracentrifugation at sedimentation equilibrium showed that in 4 M urea delta-crystallin dissociates into dimeric subunits, while in 2 M guanidine hydrochloride delta-crystallin exists as a mixture of dimeric and tetrameric subunits. Dialysis of delta-crystallin from 4 M urea resulted in reaggregation of the subunits into tetramers, about 50% of which showed native tertiary structure. Dialysis from 2 M guanidine hydrochloride also resulted in tetramer formation, and about 35% was recovered with native conformation. Removal of denaturant by dialysis produced no native teritary structure after treatment with 8 M urea, but about 15% native conformation after treatment with 6 M guanidine hydrochloride.

Animals↗
PubMed1977

Specific folding and contraction of DNA by histones H3 and H4.

We demonstrate that the arginine-rich histones H3 and H4 can introduce torsional constraints on closed circular DNA with a concomitant compaction of the nucleic acid. SV40 DNA I complexed with H3 and H4 appears relaxed in electron micrographs and contains particles of 75 +/- 10 A in diameter along the DNA. SV40 DNA I is contracted 2.75 +/- 0.25 fold by all the four smaller histones and 2.6 +/- 0.4 fold by H3 and H4 alone. The arginine-rich histones can cause the topological equivalent of unwinding the DNA close to one Watson-Crick turn per particle formed. Spherical nucleoprotein complexes morphologically similar to isolated nu bodies or nucleosomes are obtained by association of H3 and H4 with 140 base pair length DNA isolated from chromatin core particles. These reconstituted particles sediment at 9.8S, as compared to 10.8S for native core particles, and contain a tetramer of the arginine-rich histones. None of these specific alterations in DNA structure is seen om complexing the slightly lysine rich-histones H2A and H2B to DNA. Our data provide further evidence indicating that the arginine-rich histones are the major determinants of the architecture of DNA within the chromatin core particle.

Arginine↗
PubMed1977

Crosslinked histone octamer as a model of the nucleosome core.

When histones in chromatin core particles were crosslinked with dimethylsuberimidate, the resulting particles had properties closely similar to those of native core particles. A crosslinked octameric histone complex was isolated from these particles under nondenaturing conditions. Upon reaction with DNA, this octameric protein folded the DNA into a structure closely resembling that of native core particles as verified by various techniques; protein denaturants were necessary for reassociation. The histone octamer is useful as a model of the nucleosome protein core and for studying histone-DNA interactions that occur in nucleosomes.

Chromatin↗
PubMed1976

Histone compostion of chromatin subunits studied by immunosedimentation.

Chromatin subunits were prepared from HeLa cells by in situ digestion of nuclear DNA with micrococcal nuclease followed by sucrose gradient sedimentation. These 11S chromosomal particles (nucleosomes) contain a DNA fragment 140--180 base pairs long and an equal mass of histones, H2A, H2B, H3, and h4. nucleosomes were incubated with purified antibodies to histones H2A and H2B and to hemoglobin A, and the resulting complexes were analyzed by ultracentrifugation. Of these, only anti-H2B bound specifically to nucleosomes. When sufficient antibody was present, all (greater than 98%) the nucleosomes sedimented with increased velocities, indicating that all chromosomal particles contain H2B, as suggested by previous electron microscopic studies (Bustin, M., Goldblatt, D., and Sperling, R. (1976), Cell 7, 297). The amount of antibody reacting with H2B in the nucleosome was quantitated by densitometric scanning of gel electrophoresis patterns of the proteins in various nucleosome-anti-H2B complexes separated by sedimentation on isokinetic sucrose gradients. Under conditions where all particles had increased sedimentation velocities, from 1 to 3 IgG molecules are bound to each nucleosome, the ratio increasing from top to bottom of the sedimenting peak. When nucleosomes are thus dispersed on the basis of reaction with anti-H2B, the ratios of H2A to H4 and of (H2B + H3) to H4 are identical (+/- 8%) for all fractions, suggesting that each nucleosome has an identical histone complement, two each of histones H2A, H2B, H3, and H4. Confidence limits for exclusion of other possible octamers are presented. The variation in ratio of bound antibody to nucleosome probably reflects a normal distribution during the titration, although differential exposure of H2B antigenic determinants in several populations of nucleosomes cannot be excluded as an explanation. The method use should be generally applicable to further studies of the composition and function of nucleosomes.

Animals↗
PubMed1976

Removal of histone H1 exposes a fifty base pair DNA segment between nucleosomes.

Micrococcal nuclease has been used to prepare chromatin from HeLa cells and to probe the structure of HeLa chromatin under various ionic conditions and after the removal of chromatin proteins by salt extraction. The results suggest that (1) HeLa chromatin DNA exists as 150-160 base pair beads interspersed with 40-50 base pair bridges;(2) the bead and bridge conformation exists at physiologic salt concentrations; and (3) removal of histone H1 renders the 40-50 base pair bridge, but not the 150-160 base pair bead, more nuclease susceptible.

Cell Nucleus↗