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J E Godfrey

Publications and source records attributed to J E Godfrey.

16 recordsLinked to original sources
PubMed1991

Associative behavior of the histone (H3-H4)2 tetramer: dependence on ionic environment.

Mixtures of histones H3 and H4 were examined by analytical ultracentrifugation and circular dichroism to determine their association behavior and secondary structure content in high and low ionic strength solvents containing chloride, phosphate, or sulfate. H3 and H4 were also cross-linked by using DSP in order to directly trap any intermolecular interactions occurring in solution. While H3 and H4 can exist as an H3-H4 dimer under limited conditions, they behave as a stable (H3-H4)2 tetramer under most conditions, particularly those which are physiologically relevant. In chloride-containing solutions, the equilibrium between H3-H4 and (H3-H4)2 is responsive to changes in ionic strength and paralleled by large changes in alpha-helicity. In sulfate- and phosphate-containing solutions, the equilibrium is again governed by ionic strength, but there are no significant changes in secondary structure accompanying shifts in the equilibrium. Small oligomers can be formed in the presence of sulfate and phosphate and trapped by the cross-linking reagent; these oligomers are much smaller than those formed in chloride-containing solutions. However, addition of the H2A-H2B dimer into the system prevents aggregation of the (H3-H4)2 tetramer by acting as a "molecular cap" and thus regulating the assembly pathway toward the formation of tripartite octamers. The observed assembly of H3 and H4 into a stable, tetrameric complex supports the concept of the core histone octamer having a tripartite organization in solution rather than being organized as two heterotypic tetramers.

Animals↗
PubMed1991

Neutron and x-ray scatter studies of the histone octamer and amino and carboxyl domain trimmed octamers.

The structure of the nucleosome has been under intense investigation using neutron crystallography, x-ray crystallography, and neutron solution scattering. However the dimension of the histone octamer inside the nucleosome is still a subject of controversy. The radius of gyration (Rg) of the octamer obtained from solution neutron scattering of core particles at 63% 2H2O, 37% 1H2O is 33 A, and x-ray crystallography study of isolated histone octamer gives a Rg of 32.5 A, while the reported values using x-ray crystallography of core particles from two individual studies are 29.7 and 30.4 A, respectively. We report here studies of isolated histone octamer and trypsin-limited digested octamer using both neutron solution scattering and small angle x-ray scattering. The Rg of the octamer obtained is 33 A, whereas that of the trimmed octamer is 29.8 A, similar to the structure obtained from the crystals of the core particles. The N-terminal domains of the core histones in the octamer have been shown by high resolution nuclear magnetic resonance (Schroth, G.P., Yau, P., Imai, B.S., Gatewood, J.M., and Bradbury, E.M. (1990) FEBS Lett. 268, 117-120) to be mobile and flexible; it is likely that these regions are disordered and "not seen" by x-ray crystallography.

Animals↗
PubMed1990

Spectropolarimetric analysis of the core histone octamer and its subunits.

The secondary structure of the calf thymus core histone octamer, (H2A-H2B-H3-H4)2, and its two physiological subunits, the H2A-H2B dimer and (H3-H4)2 tetramer, was analyzed by ORD spectropolarimetry as a function of temperature and solvent ionic strength within the ranges of these experimental parameters where assembly of the core histone octamer exhibits pronounced sensitivity. While the secondary structure of the dimer is relatively stable from 0.1 to 2.0 M NaCl, the secondary structure of the tetramer exhibits complex changes over this range of NaCl concentrations. Both complexes exhibit only modest responses to temperature changes. ORD spectra of very high and very low concentrations of stoichiometric mixtures of the core histones revealed no evidence of changes in the ordered structure of the histones as a result of the octamer assembly process at NaCl concentrations above 0.67 M, nor were time-dependent changes detected in the secondary structure of tetramer dissolved in low ionic strength solvent. The secondary structure of the chicken erythrocyte octamer dissolved in high concentrations of ammonium sulfate, including those of our crystallization conditions, was found to be essentially unchanged from that in 2 M NaCl when examined by both ORD and CD spectropolarimetry. The two well-defined cleaved products of the H2A-H2B dimer, cH2A-H2B and cH2A-cH2B, exhibited reduced amounts of ordered structure; in the case of the doubly cleaved moiety cH2A-cH2B, the reductions were so pronounced as to suggest marked structural rearrangements.

Ammonium Sulfate↗
PubMed1990

Effect of aggregation of histone octamers in high-salt solutions on circular dichroism spectra.

The circular dichroism (CD) of freshly prepared chicken erythrocyte core histones has been reexamined in high concentrations of ammonium sulfate and sodium chloride, conditions which cause drastic changes in the solubility and aggregative properties of these proteins. After sample clarification by ultracentrifugation, no significant net changes are detected in the secondary structure of the core histones in the range of 2.0-2.5 M ammonium sulfate. There is also no significant difference between the CD spectra of histone solutions in 2 M sodium chloride and clarified solutions of histones in high concentrations of ammonium sulfate. It was observed that sample clarification by ultracentrifugation immediately prior to taking CD spectra was necessary for signal stabilization, especially under conditions which begin to favor crystallization of the histones.

Ammonium Sulfate↗
PubMed1990

A gastrectomy population: 25-30 years on.

Prior to 1960 a Polya gastrectomy was the most frequent operation for duodenal ulcer. The majority of these patients now have reached the age of sixty or older. A prospective longitudinal study of a cohort of patients who underwent gastrectomy between 1955 and 1960 was undertaken. Twenty five to thirty years later the study has revealed the extent of the nutritional problems that may arise with the passage of time and shows that these numerically far outweigh the mechanical post-gastrectomy syndromes and weight loss which tended to dominate the earlier post-gastrectomy scene. By the end of the first decade, iron deficiency was the commonest nutritional problem. Vitamin B12 deficiency assumed more importance in the second decade. During the third decade both reached equal prevalence, being found in some 90% of the female and 70% of the male residual population. Vitamin D deficiency and early osteomalacia was a lesser problem, reaching its climax in the second decade. Evidence suggested a high incidence of osteoporosis and this requires further investigation. Overall, women fared worse than men with a higher and earlier incidence of iron deficiency, particularly in the pre-menopausal group. This study emphasizes the increasing need for regular screening of post-gastrectomy patients to detect early iron, vitamin B12 and vitamin D deficiencies as patients grow older.

Celiac Disease↗
PubMed1989

Steady-state electrophoresis: a technique for measuring physical properties of macro-ions.

The basic theory of a newly discovered physical technique, steady-state electrophoresis, is described followed by analyses of several representative macro-ion systems with the technique. This method measures apparent moments of molar diminished charge (defined below) of solvated macro-ions from an analysis of a concentration gradient of the macro-ions stabilized against a semipermeable membrane by the opposing forces of diffusion and an external electric field. The experimental results confirm that the theory adequately describes the behavior of the macro-ion systems at electrophoretic steady state and suggest applications for the technique in addition to measuring macro-ion-small ion interactions.

Electrochemistry↗
PubMed1989

Examination of errors caused by random summing in in vivo prompt gamma ray analysis.

A technique is described for examining the mode of operation of radiation detectors and estimating the losses and gains caused by random summing effects in spectra acquired at high counting rates. The technique is applied to estimating the errors caused by random summing when measuring the amounts of carbon and nitrogen in the human body by the prompt gamma ray neutron activation analysis system installed in Leeds, UK. Our examination shows that the counting rate would have to increase to more than twice the value used at the method's calibration, before an error of greater than 10% is caused in the estimation of carbon by random summing effects, whilst for nitrogen a change of only 18% in the counting rate will cause a 10% error in its estimation.

Activation Analysis↗
PubMed1988

H2a-specific proteolysis as a unique probe in the analysis of the histone octamer.

We have utilized the H2a-specific protease as a unique probe to investigate the nature of the interactions between the protein subunits which form the core histone octamer. Upon incubation in high ionic strength media this protease, normally found tightly associated with isolated calf thymus chromatin, releases the 15 COOH-terminal amino acids of histone H2a by specifically cleaving the H2a polypeptide between Val114 and Leu115, yielding cleaved H2a (cH2a) and a free pentadecapeptide (Eickbush, T. H., Watson, D. K., and Moudrianakis, E. N. (1976) Cell 9, 785-792). We find that removal of this pentadecapeptide results in a marked dissociation of the octamer into its H2a:H2b dimer and H3:H4 tetramer subunits. Reconstitution experiments indicate that cH2a is capable of forming a dimer with H2b, but this cH2a:H2b dimer has a substantially lower affinity for the H3:H4 tetramer than native H2a:H2b dimer. Kinetic studies of H2a cleavage in high ionic strength solutions demonstrate that H2a molecules in the octamer are relatively resistant to proteolytic attack compared to H2a molecules in the dimer. The extent of this resistance, in response to various experimental parameters, is directly correlated to the strength of interaction between the H2a:H2b dimer and H3:H4 tetramer subunits. These reconstitution and kinetic experiments suggest that the histone domains proximal to the H2a cleavage site have an important function in maintaining the association of the histone octamer subunits.

Animals↗
PubMed1976

The flexibility of low molecular weight double-stranded DNA as a function of length. I. Isolation andphysical characterization of seven fractions.

Sonicated calf thymus DNA was fractionated by rate zonal centrifugation into seven fractions with weight average molecular weights ranging from 0.28 to 1.3 X 10(6) daltons, as determined by sedimentation equilibrium and light scattering measurements (the latter are described in the accompanying paper). Electron microscopy and sedimentation equilibrium analysis revealed these fractions to be narrowly disperse with Mw/Mn ratios averaging about 1.06. Intrinsic viscosities and sedimentation rates were measured and found to vary linearly with molecular weight in double-logarithmic plots in fair agreement with previously published functions relating these parameters for low molecular weight DNA. Thso agreeing with reported estimates of this parameter for short DNA. These data will be used in the second paper of this series to calculate the persistence length of the DNA fragments in each of the seven fractions by light scattering and hydrodynamic theories for the Kratky-Porod worm-like coil.

Animals↗
PubMed1976

The flexibility of low molecular weight double-stranded DNA as a function of length. I. Light scattering measurements and the estimation of persistence lengths from light scattering, sedimentation and viscosity.

In the preceding paper are described the isolation and physical characterization of seven narrowly disperse fractions of calf thymus DNA in the molecular weight range 0.3 to 1.3 X 10(6) daltons. Herein, we have determined by light scattering the molecular weights and root mean square radii of these fractions in a solvent comprising 0.2 M NaCl, 2 mM EDTA, 2mM Na-PO4,pH7. Measurements were made in a modified Wippler-Scheibling photometer to a 20 degree lower limit of scattering angle on solutions rendered virtually dust-free by procedures described. The optical anisotropies of the DNA fractions were measured permitting the experimental molecular weights and root mean square radii to be corrected to their true values. From these values, with appropriate polydispersity corrections, we calculate a Kratky-Porod persistence length, a, of 54.0 +/- 5.6 nm which is invariant over the molecular range examined. From the sedimentation coefficients (preceding paper) and the theory of Yamakawa and Fujii, we calculate a to be 66 nm, a value found to apply equally well to several DNA samples of various origins whose sedimentation rates are known in themolecular weight range from about 4 X 10(4) to 10(8) daltons. Similarly, from the intrinsic viscosities and the theory of Yamakawa and Fujii, we calculate a to be 59 nm, which again adequately applies to a number of DNA samples whose viscosities have been measured by other workers in the molecular wieght range 3 X 10(5) to 10(8) daltons. The Flory-Mandelkern paramerter, beta, was found to vary with molecular weight in the manner predicted by the theory of Yamakawa and Fujii. The average value of a from the three sets of measurements is 60 +/- 6nm, which we believe applies to double-stranded DNA molecules, independent of chain length, over the whole range of molecular weights from which reliable data exist.

Animals↗