Linker histone interaction shows divalent character with both supercoiled and linear DNA.

The interaction of linker histone H1 with both linear and superhelical double-stranded DNA has been investigated at low ionic strengths. Gel mobility retardation experiments demonstrate strikingly different behavior for the two forms of DNA. First, the experiments strongly suggest that linker histone binds to superhelical DNA in a negatively cooperative mode. In contrast, binding of linker histone to linear DNA under the conditions employed here shows no cooperativity. Second, binding of linker histone to linear DNA results in aggregation of histone-DNA complexes, even at very low levels of input histone H1. Because H1 has been shown to interact as a monomer, this aggregation is evidence of the divalent character of the linker histone, for without H1's ability to bind to two duplex strands of DNA, aggregation could not occur. Although aggregation can be made to occur with superhelical DNA, it can do so only at near-saturation levels of input histone H1. Finally, in direct competition, linker histone binds to superhelical DNA to the complete exclusion of linear DNA, indicating that the linker histone's function is related to the crossover structures that differentiate superhelical DNA from linear DNA. We develop a model that explains the observed behavior of binding of linker histone to superhelical DNA that is consistent with both the divalent character of the linker histone and the negative cooperativity by which linker histone and superhelical DNA interact.

Reflections on a century of protein chemistry.

The development of protein structural chemistry during the twentieth century is briefly reviewed. Emphasis is placed on certain major problems that have defined the field, and how they have been resolved, often as a consequence of technological advances. The ways in which incorrect hypotheses have affected the development of the field are also discussed.

A hypothesis concerning diffusion-limited protein-ligand interactions.

A simple assumption allows the prediction of the numerical value for a 'universal' limiting kinetic rate for wholly diffusion-limited reactions between small neutral molecules and macromolecules. This prediction is compared with appropriate experimental data for binding of ligands to myoglobin and to enzymes. It is shown that in the absence of electrostatic effects, this limit is approached but not exceeded. The model also makes very specific predictions concerning the viscosity and temperature dependence of such reactions.

Two-photon excitation microscopy of tryptophan-containing proteins.

We have examined the feasibility of observing single protein molecules by means of their intrinsic tryptophan emission after two-photon excitation. A respiratory protein from spiders, the 24-meric hemocyanin, containing 148 tryptophans, was studied in its native state under almost in vivo conditions. In this specific case, the intensity of the tryptophan emission signals the oxygen load, allowing one to investigate molecular cooperativity. As a system with even higher tryptophan content, we also investigated latex spheres covered with the protein avidin, resulting in 340 tryptophans per sphere. The ratio of the fluorescence quantum efficiency to the bleaching efficiency was found to vary between 2 and 180 after two-photon excitation for tryptophan free in buffer solution, in hemocyanin, and in avidin-coated spheres. In the case of hemocyanin, this ratio leads to about four photons detected before photobleaching. Although this number is quite small, the diffusion of individual protein molecules could be detected by fluorescence correlation spectroscopy. In avidin-coated spheres, the tryptophans exhibit a higher photostability, so that even imaging of single spheres becomes possible. As an unexpected result of the measurements, it was discovered that the population of the oxygenated state of hemocyanin can be changed by means of a one-photon process with the same laser source that monitors this population in a two-photon process.

Structures of two molluscan hemocyanin genes: significance for gene evolution.

We present here the description of genes coding for molluscan hemocyanins. Two distantly related mollusks, Haliotis tuberculata and Octopus dofleini, were studied. The typical architecture of a molluscan hemocyanin subunit, which is a string of seven or eight globular functional units (FUs, designated a to h, about 50 kDa each), is reflected by the gene organization: a series of eight structurally related coding regions in Haliotis, corresponding to FU-a to FU-h, with seven highly variable linker introns of 174 to 3,198 bp length (all in phase 1). In Octopus seven coding regions (FU-a to FU-g) are found, separated by phase 1 introns varying in length from 100 bp to 910 bp. Both genes exhibit typical signal (export) sequences, and in both cases these are interrupted by an additional intron. Each gene also contains an intron between signal peptide and FU-a and in the 3' untranslated region. Of special relevance for evolutionary considerations are introns interrupting those regions that encode a discrete functional unit. We found that five of the eight FUs in Haliotis each are encoded by a single exon, whereas FU-f, FU-g, and FU-a are encoded by two, three and four exons, respectively. Similarly, in Octopus four of the FUs each correspond to an uninterrupted exon, whereas FU-b, FU-e, and FU-f each contain a single intron. Although the positioning of the introns between FUs is highly conserved in the two mollusks, the introns within FUs show no relationship either in location nor phase. It is proposed that the introns between FUs were generated as the eight-unit polypeptide evolved from a monomeric precursor, and that the internal introns have been added later. A hypothesis for evolution of the ring-like quaternary structure of molluscan hemocyanins is presented.

Allostery in very large molecular assemblies.

In contrast to small allosteric systems (like hemoglobin) those containing very large numbers (n) of binding sites never exhibit cooperativity (as measured by the Hill coefficient, nH) even approaching the potential limit, n. The reason for this appears to be that in such macromolecules the cooperative unit always represents some sub-structure of the entire structure. On the other hand, it is frequently observed that such sub-structures, when isolated, do not exhibit cooperativity at all. This paper describes studies of some molluscan hemocyanins that explore this apparent anomaly. It is concluded that it is the higher order structure of the molecule that provides a framework within which the sub-structures may exhibit their allosteric behavior.

Sequence of the Octopus dofleini hemocyanin subunit: structural and evolutionary implications.

Sequencing of the subunit of the hemocyanin of Octopus dofleini has been completed from a cDNA library. This represents the first molluscan hemocyanin to be completely sequenced. The sequence determined is for one of the two distinguishable cDNAs which have been recognized for this protein. The protein subunit has 2896 amino acids and contains seven functional units, each carrying two sets of three invariant histidine residues constituting the binding sites (A and B) for two copper atoms. The accompanying paper identifies this site in the C-terminal functional unit (Odg). Differences in sequence for the two cDNAs, for the region in which both are available, are concentrated in the "linker regions" between functional units. The sequences of the seven units exhibit high similarity, averaging about 40% identity, with a concentration of conserved sequences in the region surrounding the copper binding sites. The sequences around the B-site show significant homology to the sequences of arthropod hemocyanins. Comparison of the functional unit sequences in terms of hydrophobicity and surface exposure profiles, as well as regions of probable secondary structure, indicate that all functional units probably have a common tertiary folding; the protein subunit is a string of similarly folded beads. A number of putative N-linked carbohydrate binding sites can be recognized in the sequence; one of these corresponds to the carbohydrate observed in the X-ray diffraction study of functional unit Odg as disclosed in the accompying paper. Phylogenetic analysis of the sequences of the O. dofleini functional units, and comparison with other available molluscan sequences indicates that the multi-domain subunit structure must have arisen over a relatively brief period, preceeding the differentiation of major molluscan types.

Crystal structure of a functional unit from Octopus hemocyanin.

Hemocyanins are giant oxygen transport proteins found in many arthropods and molluscs. Freely dissolved in the hemolymph, they are multisubunit proteins that contain many copies of the active site, a copper atom pair that reversibly binds oxygen. Octopus hemocyanin is composed of ten subunits, each of which contain seven oxygen-binding "functional units". The carboxyl-terminal 47 kDa functional unit, Odg, is a proteolytic isolate that binds oxygen reversibly while exhibiting slight Bohr and magnesium ion effects. In this work we present the X-ray structure determination and analysis of Odg at 2.3 A resolution. Odg has two structural domains: a largely alpha-helical copper binding domain, and a five-stranded anti-parallel beta-sandwich with the jelly roll topology found in many viruses. Six histidine residues ligate the copper atoms, one of which is involved in a thioether bridge. The results show that the hemocyanin from the mollusc and that from the arthropod have distinct tertiary folds in addition to the long recognized differences in their quaternary structures. Nonetheless, a comparison of Octopus and horseshoe crab hemocyanin reveals a similar active site, in a striking example of perhaps both convergent and divergent evolution.

High-affinity binding sites for histone H1 in plasmid DNA.

The interaction of histone H1 isolated from chicken erythrocytes with restriction fragments from plasmids pBR322 and pUC19 was studied by gel electrophoresis. Certain restriction fragments exhibited unusually high affinity for the histone, forming high molecular mass complexes at protein to DNA ratios at which the other fragments did not show evidence for binding. The highly preferred fragments are intrinsically curved, as judged by their electrophoretic mobility in polyacrylamide gels, by computer modeling, and by imaging with scanning force microscopy. However, control experiments with either curved portions of the same fragments or highly curved kinetoplast DNA fragments showed that the presence of curvature alone was not sufficient for preferential binding. By using various restriction fragments centered around the highly preferred sequence, it was found that the high-affinity binding required in addition the presence of specific sequences on both sides of the region of curvature. Thus, both curvature and the presence of specific sites seem to be required to generate high affinity.

Binding of the RNA polymerase I transcription complex to its promoter can modify positioning of downstream nucleosomes assembled in vitro.

We have studied the reconstitution of chromatin-like structures in vitro, using purified RNA polymerase I transcription complexes and histone octamers. The plasmid construct used in these studies is a pUC8 derivative in which we have inserted an RNA polymerase I core promoter region of Acanthamoeba castellanii upstream of four repeats of the 5 S rDNA nucleosome positioning sequence (208 base pairs) from Lytechinus variegatus. When histone octamers were reconstituted onto the naked DNA template, the expected nucleosome positioning previously observed using tandem repeats of the same 208-base pair fragment was not obtained (as assayed by restriction enzyme digestion mapping of the inserted region of the plasmid). We show that the location of the RNA polymerase I core promoter region with regard to the tandemly repeated 208-base pair positioning sequence is a major determinant in the positioning of the histone octamers. Reconstituting first with the stalled transcription complex excluded octamers from the promoter region and recovered the expected nucleosome positioning downstream on the four repeats of the 5 S positioning sequence. The observed competition between histone octamers and the transcription complex for the promoter region suggests a great similarity with what has been reported from in vitro studies of RNA polymerase II and III transcription systems. We may be looking at a mechanism of regulation of transcription for the RNA polymerase I.

Chromatin loops and transcriptional regulation.

The existence of a supermolecular structure in the eukaryotic nucleus, involving loops of chromatin attached at irregularly spaced points to the nuclear matrix, is now well established. Quite a bit is known concerning the DNA sequences involved in the attachment. However, the function of this highly organized structure remains largely unknown. In this review, we attempt to provide an overview of present knowledge of nuclear loop structure, and to critically summarize recent studies that provide new insights as to function. We derive the conclusion that the loop structure is very likely one in which DNA topology can be locally regulated by topoisomerase activity, and is most probably modified during development.

Nucleosome positioning is determined by the (H3-H4)2 tetramer.

It is demonstrated that the histone (H3-H4)2 tetramer can find specific positions on DNA, even in the absence of other histones. Purified histone (H3-H4)2 tetramers were reconstituted onto 208-base-pair (bp) DNA molecules containing a nucleosome-positioning sequence by using salt-gradient dialysis. The stoichiometry of histone tetramer to DNA was shown to be 1:1. Digestion with micrococcal nuclease led to formation of protected DNA fragments of approximately 73 bp. Cleavage of the 73-bp DNA with restriction enzymes produced a small set of defined bands, demonstrating positioning of the (H3-H4)2 tetramer on DNA. Analysis of the restriction digests shows that the 73-bp DNA corresponds mainly to two fragments, one lying on either side of the pseudo-dyad axis of the major position adopted by complete histone octamers on this DNA. This result means that a single (H3-H4)2 histone tetramer can fold approximately 146 bp of DNA with the same positioning as the complete octamer but that a region near the pseudo-dyad is only weakly protected against micrococcal nuclease attack in the absence of histones H2A and H2B.

Binding of ethidium to the nucleosome core particle. 2. Internal and external binding modes.

We have previously reported that the binding of ethidium bromide to the nucleosome core particle results in a stepwise dissociation of the structure which involves the initial release of one copy each of H2A and H2B (McMurray & van Holde, 1986). In this report, we have examined the absorbance and fluorescence properties of intercalated and outside bound forms of ethidium bromide. From these properties, we have measured the extent of external, electrostatic binding of the dye versus internal, intercalation binding to the core particle, free from contribution by linker DNA. We have established that dissociation is induced by the intercalation mode of binding to DNA within the core particle DNA, and not by binding to the histones or by nonintercalative binding to DNA. The covalent binding of [3H]-8-azidoethidium to the core particle clearly shows that less than 1.0 adduct is formed per histone octamer over a wide range of input ratios. Simultaneously, analyses of steady-state fluorescence enhancement and fluorescence lifetime data from bound ethidium complexes demonstrate extensive intercalation binding. Combined analyses from steady-state fluorescence intensity with equilibrium dialysis or fluorescence lifetime data revealed that dissociation began when approximately 14 ethidium molecules are bound by intercalation to each core particle and less than 1.0 nonintercalated ion pair was formed per core particle.

Binding of ethidium to the nucleosome core particle. 1. Binding and dissociation reactions.

We have examined binding properties of and dissociation induced by the intercalating dye ethidium bromide when it interacts with the nucleosome core particle under low ionic strength conditions. Ethidium binding to the core particle results in a reversible dissociation which requires the critical binding of 14 ethidium molecules. Under low ionic strength conditions, dissociation is about 90% completed in 5 h. The observed ethidium binding isotherm was corrected for the presence of free DNA due to particle dissociation. The corrected curve reveals that the binding of ethidium to the core particle itself is a highly cooperative process characterized by a low intrinsic binding constant of KA = 2.4 X 10(4) M-1 and a cooperativity parameter of omega = approximately 140. The number of base pairs excluded to another dye molecule by each bound dye molecule (n) is 4.5. Through the use of a chemical probe, methidiumpropyl-EDTA (MPE), we have localized the initial binding sites of ethidium in the core particle to consist of an average of 27 +/- 4 bp of DNA that are distributed near both ends of the DNA termini. MPE footprint analysis has also revealed that, prior to dissociation, the fractional population of core particles which bind the dye (f) may be as low as 50%. Comparison of the binding and dissociation data showed that the cooperative maximum of the binding curve occurred at or near the critical value, i.e., at the point where dissociation began. The data were used to generate a detailed model for the association of ethidium with chromatin at the level of the nucleosome.

The mechanism of nucleosome assembly onto oligomers of the sea urchin 5 S DNA positioning sequence.

We have used a model system composed of tandem repeats of Lytechinus variegatus 5 S rDNA (Simpson, R. T., Thoma, F., and Brubaker, J. M. (1985) Cell 42, 799-808) reconstituted into chromatin with chicken erythrocyte core histones to investigate the mechanism of chromatin assembly. Nucleosomes are assembled onto the DNA template by mixing histone octamers and DNA in 2 M NaCl followed by stepwise dialysis into very low ionic strength buffer over a 24-h period. By 1.0 M NaCl, a defined intermediate composed of arrays of H3.H4 tetramers has formed, as shown by analytical and preparative ultracentrifugation. Digestion with methidium propyl EDTA.Fe(II) indicates that these tetramers are spaced at 207 base pair intervals, i.e. one/repeat length of the DNA positioning sequence. In 0.8 M NaCl, some H2A.H2B has become associated with the H3.H4 tetramers and DNA. Surprisingly, under these conditions DNA is protected from methidium propyl EDTA.Fe(II) digestion almost as well as in the complete nucleosome, even though these structures are quite deficient in H2A.H2B. By 0.6 M NaCl, nucleosome assembly is complete, and the MPE digestion pattern is indistinguishable from that observed for oligonucleosomes at very low ionic strength. Below 0.6 M NaCl, the oligonucleosomes are involved in various salt-dependent conformational equilibria: at approximately 0.6 M, a 15% reduction in S20,w that mimics a conformational change observed previously with nucleosome core particles; at and above 0.1 M, folding into a more compact structure(s); at and above 0.1 M NaCl, a reaction involving varying amounts of dissociation of histone octamers from a small fraction of the DNA templates. In low ionic strength buffer (less than 1 mM NaCl), oligonucleosomes are present as fully loaded templates in the extended beads-on-a-string structure.