The structure of DNA in a nucleosome.

We describe the application of the hydroxyl radical footprinting technique to examine the histone-DNA interactions of a nucleosome that includes part of the 5S ribosomal RNA gene of Xenopus borealis. We establish that two distinct regions of DNA with different helical periodicities exist within the nucleosome and demonstrate a change in the helical periodicity of this DNA upon nucleosome formation. In particular, we find that on average the helical periodicity of DNA in this nucleosome is 10.18 +/- 0.05 base pairs per turn. The same DNA, when bound to a calcium phosphate surface, has a periodicity of 10.49 +/- 0.05 base pairs per turn, similar to that of random sequence DNA. Modulations in minor groove width within the naked DNA detected by the hydroxyl radical are maintained and exaggerated in nucleosomal DNA. These features correlate with regions in the DNA previously suggested to be important for nucleosome positioning.     

Nucleosome packaging and nucleosome positioning of genomic DNA

The goals of this study were to assess the extent to which bulk genomic DNA sequences contribute to their own packaging in nucleosomes and to reveal the relationship between nucleosome packaging and positioning. Using a competitive nucleosome reconstitution assay, we found that at least 95% of bulk DNA sequences have an affinity for histone octamer in nucleosomes that is similar to that of randomly synthesized DNA; they contribute little to their own packaging at the level of individual nucleosomes. An equation was developed that relates the measured free energy to the fractional occupancy of specific nucleosome positions. Evidently, the bulk of eukaryotic genomic DNA is also not evolved or constrained for significant sequence-directed nucleosome positioning at the level of individual nucleosomes. Implications for gene regulation in vivo are discussed.     

Histone H3 disulfide dimers and nucleosome structure.

The arginine-rich histone, H3, isolated from avian erythrocytes, can dimerize by forming a disulfide linkage between the single cysteine sulfhydryl residues at position 110 of the H3 polypeptide chain. The H3 dimer can be substituted for undimerized H3 in experiments in which the nucleosome is reconstituted from DNA and mixtures of the four "core" histones, H2A, H2B, H3, and H4. We report here that reconstituted nucleosomes containing H3 dimer are indistinguishable, by a number of criteria, either from native nucleosomes or from reconstitutes containing H3 monomer. The criteria include the pattern of susceptibility of the complex to nucleases, the amount of DNA supercoiling induced by histone binding, and the hydrodynamic properties of reconstituted nucleosome "core" preparations. The results suggest that the residues in the neighborhood of position 110 on each H3 molecule are in close contact in the nucleosome. If, as has been proposed, the nucleosome has a dyad axis, then the disulfide bridge between H3 molecules must lie on this axis.     

On the remarkable mechanostability of scaffoldins and the mechanical clamp motif

Protein mechanostability is a fundamental biological property that can only be measured by single-molecule manipulation techniques. Such studies have unveiled a variety of highly mechanostable modules (mainly of the Ig-like, β-sandwich type) in modular proteins subjected to mechanical stress from the cytoskeleton and the metazoan cell–cell interface. Their mechanostability is often attributed to a “mechanical clamp” of secondary structure (a patch of backbone hydrogen bonds) fastening their ends. Here we investigate the nanomechanics of scaffoldins, an important family of scaffolding proteins that assembles a variety of cellulases into the so-called cellulosome, a microbial extracellular nanomachine for cellulose adhesion and degradation. These proteins anchor the microbial cell to cellulose substrates, which makes their connecting region likely to be subjected to mechanical stress. By using single-molecule force spectroscopy based on atomic force microscopy, polyprotein engineering, and computer simulations, here we show that the cohesin I modules from the connecting region of cellulosome scaffoldins are the most robust mechanical proteins studied experimentally or predicted from the entire Protein Data Bank. The mechanostability of the cohesin modules studied correlates well with their mechanical kinetic stability but not with their thermal stability, and it is well predicted by computer simulations, even coarse-grained. This extraordinary mechanical stability is attributed to 2 mechanical clamps in tandem. Our findings provide the current upper limit of protein mechanostability and establish shear mechanical clamps as a general structural/functional motif widespread in proteins putatively subjected to mechanical stress. These data have important implications for the scaffoldin physiology and for protein design in biotechnology and nanotechnology.     

Solution structure of a multifunctional DNA- and protein-binding motif of human Werner syndrome protein

Werner syndrome (WS) is an autosomal recessive disease that results in premature aging. Mutations in the WS gene (WRN) result in a loss of expression of the WRN protein and predispose WS patients to accelerated aging. As a helicase and a nuclease, WRN is unique among the five human RecQ helicase family members and is capable of multiple functions involved in DNA replication, repair, recombination, and telomere maintenance. A 144-residue fragment of WRN was previously determined to be a multifunctional DNA- and protein-binding domain (DPBD) that interacts with structure-specific DNA and a variety of DNA-processing proteins. In addition, DPBD functions as a nucleolar targeting sequence of WRN. The solution structure of the DPBD, the first of a WRN fragment, has been solved by NMR. DPBD consists of a winged helix-like motif and an unstructured C-terminal region of approximately 20 aa. The putative DNA-binding surface of DPBD has been identified by using known structural and biochemical data. Based on the structural data and on the biochemical data, we suggest a surface on the DPBD for interacting with other proteins. In this structural model, a single winged helix domain binds to both DNA and other proteins. Furthermore, we propose that DPBD functions as a regulatory domain to regulate the enzymatic activity of WRN and to direct cellular localization of WRN through protein-protein interaction.     

DNA and protein determinants of nucleosome positioning on sea urchin 5S rRNA gene sequences in vitro.

DNA and protein determinants of nucleosome positioning have been examined after in vitro reconstitutions of native or modified histone octamers onto tandem repeats of 207- and 172-base-pair DNA sequences containing the Lytechinus variegatus 5S rRNA gene and onto monomeric sequences derived from these by digestion with various restriction endonucleases. In all cases, a major nucleosome position as well as a number of minor positions have been observed, which indicates that the generation of multiple positions is an inherent property of the 5S rRNA gene sequence. Interestingly, all positions observed differ by multiples of 10 base pairs. Data obtained under different reconstitution conditions demonstrate that the observed distributions of nucleosomes on these DNA templates are equilibrium distributions. This study has also examined the positioning of histone octamers from which histone "tails" had been removed by tryptic digestion. Results indicate that the histone tails are not determinants of nucleosome positioning. Although our results suggest that the mechanical properties of the 5S rDNA are the fundamental factors determining nucleosome positioning, they are insufficient to direct all nucleosomes into a single location.     

Histone contributions to the structure of DNA in the nucleosome.

We describe the application of the hydroxyl radical footprinting technique to examine the contribution of the core histone tails and of histones H3 and H4 to the structure of DNA in the nucleosome. We first establish that, as was previously determined for a nucleosome containing a unique sequence of DNA, mixed-sequence nucleosomes contain two distinct regions of DNA structure. The central three turns of DNA in the nucleosome have a helical periodicity of approximately 10.7 base pairs per turn, while flanking regions have a periodicity of approximately 10.0 base pairs per turn. Removal of the histone tails does not change the hydroxyl radical cleavage pattern in either mixed- or unique-sequence nucleosome samples. A tetramer of histones H3 and H4, (H3/H4)2, organizes the central 120 base pairs of DNA identically to that found in the nucleosome. Moreover, "tailless" octamers and the (H3/H4)2 tetramer recognize the same nucleosome positioning signals as the intact octamer.     

Effects of hypothyroidism on the structure and mechanical properties of bone in the ovine fetus

Thyroid hormones are important for normal bone growth and development in postnatal life. However, little is known about the role of thyroid hormones in the control of bone development in the fetus. Using computed tomography and mechanical testing, the structure and strength of metatarsal bones were measured in sheep fetuses in which thyroid hormone levels were altered by thyroidectomy or adrenalectomy. In intact fetuses, plasma concentrations of total calcium and the degradation products of C-terminal telopeptides of type I collagen increased between 100 and 144 days of gestation (term 145±2 days), in association with various indices of bone growth and development. Thyroid hormone deficiency induced by thyroidectomy at 105-110 days of gestation caused growth retardation of the fetus and significant changes in metatarsal bone structure and strength when analyzed at both 130 and 144 days of gestation. In hypothyroid fetuses, trabecular bone was stronger with thicker, more closely spaced trabeculae, despite lower bone mineral density. Plasma osteocalcin was reduced by fetal thyroidectomy. Removal of the fetal adrenal gland at 115-120 days of gestation, and prevention of the prepartum rises in cortisol and triiodothyronine, had no effect on bodyweight, limb lengths, metatarsal bone structure or strength, or circulating markers of bone metabolism in the fetuses studied near term. This study demonstrates that hypothyroidism in utero has significant effects on the structure and strength of bone, with different consequences for cortical and trabecular bone.     

Global properties of the mapping between local amino acid sequence and local structure in proteins.

Local protein structure prediction efforts have consistently failed to exceed approximately 70% accuracy. We characterize the degeneracy of the mapping from local sequence to local structure responsible for this failure by investigating the extent to which similar sequence segments found in different proteins adopt similar three-dimensional structures. Sequence segments 3-15 residues in length from 154 different protein families are partitioned into neighborhoods containing segments with similar sequences using cluster analysis. The consistency of the sequence-to-structure mapping is assessed by comparing the local structures adopted by sequence segments in the same neighborhood in proteins of known structure. In the 154 families, 45% and 28% of the positions occur in neighborhoods in which one and two local structures predominate, respectively. The sequence patterns that characterize the neighborhoods in the first class probably include virtually all of the short sequence motifs in proteins that consistently occur in a particular local structure. These patterns, many of which occur in transitions between secondary structural elements, are an interesting combination of previously studied and novel motifs. The identification of sequence patterns that consistently occur in one or a small number of local structures in proteins should contribute to the prediction of protein structure from sequence.     

Periodicity of strong nucleosome positioning sites around the chicken adult beta-globin gene may encode regularly spaced chromatin.

Positioned nucleosomes contribute to both the structure and the function of the chromatin fiber and can play a decisive role in controlling gene expression. We have mapped, at high resolution, the translational positions adopted by limiting amounts of core histone octamers reconstituted onto 4.4 kb of DNA comprising the entire chicken adult beta-globin gene, its enhancer, and flanking sequences. The octamer displays extensive variation in its affinity for different positioning sites, the range exhibited being about 2 orders of magnitude greater than that of the initial binding of the octamer. Strong positioning sites are located 5' and 3' of the globin gene and in the second intron but are absent from the coding regions. These sites exhibit a periodicity (approximately 200 bp) similar to the average spacing of nucleosomes on the inactive beta-globin gene in vivo, which could indicate their involvement in packaging the gene into higher-order chromatin structure. Overlapping, alternative octamer positioning sites commonly exhibit spacings of 20 and 40 bp, but not of 10 bp. These short-range periodicities could reflect features of the core particle structure contributing to the pronounced sequence-dependent manner in which the core histone octamer interacts with DNA.     

Modulation of nucleosome structure by histone subtypes in sea urchin embryos.

Switches of the types of histones synthesized and incorporated into chromatin occur during sea urchin embryogenesis. In an attempt to define the possible effects of these variant histones on chromatin structure, I have isolated and characterized nucleosome core particles from Strongylocentrotus purpuratus blastula (nearly 100% early histones) and pluteus (75% late histones). Both particles contain 146-base-pair lengths of DNA wrapped around an octamer of H2A, H2B, H3, and H4. Although sharing these similarities with the canonical core particle, the nucleosome structures have certain features that differ from those of typical adult tissues. Both the reversible and the irreversible conformational transitions occurring on heating core particles are destabilized in the embryonic particles vs. "typical" core particles. The blastula core particle unfolds more easily than pluteus (or other) nucleosomes under the stress of low ionic strength. The rate of DNase I digestion of pluteus core particles is about half that of particles from blastula; certain cutting sites differ in their susceptibility between the two embryonic particles and between these two and the canonical core particle. The data demonstrate that the variant histones synthesized during early embryogenesis have demonstrable effects on chromatin structure, even at this basic level.     

Identification of an ion channel-forming motif in the primary structure of CFTR, the cystic fibrosis chloride channel.

Synthetic peptides with sequences representingputative transmembrane (M) segments of CFTR (the cystic fibrosis transmembraneconductance regulator) were used as tools to identify the involvement of suchsegments in forming the ionic pore of the CFTR Cl- channel. Peptides withsequences corresponding to M2 and M6 form anion-selective channels afterreconstitution in lipid bilayers. In contrast, peptides with the sequences ofM1, M3, M4, and M5, or peptides of the same amino acid composition as M2 and M6but with scrambled sequences, do not form channels. Conductive heterooligomersof M2 and M6 exhibit a single channel conductance of 8 pS (in 0.15 M KCl) and a95% selectivity for anions over cations, properties that emulate both theconductance and the selectivity of the authentic CFTR channel. Theidentification of sequence-specific motifs that account for key functionalattributes of the CFTR channel suggests that such modules may representfundamental units of function and are plausible constituents of the pore-formingstructure of the CFTR Cl- channel.     

Calpain-I induced alterations in the cytoskeletal structure and impaired mechanical properties of single myocytes of rat heart

OBJECTIVE: The involvement of Calpain-I mediated proteolysis has been implicated in myofibrillar dysfunction of reperfused myocardium following ischemia (stunning). This study addresses the question whether ultrastructural alterations might be responsible for the depressed contractility. METHODS: Mechanical properties and protein composition of isolated myocytes after Calpain-I exposure (1.25 U/ml; 10 min; 15 degrees C; pCa 5.0) and of ischemic rat hearts following reperfusion were characterized. RESULTS: Maximal isometric force (44 +/- 5 kN/m2) at pCa 4.5 (pCa = -log[Ca2+]) decreased by 42.5% in Triton permeabilized myocytes (n = 11) after Calpain-I treatment. Force (and consequent myofilament disarrangement) during Calpain-I treatment was prevented by 40 mM BDM. The contractile force of Calpain-I exposed myocytes was significantly higher at submaximal levels of activation (pCa 5.5, 5.4 and 5.3) before maximal force development (pCa 4.5) than after maximal force development. The pCa50 value (5.40 +/- 0.02) determined from these initial test contractures did not differ significantly from that of untreated controls (5.44 +/- 0.03). However, after full activation Ca(2+)-sensitivity of force production in Calpain-I treated myocytes was significantly reduced (pCa50 5.34 +/- 0.02). This change in pCa50 was positively correlated with the reduction in maximal isometric force and was accompanied by sarcomere disorder. These findings imply that at least part of the Calpain-I induced mechanical alterations are dependent on force history. Measurements of the rate of force redevelopment after unloaded shortening suggested that Calpain-I did not affect cross-bridge kinetics. SDS gel electrophoresis and Western immunoblotting of Calpain-I treated myocytes revealed desmin degradation. The desmin content of postischemic myocardium was also reduced. CONCLUSION: Our results indicate that ultrastructural alterations may play an important role in the Calpain-I mediated cardiac dysfunction.     

Right ventricular mechanical and energetic properties

To formulate right ventricular (RV) mechanical and energetic properties in terms of the time-varying elastance model, Emax and the systolic pressure-volume area (PVA) of RV were measured in the excised cross-circulated heart preparation, while the left ventricle was beating unloaded. Emax of RV was constant, and independent of the RV volume, the stroke volume, the ejection velocity, and the pre-ejection period in the control contractile state. Enhancement of the contractile state with calcium increased Emax, and reduction of the contractile state with propranolol decreased Emax. The whole heart oxygen consumption (Vo2) was linearly regressed on PVA of RV, in both the control and the calcium-enhanced contractile state. Calcium elevated the regression line in a parallel manner. The slope of the regression line was (1.85 +/- 0.19) x 10(-5) ml O2/mmHg ml in the control state, and (1.57 +/- 0.44) in the calcium state. These slope values were similar to those in left ventricle (LV). We therefore conclude that mechanical and energetic properties of RV are similar to those of LV.     

Multiple nucleosome positioning with unique rotational setting for the Saccharomyces cerevisiae 5S rRNA gene in vitro and in vivo.

A simple no-background assay was developed for high-resolution in vivo analysis of yeast chromatin. When applied to Saccharomyces cerevisiae 5S rRNA genes (5S rDNA), this analysis shows that nucleosomes completely cover this chromosomal region, occupying alternative positions characterized by a unique helical phase. This supports the notion that sequence-intrinsic rotational signals are the major determinant of nucleosome localization. Nucleosomal core particles reconstituted in vitro occupy the same positions and have the same helically phased distribution observed in vivo, as determined by mapping of exonuclease III-resistant borders, mapping by restriction cleavages, and by DNase I and hydroxyl-radical digestion patterns.