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van Emmerik CL, van Ingen H. Unspinning chromatin: Revealing the dynamic nucleosome landscape by NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 110:1-19. [PMID: 30803691 DOI: 10.1016/j.pnmrs.2019.01.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 05/09/2023]
Abstract
NMR is an essential technique for obtaining information at atomic resolution on the structure, motions and interactions of biomolecules. Here, we review the contribution of NMR to our understanding of the fundamental unit of chromatin: the nucleosome. Nucleosomes compact the genome by wrapping the DNA around a protein core, the histone octamer, thereby protecting genomic integrity. Crucially, the imposed barrier also allows strict regulation of gene expression, DNA replication and DNA repair processes through an intricate system of histone and DNA modifications and a wide range of interactions between nucleosomes and chromatin factors. In this review, we describe how NMR has contributed to deciphering the molecular basis of nucleosome function. Starting from pioneering studies in the 1960s using natural abundance NMR studies, we focus on the progress in sample preparation and NMR methodology that has allowed high-resolution studies on the nucleosome and its subunits. We summarize the results and approaches of state-of-the-art NMR studies on nucleosomal DNA, histone complexes, nucleosomes and nucleosomal arrays. These studies highlight the particular strength of NMR in studying nucleosome dynamics and nucleosome-protein interactions. Finally, we look ahead to exciting new possibilities that will be afforded by on-going developments in solution and solid-state NMR. By increasing both the depth and breadth of nucleosome NMR studies, it will be possible to offer a unique perspective on the dynamic landscape of nucleosomes and its interacting proteins.
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Affiliation(s)
- Clara L van Emmerik
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.
| | - Hugo van Ingen
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.
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Bradbury EM. Conformations and flexibilities of histones and high mobility group (HMG) proteins in chromatin structure and function. CIBA FOUNDATION SYMPOSIUM 2008; 93:246-70. [PMID: 6220876 DOI: 10.1002/9780470720752.ch14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The packaging of the enormous lengths of eukaryotic DNA into the different conformational states of chromosomes is controlled very largely by an equal total mass of the histones, H1, H2A, H2B, H3 and H4. Histone sequences, sequence conservations, postsynthetic chemical modifications and studies of histone conformations and interactions show clearly that histones are multi-domain proteins. The N-terminal domains of all histones and the C-terminal domains of H1, H2A and H2B are flexible random coils, while the C-terminal regions of H3 and H4 and the central regions of H1, H2A and H2B are structured. Histones H3 and H4 are essential for nucleosome structure and interact with DNA to give the nucleus of the nucleosome structure, which is completed by interactions of the conserved structured regions of (H2A, H2B) dimers and H1. The flexible domains of all the histones are very basic and contain all the sites of reversible chemical modifications: acetylation of lysines in the core histones and phosphorylation of serines and threonines in histone H1. Strict correlations have been observed (i) between acetylation and DNA processing and (ii) between H1 phosphorylation and chromosome condensation. In addition to histone acetylation, active chromatin is also associated with high mobility group (HMG) proteins 14 and 17. These proteins are completely flexible under all solution conditions and their native structures must be imposed by their binding sites in active chromatin. The function of flexibility in these chromosomal proteins is not understood but is probably related to the enormous lengths of DNA which have to be controlled in the structures and function of chromosomes.
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Wang X, Hayes JJ. Physical methods used to study core histone tail structures and interactions in solutionThis paper is one of a selection of papers published in this Special Issue, entitled 27th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process. Biochem Cell Biol 2006; 84:578-88. [PMID: 16936830 DOI: 10.1139/o06-076] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The core histone tail domains are key regulatory elements in chromatin. The tails are essential for folding oligonucleosomal arrays into both secondary and tertiary structures, and post-translational modifications within these domains can directly alter DNA accessibility. Unfortunately, there is little understanding of the structures and interactions of the core histone tail domains or how post-translational modifications within the tails may alter these interactions. Here we review NMR, thermal denaturation, cross-linking, and other selected solution methods used to define the general structures and binding behavior of the tail domains in various chromatin environments. All of these methods indicate that the tail domains bind primarily electrostatically to sites within chromatin. The data also indicate that the tails adopt specific structures when bound to DNA and that tail structures and interactions are plastic, depending on the specific chromatin environment. In addition, post-translational modifications, such as acetylation, can directly alter histone tail structures and interactions.
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Affiliation(s)
- Xiaodong Wang
- Department of Biochemistry and Biophysics, Box 712, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester NY, USA
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Karantza V, Freire E, Moudrianakis EN. Thermodynamic studies of the core histones: stability of the octamer subunits is not altered by removal of their terminal domains. Biochemistry 2001; 40:13114-23. [PMID: 11669650 DOI: 10.1021/bi0110140] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have investigated the role of the labile terminal domains of the core histones on the stability of the subunits of the protein core of the nucleosome by studying the thermodynamic behavior of the products of limited trypsin digestion of these subunits. The thermal stabilities of the truncated H2A-H2B dimer and the truncated (H3-H4)/(H3-H4)(2) system were studied by high-sensitivity differential scanning calorimetry and circular dichroism spectroscopy. The thermal denaturation of the truncated H2A-H2B dimer at pH 6.0 and low ionic strength is centered at 47.3 degrees C. The corresponding enthalpy change is 35 kcal/mol of 11.5 kDa monomer unit, and the heat capacity change upon unfolding is 1.2 kcal/(K mol of 11.5 kDa monomer unit). At pH 4.5 and low ionic strength, the truncated (H3-H4)/(H3-H4)(2) system, like its full-length counterpart, is quantitatively dissociated into two truncated H3-H4 dimers. The thermal denaturation of the truncated H3-H4 dimer is characterized by the presence of a single calorimetric peak centered at 60 degrees C. The enthalpy change is 25 kcal/mol of 10 kDa monomer unit, and the change in heat capacity upon unfolding is 0.5 kcal/(K mol of 10 kDa monomer unit). The thermal stabilities of both types of truncated dimers exhibit salt and pH dependencies similar to those of the full-length proteins. Finally, like their full-length counterparts, both truncated core histone dimers undergo thermal denaturation as highly cooperative units, without the involvement of any significant population of melting intermediates. Therefore, removal of the histone "tails" does not generally affect the thermodynamic behavior of the subunits of the core histone complex, indicating that the more centrally located regions of the histone fold and the extra-fold structured elements are primarily responsible for their stability and responses to parameters of their chemical microenvironment.
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Affiliation(s)
- V Karantza
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218
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Karantza V, Freire E, Moudrianakis EN. Thermodynamic studies of the core histones: pH and ionic strength effects on the stability of the (H3-H4)/(H3-H4)2 system. Biochemistry 1996; 35:2037-46. [PMID: 8639689 DOI: 10.1021/bi9518858] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The self-associative behavior and the thermal stability of the H3/H4 histone complex was studied in low-ionic strength conditions by several physicochemical techniques, including differential scanning calorimetry and circular dichroism spectroscopy. At neutrality, the major molecular species present in solution is the (H3-H4)2 tetramer. Its thermodynamic properties cannot be studied directly though, since its thermal denaturation is completely irreversible even at the lowest salt concentrations. However, a complete thermodynamic analysis can be performed at low ionic strength and pH 4.5, where the (H3-H4)2 tetramer is quantitatively dissociated into two H3-H4 dimers and where almost complete reversibility of the thermal transitions is attained. The unfolding transition temperature of the 26.5 kDa H3-H4 dimer increases as a function of both the ionic strength of the solvent and the total protein concentration. The thermal denaturation of the H3-H4 dimer is characterized by the presence of a single calorimetric peak, centered at 58 degrees C, with a corresponding enthalpy change of 25 kcal/mol of a 13 kDa monomer unit and a change in heat capacity upon unfolding of about 0.6 kcal/(K mol of 13 kDa monomer unit). The complex between histones H3 and H4 (tetramer or dimer) is stable between pH 9.5 and 3.0. At pH 1.5, the system is almost completely unfolded at all temperatures. At low ionic strengths and pH values between 5.0 and 2.5, the H3-H4 dimer behaves as a highly cooperative system, melting as a single unit; i.e. individual H3 and H4 folded monomers are not detectable during the treatment. The two-state mechanism accounting for the unfolding of the H3-H4 dimer at pH 4.5 is the same as that described for the H2A-H2B dimer at neutrality. Just like for the H2A and H2B histones, the H3 and H4 polypeptides are properly folded only when assembled as H3-H4 dimers or in higher-order histone assemblies. Therefore, coupling along the interfaces of the two chains within the heterodimer is the major factor contributing to the stabilization of the secondary and tertiary structures of the chains as well as of the histone dimers.
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Affiliation(s)
- V Karantza
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
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Abstract
Modern NMR has revitalized the study of protein dynamics. Multidimensional spectra and the heteronuclear spectroscopy allow a substantial gain in resolution. Dynamics can be analyzed at individual sites and data on segmental and sequence-dependent flexibility are accumulating. This review summarizes the wide variety of NMR approaches for observing internal motions, including the folding processes, and the attempts to correlate dynamics to the biological activity of proteins. The implications of mobility on structure determination by NMR is also discussed.
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Affiliation(s)
- O Jardetzky
- Stanford Magnetic Resonance Laboratory, Stanford University, CA 94305-5055
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Arents G, Burlingame RW, Wang BC, Love WE, Moudrianakis EN. The nucleosomal core histone octamer at 3.1 A resolution: a tripartite protein assembly and a left-handed superhelix. Proc Natl Acad Sci U S A 1991; 88:10148-52. [PMID: 1946434 PMCID: PMC52885 DOI: 10.1073/pnas.88.22.10148] [Citation(s) in RCA: 540] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The structure of the octameric histone core of the nucleosome has been determined by x-ray crystallography to a resolution of 3.1 A. The histone octamer is a tripartite assembly in which a centrally located (H3-H4)2 tetramer is flanked by two H2A-H2B dimers. It has a complex outer surface; depending on the perspective, the structure appears as a wedge or as a flat disk. The disk represents the planar projection of a left-handed proteinaceous superhelix with approximately 28 A pitch. The diameter of the particle is 65 A and the length is 60 A at its maximum and approximately 10 A at its minimum extension; these dimensions are in agreement with those reported earlier by Klug et al. [Klug, A., Rhodes, D., Smith, J., Finch, J. T. & Thomas, J. O. (1980) Nature (London) 287, 509-516]. The folded histone chains are elongated rather than globular and are assembled in a characteristic "handshake" motif. The individual polypeptides share a common central structural element of the helix-loop-helix type, which we name the histone fold.
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Affiliation(s)
- G Arents
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
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Muller S, Couppez M, Briand JP, Gordon J, Sautière P, van Regenmortel MH. Antigenic structure of histone H2B. BIOCHIMICA ET BIOPHYSICA ACTA 1985; 827:235-46. [PMID: 2578822 DOI: 10.1016/0167-4838(85)90208-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Antigenic determinants of histone H2B were localized using a series of 23 overlapping fragments of H2B obtained either by chemical and enzymatic cleavage of the histone or by solid-phase peptide synthesis. The ability of peptides to bind H2B antibodies was measured in an enzyme-linked immunosorbent assay, using antisera directed against calf thymus and chicken erythrocyte H2B as well as four anti H2B monoclonal antibodies obtained from autoimmune mice. Seven antigenic determinants were localized in the H2B molecule in the vicinity of residues 1-11, 6-18, 15-25, 26-35, 50-65, 94-113 and 114-125. Two of these determinants (residues 6-18 and 26-35) were revealed only through the binding properties of antibodies isolated from autoimmune mice. The usual correlation between hydrophilicity and antigenicity was found to hold for four of the epitopes, and the N- and C-termini of H2B were both antigenically active.
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Van Helden PD. The influence of primary structure changes on the higher order structure of histone H2B. BIOCHIMICA ET BIOPHYSICA ACTA 1980; 623:429-38. [PMID: 7397225 DOI: 10.1016/0005-2795(80)90272-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Structural changes of histones H2B in aqueous media were studied under conditions of varying pH and ionic strength. The techniques involved intrinsic fluorescence of tyrosine residues, extrinsic fluorescence using the hydrophobic probe 8-anilinonaphthalene sulfonate and fluorescence polarization. Secondary structure predictive methods were also used to study potential effects of primary mutations. In spite of many primary structure changes, the predicted effect on a globular structure of H2B is minimal. The results indicate the formation of a major hydrophobic region, the formation of helices and the burial of tyrosine residue 83 (calf), the structural changes of which appear to be identical in all H2B's as ionic strength is increased. The effect of primary structure changes on protein-protein interaction where H2B's are concerned is likely to be negligible, whereas the major effect is likely to be the protein-DNA interaction where H2B could be at least partially responsible for differentiation.
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12
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Abstract
The complete sequence of histone 2B of Drosophila has been determined by using an improved Beckman sequenator. Comparing these data with those previously published by other investigators on the histone 2B of calf [Iwai, K., Hayashi, H., & Ishikawa, K. (1972) J. Biochem. (Tokyo) 72, 357--367], trout [Koostra, A., & Bailey, G. S. (1978) Biochemistry 17, 2504--2510], and Patella (a limpet) [van Helden, P. D., Strickland, W. N., Brandt, W. F., & von Holt, C. (1979) Eur. J. Biochem. 93, 71--78], it is possible to assess the evolutionary stability of this protein. There is little conservation of sequence in the N-terminal portion of the molecule (residues 1--26 numbering according to calf H2B), while the remainder of the protein, which we designate the C-terminal portion, is highly conserved. In the region of 27--125 residues, there are 9 substitutions in the composite data among the 98 positions, 8 of them conservative. These data indicate that very different selective pressures operate on the two different portions of the H2B molecule, implying the existence of two well-defined regions. Studies on the structure of the nucleosome by others have suggested that the C-terminal portion of H2B is involved in histone-histone interactions while the N-terminal portion is a relatively free "tail" binding to DNA. The sequence data indicate that the function of the C-terminal region of H2B requires considerable sequence specificity while that of the N-terminal region does not.
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Sonnenbichler J. Advances in chromatin research. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 1979; 66:244-50. [PMID: 381945 DOI: 10.1007/bf00571604] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Recent results in chromatin research are reviewed. The nucleosomal arrangement is described and the roles of DNA, histones and non-histones are discussed in connection with their functions.
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15
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Tancredi T, Temussi PA. Secondary structure of calf-thymus histone H1 by means of13C-NMR spectroscopy. Biopolymers 1979. [DOI: 10.1002/bip.1979.360180102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Cary PD, Moss T, Bradbury EM. High-resolution proton-magnetic-resonance studies of chromatin core particles. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 89:475-82. [PMID: 710406 DOI: 10.1111/j.1432-1033.1978.tb12551.x] [Citation(s) in RCA: 121] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The binding of histones in chromatin core particles and in core particles depleted of histones H2A and H2B has been studied by high-resolution proton nuclear magnetic resonance (NMR) at 270 MHZ. At low ionic strengths it is shown that histones H3 and H4 are bound in the core particle. Further, whereas the apolar regions of H2A and H2B are also bound to the core particle, the basic N-terminal and C-terminal regions are more mobile and give rise to sharp resonances in the NMR spectrum of the core particle. Between 0.3 and 0.6 M NaCl there is further release of basic regions of histones H3 and H4 from the complex. The dissociation of the core particle between 0.6 and 2.0 M NaCl is accompanied by the release of the structured apolar regions of the histones as evidenced by the appearance of a complex aromatic spectrum and perturbed upfield ring-current-shifted methyl resonances. Arginine residues are implicated in the binding between histones and DNA and 69% of these residues are found in the apolar regions of the histones. The interactions between histones and DNA in the core particle thus involves H3 and H4 and the apolar regions of H2A and H2B. It is suggested that these basic regions of H2A and H2B have binding sites outside the core particle.
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Friend C, Freedman HA. Effects and possible mechanism of action of dimethylsulfoxide on Friend cell differentiation. Biochem Pharmacol 1978; 27:1309-13. [PMID: 358991 DOI: 10.1016/0006-2952(78)90112-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Weischet WO, Tatchell K, Van Holde KE, Klump H. Thermal denaturation of nucleosomal core particles. Nucleic Acids Res 1978; 5:139-60. [PMID: 643604 PMCID: PMC341967 DOI: 10.1093/nar/5.1.139] [Citation(s) in RCA: 145] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Thermal denaturation of very homogeneous preparations of core particles from chicken erythrocyte chromatin is studied by several techniques. The change in absorbance, which is very closely paralleled by changes in heat capacity, which is very closely paralleled by changes in heat capacity, is a biphasic process with inflexions at 60 degrees C and 74 degrees C. In contrast, isolated DNA of the same length denatures in a single transition around 44 degrees C. Monitoring the circular dichroism of the cores during thermal denaturation reveals biphasic changes in the secondary structure of the DNA, preceding the base unstacking by 10 degrees C in the first and 3 degrees C in the second phase. However, measurable alterations in the secondary structure of the histones are confined to the second phase with a melting temperature at 71 degrees C. Increase in the ionic strength of the buffer from 1 mM to 10 mM leads to almost monophasic melting curves as measured by absorbance and CD, while not causing any measurable conformational changes at room temperature. The melting of core particles is interpreted as a denaturation of about 40 base pairs in the first phase, followed by a massive breakdown of the native structure of a tight histone-DNA complex, which frees the remaining 100 base pairs for unstacking.
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Giancotti V, Brovedan S, Fonda M, Grandinetti R, Russo E. Intrinsic and extrinsic fluorescence of histones H2A and H2B: a conformational study. Biophys Chem 1978; 7:269-77. [PMID: 623868 DOI: 10.1016/0301-4622(78)85003-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Intrinsic and extrinsic fluorescence measurements suggest that H2A and H2B histones, in a partially secondary structure, self-aggregate into assemblies in which some tyrosine groups are buried in a hydrophobic environment and show enhanced fluorescence, 2-p-toluidinylnaphthalene-6-sulfonate (TNS) indicates heterogeneity among the binding sites whose number depends on the pH values of the solutions. Warfarin, used as hydrophobic probe, shows that during the process of self-association and cross-complexing of the two histones there is the covering of some hydrophobic sites of the proteins.
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21
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Patel DJ. Mutagen-nucleic acid complexes at the polynucleotide duplex level in solution: intercalation of proflavine into poly(dA-dT) and the melting transition of the complex. Biopolymers 1977; 16:2739-54. [PMID: 597577 DOI: 10.1002/bip.1977.360161212] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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22
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Crane-Robinson C, Hayashi H, Cary PD, Briand G, Sautière P, Krieger D, Vidali G, Lewis PN, Tom-Kun J. The location of secondary structure in histone H4. EUROPEAN JOURNAL OF BIOCHEMISTRY 1977; 79:535-48. [PMID: 562748 DOI: 10.1111/j.1432-1033.1977.tb11838.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A total of eight peptides cleaved from calf thymus histone H4 have been studied at several ionic strengths by circular dichroic, infrared and nuclear magnetic resonance spectroscopies to follow the formation of alpha helix, beta structure and self-aggregates. The results are compared with data obtained previously on three other peptides and on the intact molecule in order to define the location of secondary structure in histone H4. It is concluded that there are two alpha-helical sections, the first from residues 55 to 67 and the second of about 12 residues in the region between residues 70 to 90. beta-Structure formation takes place only in the C-terminal part of the intact H4 molecule. Nuclear magnetic resonance studies of the peptides prove that it is the basic N-terminal regions of histone H4 that remain free when the molecule self-aggregates.
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23
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Macleod AR, Wong NC, Dixon GH. The amino-acid sequence of trout-testis histone H1. EUROPEAN JOURNAL OF BIOCHEMISTRY 1977; 78:281-91. [PMID: 913397 DOI: 10.1111/j.1432-1033.1977.tb11739.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The complete amino-acid sequence of 194 residues of trout testis histone H1 has been elucidated by automated Edman degradation of large peptides derived from specific cleavages at infrequent amino-acid residues. Trout testis histone H1 has a molecular weight of 19314, is only slighly microheterogeneous, and possesses pentapeptide sequences related to Ala-Ala-Ala-Lys-Lys repeated six times in the complete sequence. Although the N-terminus of histone H1 is known to be blocked, some 10% of intact trout testis H1 contains a free N-terminal alanine residue. Three seryl residues in the C-terminal half (97-194) of the molecule occur in the sequence Lys-Ser-Pro-Lys known to be phosphorylated in trout testis H1. The sequence has been compared to the known partial sequence of rabbit thymus H1. The results are consistent with a role for histone H1 in the maintenance of the higher-order structure of chromatin.
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Abstract
Laser Raman spectroscopy indicates that the inner histones which are bound to DNA in chromatin or in isolated nu bodies are similar in conformation to the inner histones which are dissociated from DNA in high-salt solutions. This structure contains, on the average, 51+/-5% alpha-helix and no substantial beta-sheet conformation. It is proposed that the protein core of the nu body has a high alpha-helix content.
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25
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Puigdoménech P, Daban JR, Palau J, Podo F, Guidoni L, Temussi PA. The interaction of histone H3 with histone H4 and with other histones studied by 19F nuclear magnetic resonance. BIOCHIMICA ET BIOPHYSICA ACTA 1977; 492:12-9. [PMID: 16662 DOI: 10.1016/0005-2795(77)90209-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The behaviour, upon variations in ionic strength, pH and temperature of 19F nuclear nuclear magnetic resonance signals of the trifluoroacetonylated derivative of histone H3 is compared with those of the H3-H4 complex and of the Hv fraction (an equimolar mixture of H2A, H2B, H3 and h4). The line width of the 19F-labelled histone H3 signals increases with ionic strength or pH, an effect consistent with aggregation of the protein. In the case of H3-H4 complex or Hv the line width decreases at intermediate ionic strengths (0.1-0.25 M NaCl). This effect is interpreted as the consequence of the formation of a well defined structure with ionic strength. At high salt concentrations the line width increases as a consequence of the final rigid quaternary structure or of the formation of higher aggregates.
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26
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Tancredi T, Temussi PA, Paolillo L, Trivellone E, Crane-Robinson C. A study of calf-thymus histone H2B using 13C magnetic resonance. EUROPEAN JOURNAL OF BIOCHEMISTRY 1976; 70:403-8. [PMID: 1009938 DOI: 10.1111/j.1432-1033.1976.tb11030.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Calf thymus histone H2B has been studied by means of 13c magnetic resonance. Most sidechain resonances have been assigned. Analysis of 13c peak intensities by a simple computer-aided method proves that 13c magnetic resonance spectroscopy can be used to monitor aggregation phenomena more accurately than 1H magnetic resonance or other physico-chemical methods. Re-examination of 1H spectral simulations shows substantial agreement with 13C results. It is concluded that in 0.1M added NaCL the H2b aggregates include the chain segment from 50 (+/-5) to 108 (+/-5).
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27
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Ramsay-Shaw B, Schmitz K. Reanalysis of histone-induced conformational changes in DNA determined by quasielastic light scattering. Biopolymers 1976; 15:2313-5. [PMID: 990416 DOI: 10.1002/bip.1976.360151121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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28
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Abstract
The secondary structures of the histones, H1, H2A, H2B, H3, and H4 have been predicted utilizing the predictive scheme of Chou and Fasman (Biochemistry 13:211, 222[1974]) and a new set of conformational parameters based on the X-ray data of 29 protein structures. The alpha-helical, beta-sheet, reverse beta-turns, and random coil regions of these proteins are carefully delineated. Structures are specified which are most probably under various environmental conditions, i.e., for changes in ionic strength, association between histones and in association with DNA. Potential conformational changes within these histones are also predicted.
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29
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Smerdon MJ, Isenberg I. Conformational changes in subfractions of calf thymus histone H1. Biochemistry 1976; 15:4233-42. [PMID: 9134 DOI: 10.1021/bi00664a016] [Citation(s) in RCA: 71] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This paper presents the first study of conformational changes in the subfractions of calf thymus H1. H1 was fractionated by the method of Kincade and Cole (Kincade, J. M., and Cole, R.D. (1966), J. Biol. Chem. 241. 5790) using a very shallow Gdn-HC1 gradient. A possible new H1 subfraction, about 5--8% of the H1, has been found and characterized by amino acid analysis and electrophoresis. The effects of salt concentration and pH on the conformation of each of the four major subfractions have been studied by measuring the fluorescence anisotropy of the tyrosine emission and the circular dichroism (CD) of the peptide bond. Upon the addition of salt to aqueous solutions at neutral pH, all four subfractions show an instantaneous change in fluorescence anisotropy, fluorescence intensity, tyrosine absorbance, and CD. The folding associated with this instantaneous change is highly cooperative, and involves the region of the molecule containing the lone tyrosine, which becomes buried in the folded form. The folding of subfraction 3a is more sensitive to salt than the other major subfractions. Upon folding, approximately 13% of the residues of subfractions 1b and 2 form alpha and beta structure; 3a and 3b have approximately 16% of the residues in alpha and beta structures. There is no evidence for interactions between the subfractions. In salt-free solutions, each of the four major subfractions show very little change in conformation in going from low to neutral pH, but each shows a very sharp transition near pH 9. This transition gives rise to a marked increase in fluorescence anisotropy and fluorescence intensity, and involves the formation of both alpha and beta strucute in a manner similar to that of the salt-induced state.
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31
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Kootstra A, Bailey GS. The primary structure of histone H2B from brown trout (Salmo trutta) testes. FEBS Lett 1976; 68:76-8. [PMID: 986955 DOI: 10.1016/0014-5793(76)80408-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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32
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Jasinskas AL, Gineitis AA. A study of histone-histone interactions by affinity chromatography. Mol Biol Rep 1976; 3:19-25. [PMID: 1004503 DOI: 10.1007/bf00357205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Homologous whole histone from calf thymus was adsorbed on Sepharose 4B columns with covalently coupled histone fractions H2a, H2b, H3 or H4 in 0.01 M phosphate buffer, pH 6.7 - 1 M NaCl. The adsorbed histones were eluted from the columns with 5 M urea in the same buffer. Electrophoretic analysis has shown that the different columns exhibit selective affinity to the histone fractions: the H2b column to histone H2b and H2a (with only weak affinity to histones H3 and H4), the H2a column to histones H2b and H3 (moderate affinity to histone H2b), and the H4 column to histone H3, H4 and H2b (weak affinity to histone H2a). Histone H1 displayed no fixation by either of the columns tested.
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33
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Carpenter BG, Baldwin JP, Bradbury EM, Ibel K. Organisation of subunits in chromatin. Nucleic Acids Res 1976; 3:1739-46. [PMID: 967672 PMCID: PMC343032 DOI: 10.1093/nar/3.7.1739] [Citation(s) in RCA: 114] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
There is considerable current interest in the organisation of nucleosomes in chromatin. A strong X-ray and neutron semi-meridional diffraction peak at approximately 10 nm had previously been attributed to the interparticle specing of a linear array of nucleosomes. This diffraction peak could also result from a close packed helical array of nucleosomes. A direct test of these proposals is whether the 10 nm peak is truly meridional as would be expected for a linear array of nucleosomes or is slightly off the meridian as expected for a helical array. Neutron diffraction studies of H1-depleted chromatin support the latter alternative. The 10 nm peak has maxima which form a cross-pattern with semi-meridional angle of 8 to 9 degrees. This is consistent with a coil of nucleosomes of pitch 10 nm and outer diameter of approximately 30 nm. These dimensions correspond to about six nucleosomes per turn of the coli.
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Abstract
The subunit structure of Neurospora chromatin which contains a full histone complement (Goff, 1976) exhibits both differences and similarities to chromatin of higher eucaryotes. The size of the DNA per subunit is only 170 +/- 5 base pairs, as compared to 200 base pairs in higher eucaryotes. However, the internal structures of the subunits are closely related. They contain 140 base pairs of DNA that are more tightly associated with the histone core and similarly arranged on the outside of the subunit. Hence the difference in structure resides in a shorter linker region of adjacent subunits in Neurospora chromatin. This is supported by a reduced primary cutting site and a lower content of lysines in histone H1. The role of H1 and its relation to the linker region are discussed.
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35
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Moss T, Cary PD, Crane-Robinson C, Bradbury EM. Physical studies on the H3/H4 histone tetramer. Biochemistry 1976; 15:2261-7. [PMID: 945069 DOI: 10.1021/bi00656a003] [Citation(s) in RCA: 77] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
High-resolution proton magnetic resonance spectroscopy (270 MHz), circular dichroism, and infrared spectroscopies and ultracentrifugation studies have been carried out on the salt-extracted (H3/H4)2 tetramer from calf thymus. The tetramer contains about 29% alpha helix and no beta structure. It is denatured in 6 M urea but can be renatured simply by dialysis to water. The proton spectrum shows a number of perturbed resonances which are not observed in the spectra of either H3 or H4 alone. The observation of these resonances demonstrates that the tetramer contains some elements of tertiary structure. The overall appearance of the spectrum however is close to that of a partially denatured protein. Sedimentation velocity studies show the tetramer to have a frictional ratio of 1.99 in 50 mM acetate/50 mM bisulfite and thus to be hydrodynamically quite different from a globular protein. Two possible structural models compatible with the data are discussed.
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36
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Strätling WH. Stimulation of transcription on chromatin by polar organic compounds. Nucleic Acids Res 1976; 3:1203-13. [PMID: 781622 PMCID: PMC342980 DOI: 10.1093/nar/3.5.1203] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Polar organic compounds, including DMSO, increase RNA synthesis on isolated chromatin by E. coli RNA polymerase and RNA polymerase II from calf thymus. Transcription is stimulated on chromatin from Friend-virus-infected erythroleukemia cells and from various other sources. Using procedures which inhibit specifically the formation of a stable initiation complex, it is shown that the stimulation does not result from an increase in initiation of both E. coli and the eukaryotic RNA polymerase. After separation of chromatin into template active and inactive fractions, DMSO increases RNA synthesis by a factor of about 1.5 using the template inactive fraction, while stimulation of transcription on the template active portion is lower (factor of 1.2). It is suggested that the effect on RNA synthesis is mediated by a weakening of the apolar interactions between histones in chromatin subunits, releasing transcription partially from the constraints imposed by histones.
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37
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Mihalakis N, Miller OJ, Erlanger BF. Antibodies to histones and histone-histone complexes: immunochemical evidence for secondary structure in histone 1. Science 1976; 192:469-71. [PMID: 3853 DOI: 10.1126/science.3853] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Highly specific antibodies were raised to histone 1 (H 1) and the histone complexes H32-H42 AND H2A-H2B, isolated by salt extraction. Antibody to H1 could detect irreversible conformational changes in acid- or urea-treated H1. The antibodies showed different reactivities with chromosomes as compared to antibodies in acid-extracted histones and should be useful in studies of native chromatin and chromosome structure.
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38
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Lilley DM, Howarth OW, Clark VM, Pardon JF, Richards BM. The existence of random coil N-terminal peptides - 'tails' - in native histone complexes. FEBS Lett 1976; 62:7-10. [PMID: 1248639 DOI: 10.1016/0014-5793(76)80004-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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39
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Liquier J, Pinot-Lafaix M, Taillandier E, Brahms J. Infrared linear dichroism investigations of deoxyribonucleic acid complexes with poly(L-arginine) and poly(L-lysine). Biochemistry 1975; 14:4191-7. [PMID: 170956 DOI: 10.1021/bi00690a007] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Complexes between DNAs from various sources and poly(L-lysine) and poly(L-arginine) were studied by means of infrared linear dichroism. The measurements of dichroic ratios allowed us to determine the orientation of the phosphate group of DNA in the complexes with basic polypeptides. At high relative humidities (higher than 90%, B form), the bisector of the less than OPO in the complexes forms an angle with respect to the helical axis which has a value lower by about 4 degrees than in the corresponding DNA sample. This change of orientation of the phosphate group of DNA indicates a modification of the B form upon binding of polylysine or polyarginine. The structural transitions B leads to A and B leads to C measured as a function of relative humidities were not affected by formation of complexes with both basic polypeptides. Similar results were obtained for complexes prepared by direct mixing or by salt gradient dialysis. The presence of A and C forms was observed in complexes of DNA with poly(L-lysine) and poly(L-arginine) at lower relative humidity. Thus, the conformational flexibility of DNA in complexes with polylysine and polyarginine is not changed despite a substantial increase in the Tm (melting temperature). These results are considered as a model for the understanding of interactions between DNA and histones particularly of the binding of the N-terminal fragment, lysine or arginine rich.
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40
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Lewis PN, Bradbury M, Crane-Robinson C. Ionic strength induced structure in histone H4 and its fragments. Biochemistry 1975; 14:3391-400. [PMID: 1170891 DOI: 10.1021/bi00686a016] [Citation(s) in RCA: 46] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The salt-induced folding and self-association of histone H4 and its fragments (1-23), (25-67), (69-84), and (69-102) have been studied at the same molar concentration (1 mM) by nuclear magnetic resonance (NMR), circular dichroism (CD), and ir spectroscopy. Byeach of these techniques intact histone H4 exhibited a fast structural change, involving the formation of alphaR helix and aggregation, and also a slow change involving beta-structure formation. Fragment (25-67) was found to behave in a manner similar to the intact molecule for the fast change, showing both helix formation and aggregation but exhibited no time-dependent effects. All the other fragments were found to be essentially noninteracting. It is concluded that (25-67) contains the rgion critical for the folding and self-association of histone H4. On the basis of these results a model is proposed for the self-association of histone H4 in which helix is located between residues 49 and 73, while the beta structure lies between 74 and the C-terminus.
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41
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Rubin RL, Moudrianakis EN. The F3-F2a1 complex as a unit in the self-assembly of nucleoproteins. Biochemistry 1975; 14:1718-26. [PMID: 1125196 DOI: 10.1021/bi00679a026] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A specific and stable interaction between histones f3 and f2a1 was demonstrated to take place in the absence of DNA. When a mixture of these histones was subjected to velocity sedimentation under conditions in which the separate histones are aggregated and precipitate, the mixture of f3 and f2a1 remained soluble and these histones appeared to cotransport through the gradient, indicating the establishment of an isolatable, stable f3-f2a1 complex. This isolated complex subsequently binds to DNA quantitatively to form nucleohistone. Stoichiometry data strongly suggest that histones f3 and f2a1 bind to DNA as a unit; this is the only type of f2a1 binding to DNA that can take place under mild conditions. Histone f1 can act as a modifier of the f3-f2a1-DNA interactions by augmenting the formation of the f3-f2a1 complex and consequently enhancing the overall binding of these histones to DNA. No significant interactions of histones f2b and f2a2 with other histones could be demonstrated. Because of the findings reported here and the known affinity characteristics of the arginine-rich histones to DNA in native chromatin (in particular their stimultaneous extraction from chromatin by salt), we suggest that the (f3 + f2a1)-DNA complex is a structural component of native chromatin. We would also like to propose that, in vivo, histones may possess a considerable amount of quaternary structure, which would greatly increase the specificity of their role as potential regulators of the structure and function of the eucaryotic chromosomes.
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42
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Adler AJ, Fulmer AW, Fasman GD. Interaction of histone f2al fragments with deoxyribonucleic acid. Circular dichroism and thermal denaturation studies. Biochemistry 1975; 14:1445-54. [PMID: 1168487 DOI: 10.1021/bi00678a015] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The glycine-arginine-rich histone, f2al (IV) (102 amino acids), from calf thymus was cleaved at residue 84 with cyanogen bromide. Complexes containing homologous DNA and each f2al fragment were reconstituted by means of Gdn-HC1 gradient dialysis. The circular dichroic (CD) spectra of these complexes were all examined in 0.14 M NaC1. The CD spectra of the DNA-f2al fragment complexes did not differ appreciably from that of DNA alone in the wavelength region above 240 nm. However, intact f2al-DNA complexes yield CD spectra which differ significantly (enhanced, blue-shifted, 273-nm band) from that of native DNA (Shih and Fasman, 1971). The small C-terminal fragment (85-102) was bound weakly to DNA under the conditions used. However, the large basic N-terminal fragment (1-83) was bound as well to DNA as was whole f2al, but produced no CD distortion. The conformation of the N-terminal fragment, unlike intact f2al, was not changed upon increasing the ionic strength to 0.14 M NaF. These results complement previous studies on f2al and its N-terminal CNBr fragment (Ziccardi and Schumaker, 1973). Thermal denaturation of the complexes in 2.5 X 10(-4) M EDTA was monitored simultaneously by changes in the absorption and CD spectra. All complexes showed a thermal transition at 45 degrees (Tml), attributable to the melting of free, double-stranded DNA. In addition, f2al-DNA and N fragment-DNA complexes displayed melting phenomena at 88 and 78 degrees (Tm2), respectively, caused by the denaturation of the histone-bound DNA. This difference in Tm2 constitutes further evidence that loss of the 18-amino-acid carboxyl end segment of f2al prohibits the unique type of interaction which occurs between DNA and the intact histone.
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43
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Bradbury EM, Cary PD, Chapman GE, Crane-Robinson C, Danby SE, Rattle HW, Boublik M, Palau J, Aviles FJ. Studies on the role and mode of operation of the very-lysine-rich histone H1 (F1) in eukaryote chromatin. The conformation of histone H1. EUROPEAN JOURNAL OF BIOCHEMISTRY 1975; 52:605-13. [PMID: 1236150 DOI: 10.1111/j.1432-1033.1975.tb04032.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Proton magnetic resonance, circular dichroism and other studies of whole and cleaved calf thymus histone H1 (formerly F1) reveal the presence of specific folded structures in the region approximately from residue 40--115. Ionic, hydrogen-bond and hydrophobic interactions all appear to contribute to the stability of the structure, which is predicted to contain alpha-helices in regions 42--55 and 58--75. No evidence was found for beta-structures, either inter or intramolecular, or for any structure formation outside the region 40--115. At 18 degrees C and a protein concentration of 2 mM the first-order exchange rate between random-coil and structured forms is slower than 80 s-1; at 40 degrees C the exchange rate is faster than 330 s-1.
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44
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Pekary AE, Li HJ, Chan SI, Hsu CJ, Wagner TE. Nuclear magnetic resonance studies of histone IV solution conformation. Biochemistry 1975; 14:1177-84. [PMID: 235281 DOI: 10.1021/bi00677a012] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The 220-MHz high-resolution proton magnetic resonance (PMR) spectrum of histone IV has been examined as a function of histone concentration, salt concentration, and pD. The hydrophobic C-terminal portion of the histone IV monomer appears to be largely PMR "invisible" indicating that this region of the polypeptide contains rigid secondary structure. Further loss of PMR resonance areas with increased histone IV concentration in neat D2O has been attributed to self-aggregation involving a monomer-dimer equilibrium. An equilibrium between the monomer and large aggregates, on the other hand, appears to dominate at NaCl concentrations above 0.01 M. pD studies reveal an abrupt increase in histone IV aggregation at pD smaller than 0.8 and precipitation of histone IV at pD values in the neighborhood of its isoelectric point, pD similar to 11.
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45
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Pekary AE, Chan SI, Hsu CJ, Wagner TE. Nuclear magnetic resonance studies on the solution conformation of histone IV fragments obtained by cyanogen bromide cleavage. Biochemistry 1975; 14:1184-9. [PMID: 1168067 DOI: 10.1021/bi00677a013] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Two histone IV fragments obtained by cleavage at Met-84 by cyanogen bromide have been examined by proton magnetic resonance (PMR) spectroscopy as a function of temperature, peptide concentration, ionic strength, and pD. Sedimentation and gel electrophoresis studies on these peptides have also been carried out. The 220-MHz PMR spectrum of the N-peptide in both the high- and low-field regions was shown to be almost identical with that calculated for an extended coil N-peptide monomer. The calculated random coil and experimental C-peptide spectra, on the other hand, differ in many respects. Evidence was obtained for the presence of rigid secondary structure in the C-peptide. In addition, the Val, Leu, Ile CH3 resonance displays a prominent high-field satellite band which shifts downfield with increasing temperature. Sedimentation studies on the N-peptide reveal the formation of extremely large, remarkably homogeneous aggregates at ionic strengths larger than or equal to 0.01. The C-peptide, on the other hand, does not appear to form aggregates of sufficient size to be detectable in velocity sedimentation studies of a few hours duration. The relative area changes which have previously been noted in the PMR spectrum of histone IV with increasing ionic strength were also observed for the N-peptide but not the C-peptide. Interpretation of these relative area changes has been made in terms of the amino acid sequence of histone IV, and an effort was made to identify that segment of the polypeptide which undergoes secondary structural change with increasing ionic strength.
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46
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Martinson HG, McCarthy BJ. Histone-histone associations within chromatin. Cross-linking studies using tetranitromethane. Biochemistry 1975; 14:1073-8. [PMID: 1168485 DOI: 10.1021/bi00676a030] [Citation(s) in RCA: 74] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Treatment of chromatin with the protein cross-linker tetranitromethane (TNM) results in a product identified as an F2a1-F2b dimer. The same product appears after treatment with TNM of HeLa cells growing in culture. Furthermore acid-extracted histones which have been fractionated into the five separate species can be recombined and mixed with DNA to produce a nucleohistone preparation which is also cross-linked by TNM to give the F2a1-F2b dimer. F1 and F3 can be excluded from the reconstitution mixture without effect on the dimer production. In contrast, the presence of F2a2 is essential to the proper reconstitution of F2a1 and F2b with DNA. The specificity of TNM and the characteristics of the reaction suggest that F2a1 and F2b are cross-linked at their specific binding sites. These results provide evidence that F2a1, F2a2, and F2b interact specifically in chromatin.
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47
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48
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Baldwin JP, Boseley PG, Bradbury EM, Ibel K. The subunit structure of the eukaryotic chromosome. Nature 1975; 253:245-9. [PMID: 1167623 DOI: 10.1038/253245a0] [Citation(s) in RCA: 248] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
New strucutral data have been obtained from neutron scattering studies of chromatin. The concentration-dependent meridional peak at 10-11 nm comes from the interparticle spacing of a subunit structure. Peaks at 5.5 and 3.7 nm have a different contrast behaviour to those at 11.0 and 3.7 nm showing that histones and DNA have a different spatial arrangement in the subunit. A globular model in which apolar segments of histones from the core surrounded by DNA complexed with the basic segments of histones agrees with the data.
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49
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Price NC, Cohn M, Schirmer RH. Fluorescent and spin label probes of the environments of the sulfhydryl groups of porcine muscle adenylate kinase. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41945-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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50
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Van Holde KE, Sahasrabuddhe CG, Shaw BR. A model for particulate structure in chromatin. Nucleic Acids Res 1974; 1:1579-86. [PMID: 10793713 PMCID: PMC343437 DOI: 10.1093/nar/1.11.1579] [Citation(s) in RCA: 180] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A model is proposed for the structure of nuclease-resistant chromatin particles. The model is novel in that it proposes that the DNA in such a particle is wound about a protein core, made up of the hydrophobic regions of histone molecules.
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