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Chikhirzhina EV, Starkova TY, Polyanichko AM. The Role of Linker Histones in Chromatin Structural Organization. 2. Interaction with DNA and Nuclear Proteins. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s0006350920020049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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2
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Lapinaite A, Carlomagno T, Gabel F. Small-Angle Neutron Scattering of RNA-Protein Complexes. Methods Mol Biol 2020; 2113:165-188. [PMID: 32006315 DOI: 10.1007/978-1-0716-0278-2_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Small-angle neutron scattering (SANS) provides structural information on biomacromolecules and their complexes in dilute solutions at the nanometer length scale. The overall dimensions, shapes, and interactions can be probed and compared to information obtained by complementary structural biology techniques such as crystallography, NMR, and EM. SANS, in combination with solvent H2O/D2O exchange and/or deuteration, is particularly well suited to probe the internal structure of RNA-protein (RNP) complexes since neutrons are more sensitive than X-rays to the difference in scattering length densities of proteins and RNA, with respect to an aqueous solvent. In this book chapter we provide a practical guide on how to carry out SANS experiments on RNP complexes, as well as possibilities of data analysis and interpretation.
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Affiliation(s)
- Audrone Lapinaite
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Teresa Carlomagno
- Centre for Biomolecular Drug Research, Leibniz University Hannover, Hannover, Germany.,Helmholtz Centre for Infection Research, Group of Structural Chemistry, Braunschweig, Germany
| | - Frank Gabel
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.
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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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Alfatama M, Lim LY, Wong TW. Alginate–C18 Conjugate Nanoparticles Loaded in Tripolyphosphate-Cross-Linked Chitosan–Oleic Acid Conjugate-Coated Calcium Alginate Beads as Oral Insulin Carrier. Mol Pharm 2018; 15:3369-3382. [DOI: 10.1021/acs.molpharmaceut.8b00391] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | - Lee Yong Lim
- Pharmacy, Centre for Optimisation of Medicines, School of Allied Health, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
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Wang D, Zhou Y, Li X, Qu X, Deng Y, Wang Z, He C, Zou Y, Jin Y, Liu Y. Mechanisms of pH-Sensitivity and Cellular Internalization of PEOz-b-PLA Micelles with Varied Hydrophilic/Hydrophobic Ratios and Intracellular Trafficking Routes and Fate of the Copolymer. ACS APPLIED MATERIALS & INTERFACES 2017; 9:6916-6930. [PMID: 28186394 DOI: 10.1021/acsami.6b16376] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
pH-responsive polymeric micelles have shown promise for the targeted and intracellular delivery of antitumor agents. The present study aimed to elucidate the possible mechanisms of pH-sensitivity and cellular internalization of PEOz-b-PLA micelles in detail, further unravel the effect of hydrophilic/hydrophobic ratio of the micelles on their cellular internalization, and examine the intracellular trafficking routes and fate of PEOz-b-PLA after internalization of the micelles. The results of variations in the size and Zeta potential of PEOz-b-PLA micelles and cross-sectional area of PEOz-b-PLA molecules with pH values suggested that electrostatic repulsion between PEOz chains resulting from ionization of the tertiary amide groups along PEOz chain at pH lower than its pKa was responsible for pH-sensitivity of PEOz-b-PLA micelles. Furthermore, the studies on internalization of PEOz-b-PLA micelles by MCF-7 cells revealed that the uptake of PEOz-b-PLA micelles was strongly influenced by their structural features, and showed that PEOz-b-PLA micelles with hydrophilic/hydrophobic ratio of 1.7-2.0 exhibited optimal cellular uptake. No evident alteration in cellular uptake of PEOz-b-PLA micelles was detected by flow cytometry upon the existence of EIPA and chlorpromazine. However, the intracellular uptake of the micelles in the presence of MβCD and genistein was effectively inhibited. Hence, the internalization of such micelles by MCF-7 cells appeared to proceed mainly through caveolae/lipid raft-mediated endocytosis without being influenced by their hydrophilic/hydrophobic ratio. Confocal micrographs revealed that late endosomes, mitochondria and endoplasmic reticulum were all involved in the intracellular trafficking of PEOz-b-PLA copolymers following their internalization via endocytosis, and then part of them was excreted from tumor cells to extracellular medium. These findings provided valuable information for developing desired PEOz-b-PLA micelles to improve their therapeutic efficacy and reducing the potential safety risks associated with their intracellular accumulation.
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Affiliation(s)
- Dishi Wang
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Yanxia Zhou
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Xinru Li
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Xiaoyou Qu
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Yunqiang Deng
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Ziqi Wang
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Chuyu He
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Yang Zou
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Yiguang Jin
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine , 27 Taiping Road, Beijing 100850, China
| | - Yan Liu
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
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Abstract
Histone H1 variants, known as linker histones, are essential chromatin components in higher eukaryotes, yet compared to the core histones relatively little is known about their in vivo functions. The filamentous fungus Neurospora crassa encodes a single H1 protein that is not essential for viability. To investigate the role of N. crassa H1, we constructed a functional FLAG-tagged H1 fusion protein and performed genomic and molecular analyses. Cell fractionation experiments showed that H1-3XFLAG is a chromatin binding protein. Chromatin-immunoprecipitation combined with sequencing (ChIP-seq) revealed that H1-3XFLAG is globally enriched throughout the genome with a subtle preference for promoters of expressed genes. In mammals, the stoichiometry of H1 impacts nucleosome repeat length. To determine if H1 impacts nucleosome occupancy or nucleosome positioning in N. crassa, we performed micrococcal nuclease digestion in the wild-type and the ΔhH1 strain followed by sequencing (MNase-seq). Deletion of hH1 did not significantly impact nucleosome positioning or nucleosome occupancy. Analysis of DNA methylation by whole-genome bisulfite sequencing (MethylC-seq) revealed a modest but global increase in DNA methylation in the ΔhH1 mutant. Together, these data suggest that H1 acts as a nonspecific chromatin binding protein that can limit accessibility of the DNA methylation machinery in N. crassa.
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Tokuda JM, Pabit SA, Pollack L. Protein-DNA and ion-DNA interactions revealed through contrast variation SAXS. Biophys Rev 2016; 8:139-149. [PMID: 27551324 PMCID: PMC4991782 DOI: 10.1007/s12551-016-0196-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/10/2016] [Indexed: 12/29/2022] Open
Abstract
Understanding how DNA carries out its biological roles requires knowledge of its interactions with biological partners. Since DNA is a polyanionic polymer, electrostatic interactions contribute significantly. These interactions are mediated by positively charged protein residues or charge compensating cations. Direct detection of these partners and/or their effect on DNA conformation poses challenges, especially for monitoring conformational dynamics in real time. Small-angle x-ray scattering (SAXS) is uniquely sensitive to both the conformation and local environment (i.e. protein partner and associated ions) of the DNA. The primary challenge of studying multi-component systems with SAXS lies in resolving how each component contributes to the measured scattering. Here, we review two contrast variation (CV) strategies that enable targeted studies of the structures of DNA or its associated partners. First, solution contrast variation enables measurement of DNA conformation within a protein-DNA complex by masking out the protein contribution to the scattering profile. We review a specific example, in which the real-time unwrapping of DNA from a nucleosome core particle is measured during salt-induced disassembly. The second method, heavy atom isomorphous replacement, reports the spatial distribution of the cation cloud around duplex DNA by exploiting changes in the scattering strength of cations with varying atomic numbers. We demonstrate the application of this approach to provide the spatial distribution of monovalent cations (Na+, K+, Rb+, Cs+) around a standard 25-base pair DNA. The CV strategies presented here are valuable tools for understanding DNA interactions with its biological partners.
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Affiliation(s)
- Joshua M. Tokuda
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 USA
| | - Suzette A. Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 USA
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8
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Gabel F. Small-Angle Neutron Scattering for Structural Biology of Protein–RNA Complexes. Methods Enzymol 2015; 558:391-415. [DOI: 10.1016/bs.mie.2015.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Sotelo P, Collazo N, Zuñiga R, Gutiérrez-González M, Catalán D, Ribeiro CH, Aguillón JC, Molina MC. An efficient method for variable region assembly in the construction of scFv phage display libraries using independent strand amplification. MAbs 2012; 4:542-50. [PMID: 22692130 DOI: 10.4161/mabs.20653] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Phage display library technology is a common method to produce human antibodies. In this technique, the immunoglobulin variable regions are displayed in a bacteriophage in a way that each filamentous virus displays the product of a single antibody gene on its surface. From the collection of different phages, it is possible to isolate the virus that recognizes specific targets. The most common form in which to display antibody variable regions in the phage is the single chain variable fragment format (scFv), which requires assembly of the heavy and light immunoglobulin variable regions in a single gene. In this work, we describe a simple and efficient method for the assembly of immunoglobulin heavy and light chain variable regions in a scFv format. This procedure involves a two-step reaction: (1) DNA amplification to produce the single strand form of the heavy or light chain gene required for the fusion; and (2) mixture of both single strand products followed by an assembly reaction to construct a complete scFv gene. Using this method, we produced 6-fold more scFv encoding DNA than the commonly used splicing by overlap extension PCR (SOE-PCR) approach. The scFv gene produced by this method also proved to be efficient in generating a diverse scFv phage display library. From this scFv library, we obtained phages that bound several non-related antigens, including recombinant proteins and rotavirus particles.
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Affiliation(s)
- Pablo Sotelo
- Centro de InmunoBioTecnología (IBT), Programa Disciplinario de Inmunología, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago, Chile
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10
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Su CJ, Chen CY, Lin MC, Chen HL, Iwase H, Koizumi S, Hashimoto T. Nucleosome-like Structure from Dendrimer-Induced DNA Compaction. Macromolecules 2012. [DOI: 10.1021/ma300308y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Chun-Jen Su
- National Synchrotron Radiation Research Center, Hsin-Chu 300, Taiwan
| | - Chun-Yu Chen
- National Synchrotron Radiation Research Center, Hsin-Chu 300, Taiwan
| | - Ming-Champ Lin
- Department of Chemical Engineering and Frontier
Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsin-Chu 30013, Taiwan
| | - Hsin-Lung Chen
- Department of Chemical Engineering and Frontier
Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsin-Chu 30013, Taiwan
| | - Hiroki Iwase
- Advanced Science Research Center, Japan Atomic Energy Agency, Naka-gun, Ibaraki Pref.
319-1195, Japan
| | - Satoshi Koizumi
- Advanced Science Research Center, Japan Atomic Energy Agency, Naka-gun, Ibaraki Pref.
319-1195, Japan
| | - Takeji Hashimoto
- Department of Chemical Engineering and Frontier
Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsin-Chu 30013, Taiwan
- Advanced Science Research Center, Japan Atomic Energy Agency, Naka-gun, Ibaraki Pref.
319-1195, Japan
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11
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Wu Z, Gogonea V, Lee X, May RP, Pipich V, Wagner MA, Undurti A, Tallant TC, Baleanu-Gogonea C, Charlton F, Ioffe A, DiDonato JA, Rye KA, Hazen SL. The low resolution structure of ApoA1 in spherical high density lipoprotein revealed by small angle neutron scattering. J Biol Chem 2011; 286:12495-508. [PMID: 21292766 DOI: 10.1074/jbc.m110.209130] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Spherical high density lipoprotein (sHDL), a key player in reverse cholesterol transport and the most abundant form of HDL, is associated with cardiovascular diseases. Small angle neutron scattering with contrast variation was used to determine the solution structure of protein and lipid components of reconstituted sHDL. Apolipoprotein A1, the major protein of sHDL, forms a hollow structure that cradles a central compact lipid core. Three apoA1 chains are arranged within the low resolution structure of the protein component as one of three possible global architectures: (i) a helical dimer with a hairpin (HdHp), (ii) three hairpins (3Hp), or (iii) an integrated trimer (iT) in which the three apoA1 monomers mutually associate over a portion of the sHDL surface. Cross-linking and mass spectrometry analyses help to discriminate among the three molecular models and are most consistent with the HdHp overall architecture of apoA1 within sHDL.
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Affiliation(s)
- Zhiping Wu
- Department of Cell Biology, Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
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12
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Peng SF, Su CJ, Wei MC, Chen CY, Liao ZX, Lee PW, Chen HL, Sung HW. Effects of the nanostructure of dendrimer/DNA complexes on their endocytosis and gene expression. Biomaterials 2010; 31:5660-70. [DOI: 10.1016/j.biomaterials.2010.03.059] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Accepted: 03/21/2010] [Indexed: 02/07/2023]
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13
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14
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Haapala OK, Nienstedt I. Chromosome ultrastructure in the basidiomycete fungus Schizophyllum commune. Hereditas 2009. [DOI: 10.1111/j.1601-5223.1976.tb01195.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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15
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Rønne M, Andersen O, Erlandsen M. Effect of colcemid exposure and methanol acetic acid fixation on human metaphase chromosome structure. Hereditas 2009; 90:195-201. [PMID: 437988 DOI: 10.1111/j.1601-5223.1979.tb01306.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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16
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Sorsa V. Beaded organization of chromatin in the salivary gland chromosome bands of Drosophila melanogaster. Hereditas 2009. [DOI: 10.1111/j.1601-5223.1977.tb01396.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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17
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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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18
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Popov EM. Current advances in the X-ray crystallography of proteins. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc1995v064n12abeh000194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Koehler JK, Würschmidt U, Larsen MP. Nuclear and chromatin structure in rat spermatozoa. ACTA ACUST UNITED AC 2005. [DOI: 10.1002/mrd.1120080406] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Payet D, Travers A. The acidic tail of the high mobility group protein HMG-D modulates the structural selectivity of DNA binding. J Mol Biol 1997; 266:66-75. [PMID: 9054971 DOI: 10.1006/jmbi.1996.0782] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
HMG-D is one of the Drosophila counterparts of the vertebrate HMG1/2 class of abundant chromosomal proteins and contains three domains: an HMG domain followed by a basic region and a short acidic carboxyterminal tail. We show that the HMG domain of HMG-D does not bind to deformed DNA structures such as DNA bulges, cis-platinated DNA or four-way junctions but does bind tightly to DNA microcircles, suggesting that in vivo the natural ligands of this domain are tightly bent DNA loops. The flanking basic region substantially increases the DNA-binding activity of the HMG domain to DNA ligands other than microcircles. We demonstrate that the acidic tail alters the structural selectivity of DNA binding by increasing the affinity for deformed DNA and decreasing the affinity for linear B-DNA. Finally, we show that the acidic tail increases the efficiency of constraining preformed negative supercoils but conversely decreases the efficiency of supercoiling relaxed DNA in the presence of topoisomerase I.
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Affiliation(s)
- D Payet
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK
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22
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Akiyama T, Hogan ME. Microscopic DNA flexibility analysis. Probing the base composition and ion dependence of minor groove compression with an artificial dna bending agent. J Biol Chem 1996; 271:29126-35. [PMID: 8910569 DOI: 10.1074/jbc.271.46.29126] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We have used an artificial DNA bending agent to monitor the local flexibility of the DNA helix as a function of Mg2+ cation concentration, sequence, and temperature. A DNA bending agent was constructed from a pair of triple helix-forming oligonucleotides connected by a flexible polymeric linker, which, when the linker is short enough, causes a bend in a minor groove region separating the two sites of triple helix formation. The unique aspect of this system is that, since the bent region is not in direct contact with the linker or the triple helix-forming oligonucleotides, the free energy reflecting the bendability of the minor helix groove can be estimated from a comparison of binding affinity between the bent and unbent triple helices. A binding competition experiment and association and dissociation kinetic assays executed at 37 degrees C in the presence of 10 mM Mg2+ have revealed an extremely small difference in binding affinity between bent (50 degrees ) and straight triple helices, suggesting that DNA flexibility with respect to minor groove compression is extremely high and virtually independent of the sequence of the distorted duplex. This unexpectedly small difference in binding affinity was detected over the temperature range from 25 to 65 degrees C, and over a Mg2+ concentration range from 0.3 to 10 mM. Thus, these findings provide evidence that DNA bendability for minor groove compression is inherently high and independent of DNA sequence, temperature, or a 30-fold variation of Mg2+ ion concentration.
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Affiliation(s)
- T Akiyama
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.
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23
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Abstract
Biological processes involved in the control and regulation of transcription are dependent on protein-induced distortions in DNA structure that enhance the recruitment of proteins to their specific DNA targets. This function is often accomplished by accessory factors that bind sequence specifically and locally bend or kink the DNA. The recent determination of the three-dimensional structures of several protein-DNA complexes, involving proteins that perform such architectural tasks, brings to light a common theme of side chain intercalation as a mechanism capable of driving the deformation of the DNA helix. The protein scaffolds orienting the intercalating side chain (or side chains) are structurally diverse, presently comprising four distinct topologies that can accomplish the same task. The intercalating side chain (or side chains), however, is exclusively hydrophobic. Intercalation can either kink or bend the DNA, unstacking one or more adjacent base pairs and locally unwinding the DNA over as much as a full turn of helix. Despite these distortions, the return to B-DNA helical parameters generally occurs within the adjacent half-turns of DNA.
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Affiliation(s)
- M H Werner
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
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Nagata Y, Kinoshita T, Takizawa A, Tsujita Y, Yoshimizu H. Interaction between anα-Helical Polypeptide Containing Side-Chain Pyridyl Groups and Poly(4-vinylpyridine) in the Ternary Cu2+Ion Complex. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1994. [DOI: 10.1246/bcsj.67.773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Pager J, Coulaud D, Delain E. Electron microscopy of the nucleocapsid from disrupted Moloney murine leukemia virus and of associated type VI collagen-like filaments. J Virol 1994; 68:223-32. [PMID: 8254732 PMCID: PMC236281 DOI: 10.1128/jvi.68.1.223-232.1994] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
To analyze the constituents of retroviruses, the Moloney murine leukemia virus was disrupted and observed by dark-field electron microscopy. Virus disruption was achieved by several methods: osmotic shock, freezing-thawing cycles, and exposure to urea up to 4 M, to NaCl up to 1 M, and to Triton X-100. Several components associated with broken Moloney murine leukemia virus were repeatedly found in preparations. These components have been described as rings, thick filaments, chain-like filaments, threads covered with proteins, threads with buckles, and naked threads. A quantitative analysis of the occurrence of these components has been carried out. Among them, the thick filaments composed of a compact helical arrangement of small beads 5 nm in diameter were considered to represent the nucleocapsid. The protease-sensitive buckles found on some threads could be a compact form of the viral RNA associated to the nucleocapsid protein NCp10. The RNase-sensitive naked threads are interpreted as the deproteinized viral RNA itself. The ubiquitous chain-like filaments possess a periodic structure identical to that of polymerized type VI collagen. It is proposed that this adhesive protein is associated with the viral envelope taken from the cell membrane during the budding process of retroviruses.
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Affiliation(s)
- J Pager
- Laboratoire de Microscopie Cellulaire et Moléculaire, URA 147 du Centre National de la Recherche Scientifique, Institut Gustave Roussy, Villejuif, France
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Arents G, Moudrianakis EN. Topography of the histone octamer surface: repeating structural motifs utilized in the docking of nucleosomal DNA. Proc Natl Acad Sci U S A 1993; 90:10489-93. [PMID: 8248135 PMCID: PMC47802 DOI: 10.1073/pnas.90.22.10489] [Citation(s) in RCA: 238] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The histone octamer core of the nucleosome is a protein superhelix of four spirally arrayed histone dimers. The cylindrical face of this superhelix is marked by intradimer and interdimer pseudodyad axes, which derive from the nature of the histone fold. The histone fold appears as the result of a tandem, parallel duplication of the "helix-strand-helix" motif. This motif, by its occurrence in the four dimers, gives rise to repetitive structural elements--i.e., the "parallel beta bridges" and the "paired ends of helix I" motifs. A preponderance of positive charges on the surface of the octamer appears as a left-handed spiral situated at the expected path of the DNA. We have matched a subset of DNA pseudodyads with the octamer pseudodyads and thus have built a model of the nucleosome. In it, the two DNA strands coincide with the path of the histone-positive charges, and the central 12 turns of the double helix contact the surface of the octamer at the repetitive structural motifs. The properties of these complementary contacts appear to explain the preference of histones for double-helical DNA and to suggest a possible basis for allosteric regulation of nucleosome function.
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Affiliation(s)
- G Arents
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
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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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Choli T, Henning P, Wittmann-Liebold B, Reinhardt R. Isolation, characterization and microsequence analysis of a small basic methylated DNA-binding protein from the Archaebacterium, Sulfolobus solfataricus. BIOCHIMICA ET BIOPHYSICA ACTA 1988; 950:193-203. [PMID: 3132977 DOI: 10.1016/0167-4781(88)90011-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
DNA-binding proteins have been extracted from the thermoacidophilic archaebacterium Sulfolobus solfataricus strain P1, grown at 86 degrees C and pH 4.5. These proteins, which may have a histone-like function, were isolated and purified under standard, non-denaturing conditions, and can be grouped into three molecular mass classes of 7, 8 and 10 kDa. We have purified to homogenity the main 7 kDa protein and determined its DNA-binding affinity by filter binding assays and electron microscopy. The Stokes radius of gyration indicates that the protein occurs as a monomer. The complete amino-acid sequence of this protein contains 14 lysine residues out of 63 amino acids and the calculated Mr is 7149. Five of the lysine residues are partially monomethylated to varying extents and the methylated residues are located exclusively in the N-terminal (positions 4 and 6) and the C-terminal (positions 60, 62 and 63) regions only. The protein is strongly homologous to the 7 kDa proteins of Sulfolobus acidocaldarius with the highest homology to protein 7d. Accordingly, the name of this protein from S. solfataricus was assigned as DNA-binding protein Sso7d.
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Affiliation(s)
- T Choli
- Abteilung Wittmann, Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
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Bradbury EM, Baldwin JP. Neutron scatter and diffraction techniques applied to nucleosome and chromatin structure. CELL BIOPHYSICS 1986; 9:35-66. [PMID: 2436800 DOI: 10.1007/bf02797374] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Neutron scatter and diffraction techniques have made substantial contributions to our understanding of the structure of the nucleosome, the structure of the 10-nm filament, the "10-nm----30-nm" filament transition, and the structure of the "34-nm" supercoil or solenoid of nucleosomes. Neutron techniques are unique in their properties, which allows for the separation of the spatial arrangements of histones and DNA in nucleosomes and chromatin. They have equally powerful applications in structural studies of any complex two-component biological system. A major success for the application of neutron techniques was the first clear proof that DNA was located on the outside of the histone octamer in the core particle. A full analysis of the neutron-scatter data gave the parameters of Table 3 and the low-resolution structure of the core particle in solution shown in Fig. 6. Initial low-resolution X-ray diffraction studies of core particle crystals gave a model with a lower DNA pitch of 2.7 nm. Higher-resolution X-ray diffraction studies now give a structure with a DNA pitch of 3.0 nm and a hole of 0.8 nm along the axis of the DNA supercoil. The neutron-scatter solution structure and the X-ray crystal structure of the core particle are thus in full agreement within the resolution of the neutron-scatter techniques. The model for the chromatosome is largely based on the structural parameters of the DNA supercoil in the core particle, nuclease digestion results showing protection of a 168-bp DNA length by histone H1 and H1 peptide, and the conformational properties of H1. The path of the DNA outside the chromatosome is not known, and this information is crucial for our understanding of higher chromatin structure. The interactions of the flexible basic and N- and C-terminal regions of H1 within chromatin and how these interactions are modulated by H1 phosphorylation are not known. The N- and C-terminal regions of H1 represent a new type of protein behavior, i.e., extensive protein domains that are designed not to fold up into secondary and tertiary protein structures. This behavior is increasingly observed in DNA and chromatin binding proteins, and in the case of the high-mobility group proteins HMG 14 and 17, the entire polypeptide chain is a flexible random coil over a wide range of solution, ionic, and pH conditions. It follows that the native conformations are probably imposed on these flexible domains and molecules by their binding sites in chromatin.(ABSTRACT TRUNCATED AT 400 WORDS)
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Shimidzu M, Shindo H, Matsumoto U, Mita K, Zama M. Distinction and similarity in the structure of histones H1 and H5 as indicated by 13C nuclear-magnetic-resonance spectroscopy. EUROPEAN JOURNAL OF BIOCHEMISTRY 1985; 148:431-6. [PMID: 2986962 DOI: 10.1111/j.1432-1033.1985.tb08857.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The 13C nuclear magnetic resonance studies have been carried out on histones H1 and H5, by focusing our interest on possible formation of specific salt bridges between acidic and basic amino acid residues in the proteins and also on the structural difference between the two proteins. The 13C chemical shift and pKa values of the carboxyl group of glutamic acid residues in the histones coincided with those of free glutamic acid. Based on this result and another experiment using completely modified lysine residues in the histones, no evidence for a specific interaction between acidic and basic residues has been found. It has also been shown that the pH-effects of aliphatic and aromatic resonances are quite different between H1 and H5, suggesting that the globular domain of H5 is more stable than that of H1. The correlation time (1.5 ns) for the alpha-carbons of H5 estimated from 13C nuclear Overhauser enhancement was twice as long as that of H1 (0.9 ns), indicating that the backbone in the N-terminal and C-terminal domains of H5 is less mobile than that of H1.
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32
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Aboukarsh N, Kunkle M. Ultrastructural organization of heterochromatin within sea urchin sperm nuclei. ACTA ACUST UNITED AC 1985. [DOI: 10.1002/mrd.1120120107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Kurokawa M, MacLeod MC. Separation of histones by reverse-phase high-performance liquid chromatography: analysis of the binding of carcinogens to histones. Anal Biochem 1985; 144:47-54. [PMID: 3920929 DOI: 10.1016/0003-2697(85)90082-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Reverse-phase high-performance liquid chromatography (RP-HPLC) has been examined as an approach to the rapid analysis of carcinogen-modified histones. H1 and core histone fractions were prepared by differential acid extraction of 0.35 M NaCl-extracted rat liver nuclei previously exposed to [3H]-7r,8t-dihydroxy-9t, 10t-oxy-7,8,9, 10-tetrahydrobenzo(a)pyrene [( 3H]BPDE-I). Using a sodium perchlorate-phosphate (PCP)/acetonitrile solvent system, the H1 histone fraction was eluted from an Aquapore RP-300 column in five peaks (P1-P5). The core histone fraction was resolved into eight peaks (C1-C8) using a PCP/acetonitrile-methanol solvent system. The histones of each peak were identified by sodium dodecyl sulfate and Triton/acid/urea gel electrophoresis or amino acid analysis as follows: P1, H1 degrees; P2-P5, four different H1 variant fractions; C1, H4 + A24; C2, H2B; C3, H2A X 2 + to one H2A variant; C4, H2A.1; C5, H2A.1 + two H2A variants; C6, H3.2; C7, H3.3; C8, H3.1. The bulk of radioactivity was covalently bound to histone H2A, which had higher specific activities of BPDE-I than other histones. Significant amounts of radioactivity were observed in histones H3 and H1, but not in histones H2B and H4. These RP-HPLC systems have the advantages of an analysis time within 60 min, the identification of H1, H2A, and H3 variants, and the quantitative analysis of radioactive histones. These results indicate that these RP-HPLC systems are very useful to analyze the binding of carcinogens to histones.
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Langmore JP, Paulson JR. Low angle x-ray diffraction studies of chromatin structure in vivo and in isolated nuclei and metaphase chromosomes. J Biophys Biochem Cytol 1983; 96:1120-31. [PMID: 6682117 PMCID: PMC2112310 DOI: 10.1083/jcb.96.4.1120] [Citation(s) in RCA: 102] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Diffraction of x-rays from living cells, isolated nuclei, and metaphase chromosomes gives rise to several major low angle reflections characteristic of a highly conserved pattern of nucleosome packing within the chromatin fibers. We answer three questions about the x-ray data: Which reflections are characteristic of chromosomes in vivo? How can these reflections be preserved in vitro? What chromosome structures give rise to the reflections? Our consistent observation of diffraction peaks at 11.0, 6.0, 3.8, 2.7 and 2.1 nm from a variety of living cells, isolated nuclei, and metaphase chromosomes establishes these periodicities as characteristic of eukaryotic chromosomes in vivo. In addition, a 30-40- nm peak is observed from all somatic cells that have substantial amounts of condensed chromatin, and a weak 18-nm reflection is observed from nucleated erythrocytes. These observations provide a standard for judging the structural integrity of isolated nuclei, chromosomes, and chromatin, and thus resolve long standing controversy about the "tru" nature of chromosome diffraction. All of the reflection seen in vivo can be preserved in vitro provided that the proper ionic conditions are maintained. Our results show clearly that the 30-40-nm maximum is a packing reflection. The packing we observe in vivo is directly correlated to the side-by-side arrangement of 20- 30-nm fibers observed in thin sections of fixed and dehydrated cells and isolated chromosomes. This confirms that such packing is present in living cells and is not merely an artifact of electron microscopy. As expected, the packing reflection is shifted to longer spacings when the fibers are spread apart by reducing the concentration of divalent cations in vitro. Because the 18-, 11.0-, 6.0-, 3.8-, 2.7-, and 2.1-nm reflections are not affected by the decondensation caused by removal of divalent cations, these periodicities must reflect the internal structure of the chromaticn fibers.
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Yau P, Thorne AW, Imai BS, Matthews HR, Bradbury EM. Thermal denaturation studies of acetylated nucleosomes and oligonucleosomes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1982; 129:281-8. [PMID: 7151800 DOI: 10.1111/j.1432-1033.1982.tb07050.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The thermal melting behaviors of control and acetylated mononucleosomes, dinucleosomes and trinucleosomes have been studied. Along each series of oligonucleosomes, the melting profiles change in a manner consistent with the increasing number of nucleosomes. For the control mononucleosome, the melting profile exhibits a premelting region at about 61-64 degrees C and a major cooperative transition at 75-77 degrees C. The melting profiles of the control dinucleosomes and trinucleosomes show a premelt at 61-62 degrees C (similar to that of the nucleosome core); an intermediate transition at 73-74 degrees C for the dinucleosome and at 76-77 degrees C for the trinucleosome and a major cooperative transition at 79-80 degrees C for the dinucleosome and at 81-82 degrees C for the trinucleosome. The major cooperative transition at the highest melting temperatures in the melting profiles of the mononucleosome, dinucleosome and trinucleosome comes from the melting of the central region of DNA in the nucleosome which complexed with the core histones; the premelt region is attributed to two DNA segments per nucleosome which flank this central DNA region and are free or weakly complexed with histones. The origin of the intermediate transition found for the dinucleosomes and trinucleosomes is not fully understood but probably results from the melting of DNA at the entry to and exit from the nucleosome and the linker DNA which are complexed with histones. A very similar pattern of behavior is observed for the acetylated oligonucleosomes. Direct comparison of the melting profiles of acetylated and control mononucleosomes, dinucleosomes and trinucleosomes show that the premelt region is unaffected by histone acetylation whereas the intermediate and major cooperative transitions for the acetylated oligonucleosomes are broader and occur consistently at lower temperatures than for the controls. These differences support proposals that the N-terminal regions of core histones interact within the nucleosome and on linker DNA.
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In vitro mercaptoacetylation of chromosomal proteins. Selective recovery of newly modified protein molecules. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)33528-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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38
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Duerre JA, Quick DP, Traynor MD, Onisk DV. Effect of polyamines and cations on the in vitro methylation of histones. BIOCHIMICA ET BIOPHYSICA ACTA 1982; 719:18-23. [PMID: 7171622 DOI: 10.1016/0304-4165(82)90301-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Na+ (0.05-0.15 M) increases both the rate and extent of methylation of chromosomal bound histone H4, while spermidine markedly inhibits this reaction. The effects of spermidine could be mimicked by increasing the concentration of Mg2+ or Ca2+ to 5-10 mM. At the concentrations listed above, these cations have no significant effect on the methylation of free or chromosomal bound histone H3, nor do they affect the rate r extent of methylation of soluble histone H4. Apparently, the accessibility of histone H4 to the methyltransferase is influenced by chromatin structure. Increasing concentrations of Na+ alter the conformation of chromatin (DNA) in such a way as to expose lysing residues in the N-terminal region of histone H4 to the methyltransferase, whereas Mg2+ or spermidine acts in an opposite manner.
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39
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Moore FD, Sastry KS. Intracellular potassium: 40K as a primordial gene irradiator. Proc Natl Acad Sci U S A 1982; 79:3556-9. [PMID: 6954503 PMCID: PMC346460 DOI: 10.1073/pnas.79.11.3556] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We have been interested in the possibility that the low energy electrons (Auger and Coster-Kronig) emitted after the electron capture decay of 40K may have highly localized radiochemical effects on the genetic material--effects dependent upon the intracellular locus of potassium. We report here that these effects are such that the likelihood of mutagenesis by their impact on DNA is substantial. This suggests that intracellular 40K has played a significant role as a mutagenic agent in evolution.
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Kurokawa M, Hibino Y, Sugano N. Associations of benzo[a]pyrene with rat-liver chromatin and the chromatin protein. Chem Biol Interact 1982; 39:17-30. [PMID: 6277523 DOI: 10.1016/0009-2797(82)90003-5] [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: 01/19/2023]
Abstract
Rat-liver nuclei were prepared in the course of time after the i.p. injection of [G-3H]benzo[a]pyrene ([3H]BP). The nuclei were lysed in the hypotonic buffer and centrifuged at 4000 X g. The recovery of the radioactivity of resulting supernatant (chromatin) was thus 91% at 24 h, 68% at 48 h and 74% at 168 h after the i.p. injection. The incorporation into nucleosome-oligomer fraction was always much more than into those of monomer and DNA-rich fractions. The preferential incorporation was found in the fraction which was enriched in non-histone chromatin proteins (NHCPs) of 49 000-55 000 daltons. This fraction steadily raised the incorporation level until at 168 h after the i.p. injection. In contrast, the levels of histone and DNA fractions were always very low. The significant incorporation was observed in the fraction which was composed of five classes of histones and low molecular-weight NHCPs (less than 30 000 daltons), despite the very low incorporation into the histone fraction. The fluorographic analysis revealed the predominant incorporations at the positions of molecular weight of 65 000, 52 000 and 44 000 daltons. In addition, the incorporations were clearly observed at the positions of 59 000, 49 000, 45 000, H1 histone, A24 protein and another one. On the other hand, these fractions were, at the final preparation steps, subjected to either dialysis of SDS-phenol treatment and/or acetone precipitation. The total recovery of radioactivity was thus 21% at 24 h, 32% at 48 h and 52% at 168 h after the i.p. injection. These results suggest that the chromatin contains considerable amounts of water-soluble, phenol and/or acetone-soluble BP-conjugates in the early period after the i.p. injection.
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Chinsky L, Turpin PY. Poly(dA-dT) complexes with histone H1 and pancreatic ribonuclease: specific base recognition evidenced by ultraviolet resonance raman spectroscopy. Biopolymers 1982; 21:277-86. [PMID: 7059655 DOI: 10.1002/bip.360210204] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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42
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A comparison of the amino acid sequences of histones h1 from the sperm of Echinolampas crassa and Parechinus angulosus. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/0167-4838(82)90300-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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43
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Moore PB. 8. Small-Angle Scattering Techniques for the Study of Biological Macromolecules and Macromolecular Aggregates. METHODS IN EXPERIMENTAL PHYSICS 1982. [DOI: 10.1016/s0076-695x(08)60157-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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44
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Lawrence JJ, Goeltz P. Involvement of histone H1 in the structure of the linker DNA in nucleosomes as revealed by nucleases. Mol Biol Rep 1981; 8:45-9. [PMID: 6276719 DOI: 10.1007/bf00798384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
This report describes experiments designed to study the organization of the linker DNA in nucleosomes. When rat liver nucleosomes (145 to 188 base pairs in length) were digested by Exonuclease III and then by nuclease S1 a series of bands on sizes 90 - 102 - 112 - 125 - 135 - 142 - 154 - 166 - 172 - 181 - bases was observed in denaturing electrophoretic gels. Digestion of H1-depleted nucleosomes under the same conditions results in a series of products of sizes (10.4) xn in base (n less than or equal to 14) only. This result is interpreted as reflecting a particular arrangement of linker DNA under the influence of histone H1.
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Hagiwara H, Miyazaki K, Matuo Y, Yamashita J, Horio T. Purification and characterization of alkaline protease and neutral protease from chromatin of rats. BIOCHIMICA ET BIOPHYSICA ACTA 1981; 660:73-82. [PMID: 7023544 DOI: 10.1016/0005-2744(81)90110-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
It was previously reported that, in addition to a known chymotrypsin-like protease capable of hydrolyzing histones with an optimum pH of 8 (neutral protease), another protease is bound to the chromatin of various rat tissues and in situ hydrolyzes casein more quickly than histones with an optimum pH of 10 (alkaline protease). In the present study, the alkaline protease was purified 14 000-fold to approx. 75% purity from the chromatin of Rhodamine sarcoma. This tumor contains both proteases at higher levels than normal tissues. For purification, affinity columns of Sepharose with bound soybean trypsin inhibitor, casein and histones were successively used. Also, the neutral protease was purified 920-fold to an apparently homogeneous state by affinity chromatography on a Sepharose column with bound soybean trypsin inhibitor under conditions, in which an excess amount of the enzyme was applied on the column so that part of the enzyme would pass through the column without adsorption and the enzyme thus adsorbed was then eluted. The purified alkaline and neutral proteases had molecular weights of approx. 18 000 and 27 000, respectively, and isoelectric points of approx. 11. The former enzyme hydrolyzed casein (100) in preference to histones (18) with an optimum pH of 9.5, whereas the latter enzyme preferred histones (100) to casein (32) with an optimum pH of 8. Their actions against other proteins and synthetic substrates were also studied.
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46
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Moyne G, Freeman R, Saragosti S, Yaniv M. A high-resolution electron microscopy study of nucleosomes from simian virus 40 chromatin. J Mol Biol 1981; 149:735-44. [PMID: 6273589 DOI: 10.1016/0022-2836(81)90355-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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47
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Braddock GW, Baldwin JP, Bradbury EM. Neutron-scattering studies of the structure of chromatin core particles in solution. Biopolymers 1981; 20:327-343. [PMID: 7459423 DOI: 10.1002/bip.1981.360200206] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Gordon W Braddock
- Biophysics Laboratory, School of Biological Sciences, Portsmouth Polytechnic, Portsmouth, United Kingdom
| | - John P Baldwin
- Biophysics Laboratory, School of Biological Sciences, Portsmouth Polytechnic, Portsmouth, United Kingdom
| | - E Morton Bradbury
- Department of Biological Chemistry, School of Medicine, University of California, Davis, California 95616
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Zegarelli-Schmidt EC, Goodman R. The diptera as a model system in cell and molecular biology. INTERNATIONAL REVIEW OF CYTOLOGY 1981; 71:245-363. [PMID: 7016803 DOI: 10.1016/s0074-7696(08)61184-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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