Cryo-electron microscopy of chromosome fibers is consistent with the crossed-linker model for chromatin structure

1987 ◽  
Vol 45 ◽  
pp. 648-649
Author(s):  
B. Athey ◽  
J. Langmore ◽  
S. Williams ◽  
M. Smith ◽  
C.F. Chang ◽  
...  
Keyword(s):  
Chromatin Structure ◽  
Double Helix ◽  
Histone Octamer ◽  
Left Handed ◽  
Variable Diameter ◽  
Cryo Electron Microscopy ◽  
Constant Diameter ◽  
Constant Pitch ◽  
Conserved Core ◽  
Helical Parameters

Although there is general agreement that inactive chromosome fibers consist of helically packed nucleosomes, the pattern of packing is still disputed. The nucleosome itself is composed of a highly conserved “core” comprised of 146bp of DNA and a histone octamer, and a variable “linker” comprised of 20-100bp of DNA bound to histone H1. The models of chromatin structure can be distinguished by their dependence upon linker length. The solenoid model for chromatin structure is a single helix with constant pitch (11 nm) and constant diameter (25-30nm). The twisted-ribbon model is a double helix with variable pitch (26-40nm) and constant diameter (30nm). The crossed-linker model is a double helix with conserved pitch (26-28nm) and variable diameter (26-40nm). Measurements of the diameter and apparent helical parameters of negatively-stained chromatin from Thyone sperm (87bp linker) and Necturus erythrocytes (48bp linker) are in agreement with a left-handed crossed-linker model, and in disagreement with the solenoid and twisted-ribbon models.

scholarly journals A Left-Handed RNA Double Helix Bound by the Zα Domain of the RNA-Editing Enzyme ADAR1

Structure ◽  
2007 ◽  
Vol 15 (4) ◽  
pp. 395-404 ◽  
Author(s):  
Diana Placido ◽  
Bernard A. Brown ◽  
Ky Lowenhaupt ◽  
Alexander Rich ◽  
Alekos Athanasiadis
Keyword(s):  
Rna Editing ◽  
Double Helix ◽  
Left Handed ◽  
Editing Enzyme

scholarly journals The molecular structure of the left-handed Z-DNA double helix at 1.0-Å atomic resolution

1989 ◽  
Vol 264 (14) ◽  
pp. 7921-7935
Author(s):  
R V Gessner ◽  
C A Frederick ◽  
G J Quigley ◽  
A Rich ◽  
A H J Wang
Keyword(s):  
Molecular Structure ◽  
Double Helix ◽  
Atomic Resolution ◽  
Left Handed ◽  
Z Dna ◽  
Dna Double Helix

Z-RNA: A Left-Handed Double Helix

1986 ◽  
pp. 55-68 ◽  
Author(s):  
Ignacio Tinoco ◽  
Phillip Cruz ◽  
Peter Davis ◽  
Kathleen Hall ◽  
Charles C. Hardin ◽  
...  
Keyword(s):  
Double Helix ◽  
Left Handed

scholarly journals The tetramer d(CpGpCpG) crystallizes as a left-handed double helix.

1980 ◽  
Vol 77 (7) ◽  
pp. 4016-4020 ◽  
Author(s):  
J. L. Crawford ◽  
F. J. Kolpak ◽  
A. H. Wang ◽  
G. J. Quigley ◽  
J. H. van Boom ◽  
...  
Keyword(s):  
Double Helix ◽  
Left Handed

Structures of major pilins in Clostridium perfringens demonstrate dynamic conformational change

2019 ◽  
Vol 75 (8) ◽  
pp. 718-732 ◽  
Author(s):  
Eiji Tamai ◽  
Seiichi Katayama ◽  
Hiroshi Sekiya ◽  
Hirofumi Nariya ◽  
Shigehiro Kamitori
Keyword(s):  
Conformational Change ◽  
Clostridium Perfringens ◽  
Bacterial Cell ◽  
Double Helix ◽  
Gram Positive Bacteria ◽  
Left Handed ◽  
Initial Adhesion ◽  
Practical Model ◽  
Host Tissues

Pili in Gram-positive bacteria are flexible rod proteins associated with the bacterial cell surface, and they play important roles in the initial adhesion to host tissues and colonization. The pilus shaft is formed by the covalent polymerization of major pilins, catalyzed by sortases, a family of cysteine transpeptidases. Here, X-ray structures of the major pilins from Clostridium perfringens strains 13 and SM101 and of sortase from strain SM101 are presented with biochemical analysis to detect the formation of pili in vivo. The major pilin from strain 13 adopts an elongated structure to form noncovalently linked polymeric chains in the crystal, yielding a practical model of the pilus fiber structure. The major pilin from strain SM101 adopts a novel bent structure and associates to form a left-handed twist like an antiparallel double helix in the crystal, which is likely to promote bacterial cell–cell interactions. A modeling study showed that pilin with a bent structure interacts favorably with sortase. The major pilin from strain SM101 was considered to be in an equilibrium state between an elongated and a bent structure through dynamic conformational change, which may be involved in pili-mediated colonization and sortase-mediated polymerization of pili.

scholarly journals The Effect of Calcium and Halide Ions on the Gramicidin A Molecular State and Antimicrobial Activity

2020 ◽  
Vol 21 (17) ◽  
pp. 6177
Author(s):  
Kathleen D. Carillo ◽  
Chi-Jen Lo ◽  
Der-Lii M. Tzou ◽  
Yi-Hung Lin ◽  
Shang-Ting Fang ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Calcium Salt ◽  
Double Helix ◽  
Single Species ◽  
Molecular State ◽  
Vital Role ◽  
Gramicidin A ◽  
Halide Anion ◽  
Left Handed ◽  
State 1

Gramicidin A (gA) forms several convertible conformations in different environments. In this study, we investigated the effect of calcium halides on the molecular state and antimicrobial activity of gramicidin A. The molecular state of gramicidin A is highly affected by the concentration of calcium salt and the type of halide anion. Gramicidin A can exist in two states that can be characterized by circular dichroism (CD), mass, nuclear magnetic resonance (NMR) and fluorescence spectroscopy. In State 1, the main molecular state of gramicidin A is as a dimer, and the addition of calcium salt can convert a mixture of four species into a single species, which is possibly a left-handed parallel double helix. In State 2, the addition of calcium halides drives gramicidin A dissociation and denaturation from a structured dimer into a rapid equilibrium of structured/unstructured monomer. We found that the abilities of dissociation and denaturation were highly dependent on the type of halide anion. The dissociation ability of calcium halides may play a vital role in the antimicrobial activity, as the structured monomeric form had the highest antimicrobial activity. Herein, our study demonstrated that the molecular state was correlated with the antimicrobial activity.

scholarly journals A critical analysis of a left-handed double helix model for B-DNA fibers

1982 ◽  
Vol 10 (13) ◽  
pp. 4027-4034 ◽  
Author(s):  
G. Albiser ◽  
S. Premilat
Keyword(s):  
Critical Analysis ◽  
Double Helix ◽  
Left Handed

Protein hyperacylation links mitochondrial dysfunction with nuclear organization

2020 ◽  
Author(s):  
John Smestad ◽  
Micah McCauley ◽  
Matthew Amato ◽  
Yuning Xiong ◽  
Juan Liu ◽  
...  
Keyword(s):  
Chromatin Structure ◽  
Metabolic Regulation ◽  
Tca Cycle ◽  
Interphase Chromatin ◽  
Histone Octamer ◽  
The Tca Cycle ◽  
Transport Chain ◽  
Topologically Associated Domains ◽  
Biophysical Effects ◽  
Liquid Liquid Phase Separation

SummaryCellular metabolism is linked to epigenetics, but the biophysical effects of metabolism on chromatin structure and implications for gene regulation remain largely unknown. Here, using a broken tricarboxylic acid (TCA) cycle and disrupted electron transport chain (ETC) exemplified by succinate dehydrogenase subunit C (SDHC) deficiency, we investigated the effects of metabolism on chromatin architecture over multiple distance scales [nucleosomes (∼102 bp), topologically-associated domains (TADs; ∼105 – 106 bp), and chromatin compartments (106 – 108 bp)]. Metabolically-driven hyperacylation of histones led to weakened nucleosome positioning in multiple types of chromatin, and we further demonstrate that lysine acylation directly destabilizes histone octamer-DNA interactions. Hyperacylation of cohesin subunits correlated with decreased mobility on interphase chromatin and increased TAD boundary strength, suggesting that cohesin is metabolically regulated. Erosion of chromatin compartment distinctions reveals metabolic regulation of chromatin liquid-liquid phase separation. The TCA cycle and ETC thus modulate chromatin structure over multiple distance scales.

Synthesis of Concave Helical Compression Springs

2015 ◽  
Author(s):  
Naresh Kumar Gandham ◽  
Hong Zhou
Keyword(s):  
Cylindrical Shape ◽  
Control Parameters ◽  
Spline Curve ◽  
Variable Diameter ◽  
Compression Spring ◽  
Spring Wire ◽  
Coil Diameter ◽  
Constant Pitch ◽  
The Common ◽  
Compression Springs

Helical compression springs are used to resist compressive forces or store energy in push mode. They are found in many applications that include automotive, aerospace and medical devices. The common configuration of helical compression springs is straight cylindrical shape that has constant coil diameter, constant pitch and constant spring rate. Unlike cylindrical helical compression springs, concave helical compression springs have a larger diameter at each end and a smaller diameter in the middle of the spring. The variable coil diameter enables them to produce desired load deflection characteristics, reduce solid height, buckling and surging, and keep them centered on a larger diameter hole. The unique features of concave helical compression springs also raise their synthesis challenges. In this paper, a method is introduced to synthesize concave helical compression springs. The variable coil diameter of a concave helical compression spring is described by a spline curve. A cylinder with variable diameter is generated by revolving the spline curve on spring axis. The concave helical compression spring is then modeled by wrapping a spring wire on the variable diameter cylinder. The synthesis of a concave helical compression spring is systemized as the optimization of the geometric control parameters of its wrapped spring wire. A synthesis example is presented in the paper to verify the effectiveness and demonstrate the procedure of the introduced method.

scholarly journals The tetraribonucleotiderCpGpCpG forms a left-handed Z-RNA double-helix

1986 ◽  
Vol 14 (3) ◽  
pp. 1279-1291 ◽  
Author(s):  
Peter W. Davis ◽  
Kathleen Hall ◽  
Phillip Cruz ◽  
Ignacio Tinoco ◽  
Thomas Neilson
Keyword(s):  
Double Helix ◽  
Left Handed
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