scholarly journals The effect of linker DNA on the structure and interaction of nucleosome core particles

Soft Matter ◽  
2018 ◽  
Vol 14 (45) ◽  
pp. 9096-9106 ◽  
Author(s):  
Yen-Chih Huang ◽  
Chun-Jen Su ◽  
Nikolay Korolev ◽  
Nikolay V. Berezhnoy ◽  
Sai Wang ◽  
...  
Keyword(s):  
Small Angle ◽  
Core Particle ◽  
Nucleosome Core Particle ◽  
X Ray ◽  
Nucleosome Core ◽  
Nucleosome Core Particles ◽  
X Ray Scattering ◽  
Nucleosomal Dna ◽  
The Impact

Small angle X-ray scattering reveals linker DNA-induced partial unwrapping of nucleosomal DNA on the nucleosome core particle (NCP) and the impact on NCP interaction demonstrating the crucial role of linker DNA.

Helical repeat of DNA in the nucleosome core particle

2000 ◽  
Vol 28 (4) ◽  
pp. 373-376 ◽  
Author(s):  
R. Negri ◽  
M. Buttinelli ◽  
G. Panetta ◽  
V. De Arcangelis ◽  
E. Di Mauro ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Linker Histone ◽  
Core Particle ◽  
Nucleosome Core Particle ◽  
Apparent Paradox ◽  
Nucleosome Core ◽  
Nucleosome Core Particles ◽  
High Affinity Site ◽  
Hydroxyl Radical Cleavage ◽  
Radical Cleavage

Although the crystal structure of nucleosome core particle is essentially symmetrical in the vicinity of the dyad, the linker histone binds asymmetrically in this region to select a single high-affinity site from potentially two equivalent sites. To try to resolve this apparent paradox we mapped to base-pair resolution the dyads and rotational settings of nucleosome core particles reassembled on synthetic tandemly repeating 20 bp DNA sequences. In agreement with previous observations, we observed (1) that the helical repeat on each side of the dyad cluster is 10 bp maintaining register with the sequence repeat and (2) that this register changes by 2 bp in the vicinity of the dyad. The additional 2 bp required to effect the change in the rotational settings is accommodated by an adjustment immediately adjacent to the dyad. At the dyad the hydroxyl radical cleavage is asymmetric and we suggest that the inferred structural asymmetry could direct the binding of the linker histone to a single preferred site.

scholarly journals The Role of Intersubunit Interactions for the Stabilization of the T State ofEscherichia coliAspartate Transcarbamoylase

2002 ◽  
Vol 277 (51) ◽  
pp. 49755-49760 ◽  
Author(s):  
Robin S. Chan ◽  
Jessica B. Sakash ◽  
Christine P. Macol ◽  
Jay M. West ◽  
Hiro Tsuruta ◽  
...  
Keyword(s):  
Small Angle ◽  
Structural State ◽  
Aspartate Transcarbamoylase ◽  
Wild Type ◽  
X Ray ◽  
X Ray Scattering ◽  
Intersubunit Interactions ◽  
T State ◽  
Ray Scattering

Homotropic cooperativity inEscherichia coliaspartate transcarbamoylase results from the substrate-induced transition from the T to the R state. These two alternate states are stabilized by a series of interdomain and intersubunit interactions. The salt link between Lys-143 of the regulatory chain and Asp-236 of the catalytic chain is only observed in the T state. When Asp-236 is replaced by alanine the resulting enzyme exhibits full activity, enhanced affinity for aspartate, no cooperativity, and no heterotropic interactions. These characteristics are consistent with an enzyme locked in the functional R state. Using small angle x-ray scattering, the structural consequences of the D236A mutant were characterized. The unliganded D236A holoenzyme appears to be in a new structural state that is neither T, R, nor a mixture of T and R states. The structure of the native D236A holoenzyme is similar to that previously reported for another mutant holoenzyme (E239Q) that also lacks intersubunit interactions. A hybrid version of aspartate transcarbamoylase in which one catalytic subunit was wild-type and the other had the D236A mutation was also investigated. The hybrid holoenzyme, with three of the six possible interactions involving Asp-236, exhibited homotropic cooperativity, and heterotropic interactions consistent with an enzyme with both T and R functional states. Small angle x-ray scattering analysis of the unligated hybrid indicated that the enzyme was in a new structural state more similar to the T than to the R state of the wild-type enzyme. These data suggest that three of the six intersubunit interactions involving D236A are sufficient to stabilize a T-like state of the enzyme and allow for an allosteric transition.

Small-Angle X-Ray Scattering for the Discerning Macromolecular Crystallographer

2014 ◽  
Vol 67 (12) ◽  
pp. 1786 ◽  
Author(s):  
Lachlan W. Casey ◽  
Alan E. Mark ◽  
Bostjan Kobe
Keyword(s):  
Structural Biology ◽  
Small Angle ◽  
Significant Risk ◽  
Macromolecular Crystallography ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

The role of small-angle X-ray scattering (SAXS) in structural biology is now well established, and its usefulness in combination with macromolecular crystallography is clear. However, the highly averaged SAXS data present a significant risk of over-interpretation to the unwary practitioner, and it can be challenging to frame SAXS results in a manner that maximises the reliability of the conclusions drawn. In this review, a series of recent examples are used to illustrate both the challenges for interpretation and approaches through which these can be overcome.

Crystalline and Lamellar Structure of Polypropylene Fibrillated Fibres

2013 ◽  
Vol 203-204 ◽  
pp. 439-442
Author(s):  
Marcin Bączek ◽  
Czesław Ślusarczyk ◽  
Jan Broda
Keyword(s):  
Small Angle ◽  
Crystalline Phase ◽  
Lamellar Structure ◽  
Draw Ratio ◽  
Crystallinity Index ◽  
Orientation Factor ◽  
Processing Conditions ◽  
X Ray ◽  
X Ray Scattering ◽  
The Impact

The effects of processing conditions on the structure of polypropylene fibrillated fibres were studied using a combination of wide- and small-angle X-ray scattering methods. In particular the impact of selected stages of processing on the crystalline and lamellar structure of PP were analyzed. It was stated that crystalline phase is built from α crystals. The crystallinity index as well as the Herman orientation factor of the crystalline phase is found to have a correlation only with the draw ratio of the PP film. The lamellar structure also changes with the draw ratio.

scholarly journals Dynamics of the Nucleosome Core Particle Revealed from a New Database of High-Resolution X-Ray Crystallographic and Simulated Structures

2015 ◽  
Vol 108 (2) ◽  
pp. 541a
Author(s):  
Gautam Singh ◽  
Andrew V. Colasanti ◽  
Nicolas Clauvelin ◽  
Wilma K. Olson
Keyword(s):  
High Resolution ◽  
Core Particle ◽  
Nucleosome Core Particle ◽  
X Ray ◽  
Nucleosome Core
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