scholarly journals Structural basis of a nucleosome containing histone H2A.B/H2A.Bbd that transiently associates with reorganized chromatin

2013 ◽  
Vol 3 (1) ◽  
Author(s):  
Yasuhiro Arimura ◽  
Hiroshi Kimura ◽  
Takashi Oda ◽  
Koichi Sato ◽  
Akihisa Osakabe ◽  
...  
Keyword(s):  
Dna Replication ◽  
Small Angle ◽  
Living Cells ◽  
Structural Basis ◽  
Base Pairs ◽  
X Ray ◽  
X Ray Scattering ◽  
Biochemical Function ◽  
Dna Replication And Repair ◽  
Chromatin Reorganization

Abstract Human histone H2A.B (formerly H2A.Bbd), a non-allelic H2A variant, exchanges rapidly as compared to canonical H2A and preferentially associates with actively transcribed genes. We found that H2A.B transiently accumulated at DNA replication and repair foci in living cells. To explore the biochemical function of H2A.B, we performed nucleosome reconstitution analyses using various lengths of DNA. Two types of H2A.B nucleosomes, octasome and hexasome, were formed with 116, 124, or 130 base pairs (bp) of DNA and only the octasome was formed with 136 or 146 bp DNA. In contrast, only hexasome formation was observed by canonical H2A with 116 or 124 bp DNA. A small-angle X-ray scattering analysis revealed that the H2A.B octasome is more extended, due to the flexible detachment of the DNA regions at the entry/exit sites from the histone surface. These results suggested that H2A.B rapidly and transiently forms nucleosomes with short DNA segments during chromatin reorganization.

scholarly journals Structural Basis of Cellulosome Efficiency Explored by Small Angle X-ray Scattering

2005 ◽  
Vol 280 (46) ◽  
pp. 38562-38568 ◽  
Author(s):  
Michal Hammel ◽  
Henri-Pierre Fierobe ◽  
Mirjam Czjzek ◽  
Vandana Kurkal ◽  
Jeremy C. Smith ◽  
...  
Keyword(s):  
Small Angle ◽  
Structural Basis ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

scholarly journals Supramolecular Dimerization in a Polymer Melt from Small-Angle X-ray Scattering and Rheology: A Miscible Model System

Polymers ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 880
Author(s):  
Mariapaola Staropoli ◽  
Margarita Kruteva ◽  
Jürgen Allgaier ◽  
Andreas Wischnewski ◽  
Wim Pyckhout-Hintzen
Keyword(s):  
Hydrogen Bonding ◽  
Small Angle ◽  
Full Range ◽  
Polymer Melt ◽  
Self Healing ◽  
Temperature Dependent ◽  
Base Pairs ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

We present a structural and dynamic study on the simplest supramolecular hetero-association, recently investigated by the authors to prepare architectural homogeneous structures in the melt state, based on the bio-inspired hydrogen-bonding of thymine/diaminotriazine (thy–DAT) base-pairs. In the combination with an amorphous low Tg poly(butylene oxide) (PBO), no micellar structures are formed, which is expected for nonpolar polymers because of noncompatibility with the highly polar supramolecular groups. Instead, a clear polymer-like transient architecture is retrieved. This makes the heterocomplementary thy–DAT association an ideal candidate for further exploitation of the hydrogen-bonding ability in the bulk for self-healing purposes, damage management in rubbers or even the development of easily processable branched polymers with built-in plasticizer. In the present work, we investigate the temperature range from Tg + 20 °C to Tg + 150 °C of an oligomeric PBO using small-angle X-ray scattering (SAXS) and linear rheology on the pure thy and pure DAT monofunctionals and on an equimolar mixture of thy/DAT oligomers. The linear rheology performed at low temperature is found to correspond to fully closed-state dimeric configurations. At intermediate temperatures, SAXS probes the equilibrium between open and closed states of the thy–DAT mixtures. The temperature-dependent association constant in the full range between open and closed H-bonds and an enhancement of the monomeric friction coefficient due to the groups is obtained. The thy–DAT association in the melt is more stable than the DAT–DAT, whereas the thy–thy association seems to involve additional long-lived interactions.

scholarly journals Structural diversity of proline catabolic enzymes revealed by small angle x-ray scattering, x-ray crystallography and light scattering

2012 ◽  
Author(s):  
◽  
Ranjan Kumar Singh
Keyword(s):  
Small Angle ◽  
Quaternary Structure ◽  
Structural Basis ◽  
Sequence Alignments ◽  
X Ray ◽  
Catabolic Enzymes ◽  
Bifunctional Enzymes ◽  
X Ray Scattering ◽  
Proline Utilization ◽  
Ray Scattering

The proline catabolic enzymes catalyze the 4-electron oxidation of proline to glutamate. The reaction involves two enzymes, proline dehydrogenase (PRODH) and Î"1-pyrroline -5-carboxylate dehydrogenase (P5CDH). Some bacterial organisms have both of these enzymes fused together, and the fused bifunctional enzymes are called Proline utilization A (PutA). In addition to these bifunctional enzymes, some PutAs are trifunctional, because they moonlight as transcription repressors of their own gene. Our lab recently reported that the quaternary structure of the bifunctional PutA from B. japonicam (BjPutA) is a ring-shaped tetramer. However, the structural organization of PutAs from other organisms is still unknown. In particular, there are no structures available for moonlighting trifunctional PutAs. We therefore utilized small angle X-ray scattering (SAXS) to obtain the overall shape of a trifunctional PutA from Escherichia coli (EcPutA). In addition, rigid body modeling of full-length PutA has been done with the help of SAXS data and crystal structures of DNA-binding and PRODH domains of EcPutA, and BjPutA crystal structure. Unique structural features of PutA have also been explored through multiple sequence alignments and homology modeling using the webservers like ClustalW, Espript, Phyre, and Swiss Model. The results obtained from sequence alignment study led us to work on finding the diversity in oligomeric states of PutAs. Finally, the structural basis of HPII disease that is related to disorder in human P5CDH was determined through X-ray crystallographic studies.

scholarly journals Rapid screening of in cellulo grown protein crystals via a small-angle X-ray scattering/X-ray powder diffraction synergistic approach

2020 ◽  
Vol 53 (5) ◽  
pp. 1169-1180 ◽  
Author(s):  
Janine Mia Lahey-Rudolph ◽  
Robert Schönherr ◽  
Cy M. Jeffries ◽  
Clément E. Blanchet ◽  
Juliane Boger ◽  
...  
Keyword(s):  
Cell Culture ◽  
Small Angle ◽  
Living Cells ◽  
Protein Crystals ◽  
Rapid Screening ◽  
X Ray ◽  
X Ray Scattering ◽  
A Cell ◽  
The Impact ◽  
Ray Scattering

Crystallization of recombinant proteins in living cells is an exciting new approach for structural biology that provides an alternative to the time-consuming optimization of protein purification and extensive crystal screening steps. Exploiting the potential of this approach requires a more detailed understanding of the cellular processes involved and versatile screening strategies for crystals in a cell culture. Particularly if the target protein forms crystalline structures of unknown morphology only in a small fraction of cells, their detection by applying standard visualization techniques can be time consuming and difficult owing to the environmental challenges imposed by the living cells. In this study, a high-brilliance and low-background bioSAXS beamline is employed for rapid and sensitive detection of protein microcrystals grown within insect cells. On the basis of the presence of Bragg peaks in the recorded small-angle X-ray scattering profiles, it is possible to assess within seconds whether a cell culture contains microcrystals, even in a small percentage of cells. Since such information cannot be obtained by other established detection methods in this time frame, this screening approach has the potential to overcome one of the bottlenecks of intracellular crystal detection. Moreover, the association of the Bragg peak positions in the scattering curves with the unit-cell composition of the protein crystals raises the possibility of investigating the impact of environmental conditions on the crystal structure of the intracellular protein crystals. This information provides valuable insights helping to further understand the in cellulo crystallization process.

scholarly journals Super resolution for X-ray scattering and biological insights from its applications to dynamic DNA replication and repair complexes

2017 ◽  
Vol 73 (a1) ◽  
pp. a314-a314
Author(s):  
John A. Tainer ◽  
Susan E. Tsutakawa ◽  
Greg L. Hura ◽  
Michal Hammel
Keyword(s):  
Dna Replication ◽  
Super Resolution ◽  
X Ray ◽  
X Ray Scattering ◽  
Dna Replication And Repair ◽  
Ray Scattering

A Revised O2 Reduction Model in Li-O2 Batteries as Revealed by in Situ Small Angle X-Ray Scattering

2019 ◽  
Author(s):  
Christian Prehal ◽  
Aleksej Samojlov ◽  
Manfred Nachtnebel ◽  
Manfred Kriechbaum ◽  
Heinz Amenitsch ◽  
...  
Keyword(s):  
Small Angle ◽  
Wide Angle ◽  
Reduction Mechanism ◽  
Reduction Model ◽  
X Ray ◽  
X Ray Scattering ◽  
O2 Reduction ◽  
Ray Scattering

<b>Here we use in situ small and wide angle X-ray scattering to elucidate unexpected mechanistic insights of the O2 reduction mechanism in Li-O2 batteries.<br></b>

In situ Time-Resolved Small-Angle X-ray Scattering Reveals the Formation Kinetics of Polyelectrolyte Complex Micelles

2019 ◽  
Author(s):  
Hao Wu ◽  
Jeffrey Ting ◽  
Siqi Meng ◽  
Matthew Tirrell
Keyword(s):  
Small Angle ◽  
Self Assembly ◽  
Electrostatic Interactions ◽  
Polyelectrolyte Complex ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Kinetics Of ◽  
Ray Scattering

We have directly observed the <i>in situ</i> self-assembly kinetics of polyelectrolyte complex (PEC) micelles by synchrotron time-resolved small-angle X-ray scattering, equipped with a stopped-flow device that provides millisecond temporal resolution. This work has elucidated one general kinetic pathway for the process of PEC micelle formation, which provides useful physical insights for increasing our fundamental understanding of complexation and self-assembly dynamics driven by electrostatic interactions that occur on ultrafast timescales.

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