scholarly journals SIR proteins create compact heterochromatin fibers

2018 ◽  
Vol 115 (49) ◽  
pp. 12447-12452 ◽  
Author(s):  
Sarah G. Swygert ◽  
Subhadip Senapati ◽  
Mehmet F. Bolukbasi ◽  
Scot A. Wolfe ◽  
Stuart Lindsay ◽  
...  
Keyword(s):  
Genomic Stability ◽  
Histone H4 ◽  
Complicated Structure ◽  
Force Microscopy ◽  
Structure And Dynamics ◽  
Sir Proteins ◽  
Atomic Force ◽  
Condensed Structure ◽  
Chromatin Fibers ◽  
Heterochromatin Assembly

Heterochromatin is a silenced chromatin region essential for maintaining genomic stability and driving developmental processes. The complicated structure and dynamics of heterochromatin have rendered it difficult to characterize. In budding yeast, heterochromatin assembly requires the SIR proteins—Sir3, believed to be the primary structural component of SIR heterochromatin, and the Sir2–4 complex, responsible for the targeted recruitment of SIR proteins and the deacetylation of lysine 16 of histone H4. Previously, we found that Sir3 binds but does not compact nucleosomal arrays. Here we reconstitute chromatin fibers with the complete complement of SIR proteins and use sedimentation velocity, molecular modeling, and atomic force microscopy to characterize the stoichiometry and conformation of SIR chromatin fibers. In contrast to fibers with Sir3 alone, our results demonstrate that SIR arrays are highly compact. Strikingly, the condensed structure of SIR heterochromatin fibers requires both the integrity of H4K16 and an interaction between Sir3 and Sir4. We propose a model in which a dimer of Sir3 bridges and stabilizes two adjacent nucleosomes, while a Sir2–4 heterotetramer interacts with Sir3 associated with a nucleosomal trimer, driving fiber compaction.

scholarly journals SIR proteins create compact heterochromatin fibers

2018 ◽  
Author(s):  
Sarah G. Swygert ◽  
Subhadip Senapati ◽  
Mehmet F. Bolukbasi ◽  
Scot A. Wolfe ◽  
Stuart Lindsay ◽  
...  
Keyword(s):  
Genomic Stability ◽  
Histone H4 ◽  
Complicated Structure ◽  
Force Microscopy ◽  
Structure And Dynamics ◽  
Sir Proteins ◽  
Atomic Force ◽  
Condensed Structure ◽  
Chromatin Fibers ◽  
Heterochromatin Assembly

SummaryHeterochromatin is a silenced chromatin region essential for maintaining genomic stability and driving developmental processes. The complicated structure and dynamics of heterochromatin have rendered it difficult to characterize. In budding yeast, heterochromatin assembly requires the SIR proteins -- Sir3, believed to be the primary structural component of SIR heterochromatin, and the Sir2/4 complex, responsible for the targeted recruitment of SIR proteins and the deacetylation of lysine 16 of histone H4. Previously, we found that Sir3 binds but does not compact nucleosomal arrays. Here we reconstitute chromatin fibers with the complete complement of SIR proteins and use sedimentation velocity, molecular modeling, and atomic force microscopy to characterize the stoichiometry and conformation of SIR chromatin fibers. In contrast to previous studies, our results demonstrate that SIR arrays are highly compact. Strikingly, the condensed structure of SIR heterochromatin fibers requires both the integrity of H4K16 and an interaction between Sir3 and Sir4. We propose a model in which two molecules of Sir3 bridge and stabilize two adjacent nucleosomes, while a single Sir2/4 heterodimer binds the intervening linker DNA, driving fiber compaction.

Dynamics and metastable surface structure of double atomic layer of water molecules and ions at the interface between KBr(c) and water

2004 ◽  
Vol 76 (1) ◽  
pp. 115-122 ◽  
Author(s):  
K. Ichikawa ◽  
S. Sato ◽  
N. Shimomura
Keyword(s):  
Surface Structure ◽  
Vertical Motion ◽  
Atomic Layer ◽  
Water Molecules ◽  
Potassium Ions ◽  
Force Microscopy ◽  
Structure And Dynamics ◽  
Atomic Force ◽  
Bromide Ions

The metastable surface structure and dynamics of water molecules, cations, and anions at the interface between KBr(001) and water have been demonstrated from the images in situ observed in atomic resolution using atomic force microscopy. The vertical motion of potassium ions, which means their own transfer from the equilibrium sites to the upper height right on the underlying bromide ions, has been observed at the interface. They are used to be located in some steady state stabilized by their interaction with water molecules in the double atomic layer at the interface. The observed water molecules bridge two bromide ions by hydrogen bond; the water molecules are sandwiched by the potassium ions and vice versa.

scholarly journals Structure and Dynamics of Membrane-embedded KcsA Potassium Channel Revealed by Atomic Force Microscopy

2015 ◽  
Vol 55 (1) ◽  
pp. 005-010 ◽  
Author(s):  
Ayumi SUMINO ◽  
Daisuke YAMAMOTO ◽  
Takashi SUMIKAMA ◽  
Masayuki IWAMOTO ◽  
Takehisa DEWA ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Potassium Channel ◽  
Force Microscopy ◽  
Structure And Dynamics ◽  
Atomic Force ◽  
Kcsa Potassium Channel

scholarly journals A comparison of the network structure and inner dynamics of homogeneously and heterogeneously crosslinked PNIPAM microgels with high crosslinker content

Soft Matter ◽  
2019 ◽  
Vol 15 (5) ◽  
pp. 1053-1064 ◽  
Author(s):  
Judith Witte ◽  
Tetyana Kyrey ◽  
Jana Lutzki ◽  
Anna Margarethe Dahl ◽  
Judith Houston ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Network Structure ◽  
Force Microscopy ◽  
Structure And Dynamics ◽  
Atomic Force ◽  
Crosslinker Content

The network structure and dynamics of different PNIPAM microgels is studied with various scattering methods and atomic force microscopy.

Micromechanics and Microdynamics Via Atomistic Simulations

1988 ◽  
Vol 140 ◽  
Author(s):  
Uzi Landman ◽  
W. D. Luedtke ◽  
M. W. Ribarsky
Keyword(s):  
Microscopic Level ◽  
Atomistic Simulations ◽  
Dynamical Response ◽  
Natural Phenomena ◽  
Force Microscopy ◽  
Structure And Dynamics ◽  
External Perturbations ◽  
Atomic Force ◽  
Basic Understanding ◽  
Dynamics Simulations

AbstractBasic understanding of the structure and dynamics of materials and their response to external perturbations requires knowledge on the microscopic level, of the underlying energetics and atomic dynamics, whose consequences we observe and measure. Coupled with the above is the everlasting quest to observe and understand natural phenomena on refined microscopic scales, which provides the impetus for the development of experimental and theoretical techniques for the interrogation of materials with refined spatial and temporal resolution. In this paper we review the development of molecular dynamics simulations for studies of the energetics and dynamical response of materials to external mechanical perturbations. Applications to investigations of solid and liquid interfacial systems under stress and to studies of the consequences of tip-substrate interactions in atomic force microscopy are demonstrated.

scholarly journals High-Speed Atomic Force Microscopy Reveals the Structural Dynamics of the Amyloid-β and Amylin Aggregation Pathways

2020 ◽  
Vol 21 (12) ◽  
pp. 4287
Author(s):  
Takahiro Watanabe-Nakayama ◽  
Bikash R. Sahoo ◽  
Ayyalusamy Ramamoorthy ◽  
Kenjiro Ono
Keyword(s):  
Atomic Force Microscopy ◽  
Protein Structure ◽  
Real Time ◽  
Structural Dynamics ◽  
High Speed ◽  
Amyloid Β ◽  
Force Microscopy ◽  
Structure And Dynamics ◽  
Atomic Force ◽  
Novel Therapeutic Strategies

Individual Alzheimer’s disease (AD) patients have been shown to have structurally distinct amyloid-β (Aβ) aggregates, including fibrils, in their brain. These findings suggest the possibility of a relationship between AD progression and Aβ fibril structures. Thus, the characterization of the structural dynamics of Aβ could aid the development of novel therapeutic strategies and diagnosis. Protein structure and dynamics have typically been studied separately. Most of the commonly used biophysical approaches are limited in providing substantial details regarding the combination of both structure and dynamics. On the other hand, high-speed atomic force microscopy (HS-AFM), which simultaneously visualizes an individual protein structure and its dynamics in liquid in real time, can uniquely link the structure and the kinetic details, and it can also unveil novel insights. Although amyloidogenic proteins generate heterogeneously aggregated species, including transient unstable states during the aggregation process, HS-AFM elucidated the structural dynamics of individual aggregates in real time in liquid without purification and isolation. Here, we review and discuss the HS-AFM imaging of amyloid aggregation and strategies to optimize the experiments showing findings from Aβ and amylin, which is associated with type II diabetes, shares some common biological features with Aβ, and is reported to be involved in AD.

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