Hydration Structure at the α-Al2O3 (0001) Surface: Insights from Experimental Atomic Force Spectroscopic Data and Atomistic Molecular Dynamics Simulations

2013 ◽  
Vol 117 (20) ◽  
pp. 10433-10444 ◽  
Author(s):  
Dimitrios Argyris ◽  
Anh Phan ◽  
Alberto Striolo ◽  
Paul D. Ashby
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Spectroscopic Data ◽  
Atomic Force ◽  
Hydration Structure ◽  
Α Al2o3 ◽  
Dynamics Simulations

Effects of temperature, concentration, and isomer on the hydration structure in monosaccharide solutions

2017 ◽  
Vol 19 (23) ◽  
pp. 15239-15246 ◽  
Author(s):  
Katsufumi Tomobe ◽  
Eiji Yamamoto ◽  
Masato Yasui ◽  
Kenji Yasuoka
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Hydration Structure ◽  
Effects Of Temperature ◽  
Dynamics Simulations

In this study, we elucidated the effects of temperature, concentration, and isomer on the hydration structure in monosaccharide solutions using molecular dynamics simulations.

scholarly journals Atomic force microscope adhesion measurements and atomistic molecular dynamics simulations at different humidities

2017 ◽  
Vol 28 (3) ◽  
pp. 034004 ◽  
Author(s):  
Jeremias Seppä ◽  
Bernhard Reischl ◽  
Hannu Sairanen ◽  
Virpi Korpelainen ◽  
Hannu Husu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Atomic Force Microscope ◽  
Molecular Dynamics Simulations ◽  
Atomic Force ◽  
Dynamics Simulations

scholarly journals Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy

2021 ◽  
Author(s):  
Hiroki Koide ◽  
Noriyuki Kodera ◽  
Shveta Bisht ◽  
Shoji Takada ◽  
Tsuyoshi Terakawa
Keyword(s):  
Molecular Dynamics ◽  
Atomic Force Microscopy ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Force Microscopy ◽  
Atomic Force ◽  
Dna Loop ◽  
Dynamics Simulations ◽  
Dsdna Binding ◽  
Hinge Domain

The condensin protein complex compacts chromatin during mitosis using its DNA-loop extrusion activity. Previous studies proposed scrunching and loop-capture models as molecular mechanisms for the loop extrusion process, both of which assume the binding of double-strand (ds) DNA to the so-called hinge domain formed at the interface of the condensin subunits Smc2 and Smc4. However, how the hinge domain contacts dsDNA has remained unknown, potentially due to its conformational plasticity. Here, we conducted atomic force microscopy imaging of the budding yeast condensin holo-complex and used this data as basis for coarse-grained molecular dynamics simulations to model the hinge structure in a transient open conformation. We then simulated the dsDNA binding to open and closed hinge conformations, predicting that dsDNA binds to the outside surface when closed and to the outside and inside surfaces when open. Our simulations also suggested that the hinge can close around dsDNA bound to the inside surface. The conformational change of the hinge domain might be essential for the dsDNA binding regulation and play important roles in condensin-mediated DNA-loop extrusion.

Sign in / Sign up

Export Citation Format

Share Document