Structure and Orientation of Interfacial Water Determine Atomic Force Microscopy Results: Insights from Molecular Dynamics Simulations

ACS Nano ◽  
2011 ◽  
Vol 5 (3) ◽  
pp. 2215-2223 ◽  
Author(s):  
Dimitrios Argyris ◽  
Paul D. Ashby ◽  
Alberto Striolo
Keyword(s):  
Molecular Dynamics ◽  
Atomic Force Microscopy ◽  
Molecular Dynamics Simulations ◽  
Interfacial Water ◽  
Force Microscopy ◽  
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.

scholarly journals From nanoaggregates to mesoscale ribbons: the multistep self-organization of amphiphilic peptides

2021 ◽  
Author(s):  
Grazia Maria Laura Messina ◽  
Claudia Mazzuca ◽  
Monica Dettin ◽  
Annj Zamuner ◽  
Benedetta Di Napoli ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Atomic Force Microscopy ◽  
Molecular Dynamics Simulations ◽  
Organization Structure ◽  
Self Organization ◽  
Force Microscopy ◽  
Amphiphilic Peptides ◽  
Atomic Force ◽  
Dynamics Simulations

The paper reports Atomic Force Microscopy results and Molecular Dynamics simulations on the striking differences of long-term self-organization structure for the negatively charged (AcA4)2KD (“double tail”) and AcA4D (“single tail”)...

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