Pairwise energies for polypeptide coarse-grained models derived from atomic force fields

2009 ◽  
Vol 130 (19) ◽  
pp. 195103 ◽  
Author(s):  
Marcos R. Betancourt ◽  
Sheyore J. Omovie
Keyword(s):  
Force Fields ◽  
Coarse Grained ◽  
Atomic Force

A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding

2017 ◽  
Vol 19 (21) ◽  
pp. 13629-13639 ◽  
Author(s):  
Jie Hu ◽  
Tao Chen ◽  
Moye Wang ◽  
Hue Sun Chan ◽  
Zhuqing Zhang
Keyword(s):  
Protein Folding ◽  
Force Fields ◽  
Coarse Grained ◽  
Unfolded Proteins ◽  
Critical Comparison ◽  
Atomic Models ◽  
Atomic Force

The predicted dimension of unfolded proteins is quite different using native-centric Gō-like models and transferrable (non-structure-based) models based on current atomic force fields.

Transferability of coarse-grained force fields: The polymer case

2008 ◽  
Vol 128 (6) ◽  
pp. 064904 ◽  
Author(s):  
Paola Carbone ◽  
Hossein Ali Karimi Varzaneh ◽  
Xiaoyu Chen ◽  
Florian Müller-Plathe
Keyword(s):  
Force Fields ◽  
Coarse Grained

scholarly journals A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields

2018 ◽  
Vol 39 (28) ◽  
pp. 2360-2370 ◽  
Author(s):  
Adam K. Sieradzan ◽  
Artur Giełdoń ◽  
Yanping Yin ◽  
Yi He ◽  
Harold A. Scheraga ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Force Field ◽  
Force Fields ◽  
Coarse Grained ◽  
Protein Nucleic Acid ◽  
New Protein

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.

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