Charge-State Dependent Compaction and Dissociation of Protein Complexes: Insights from Ion Mobility and Molecular Dynamics

2012 ◽  
Vol 134 (7) ◽  
pp. 3429-3438 ◽  
Author(s):  
Zoe Hall ◽  
Argyris Politis ◽  
Matthew F. Bush ◽  
Lorna J. Smith ◽  
Carol V. Robinson
Keyword(s):  
Molecular Dynamics ◽  
Charge State ◽  
Ion Mobility ◽  
Protein Complexes ◽  
State Dependent

scholarly journals Results Regarding the Resolving of Membrane-Protein Complexes using Neutron Reflection in Molecular Dynamics

2018 ◽  
Vol 114 (3) ◽  
pp. 341a
Author(s):  
Bradley W. Treece ◽  
Arvind Ramanathan ◽  
Frank Heinrich ◽  
Mathias Lösche
Keyword(s):  
Molecular Dynamics ◽  
Membrane Protein ◽  
Protein Complexes ◽  
Neutron Reflection ◽  
Membrane Protein Complexes

Charge-state-dependent atomic geometries for isolated metal adatoms on GaAs(110)

1989 ◽  
Vol 40 (8) ◽  
pp. 5810-5813 ◽  
Author(s):  
John E. Klepeis ◽  
Walter A. Harrison
Keyword(s):  
Charge State ◽  
State Dependent

scholarly journals DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations

2021 ◽  
Author(s):  
Stefanos S Nomidis ◽  
Enrico Carlon ◽  
Stephan Gruber ◽  
John F Marko
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Protein Complexes ◽  
Power Stroke ◽  
End Points ◽  
Domains Of Life ◽  
Dynamics Simulations ◽  
Fixed End ◽  
Atp Binding And Hydrolysis ◽  
Low Tension

Structural Maintenance of Chromosomes (SMC) protein complexes play essential roles in genome folding and organization across all domains of life. In order to determine how the activities of these large (about 50 nm) complexes are controlled by ATP binding and hydrolysis, we have developed a molecular dynamics (MD) model that realistically accounts for thermal conformational motions of SMC and DNA. The model SMCs make use of DNA flexibility and looping, together with an ATP-induced "power stroke", to capture and transport DNA segments, so as to robustly translocate along DNA. This process is sensitive to DNA tension: at low tension (about 0.1 pN), the model performs steps of roughly 60 nm size, while, at higher tension, a distinct inchworm-like translocation mode appears, with steps that depend on SMC arm flexibility. By permanently tethering DNA to an experimentally-observed additional binding site ("safety belt"), the same model performs loop extrusion. We find that the dependence of loop extrusion on DNA tension is remarkably different when DNA tension is fixed vs when DNA end points are fixed: Loop extrusion reversal occurs above 0.5 pN for fixed tension, while loop extrusion stalling without reversal occurs at about 2 pN for fixed end points. Our model quantitatively matches recent experimental results on condensin and cohesin, and makes a number of clear predictions. Finally we investigate how specific structural changes affect the SMC function, which is testable in experiments on varied or mutant SMCs.

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