Structural changes induced in thionins by chloride anions as determined by molecular dynamics simulations

2010 ◽  
Vol 147 (1-2) ◽  
pp. 42-52 ◽  
Author(s):  
Svetlana V. Oard ◽  
Frederick M. Enright ◽  
Bin Li
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structural Changes ◽  
Dynamics Simulations

scholarly journals Structural variability and concerted motions of the T cell receptor – CD3 complex

2021 ◽  
Author(s):  
Prithvi R. Pandey ◽  
Bartosz Różycki ◽  
Reinhard Lipowsky ◽  
Thomas R. Weikl
Keyword(s):  
Molecular Dynamics ◽  
T Cell ◽  
Molecular Dynamics Simulations ◽  
T Cell Receptor ◽  
Tilt Angle ◽  
Structural Changes ◽  
Cell Receptor ◽  
Transmembrane Helices ◽  
Dynamics Simulations ◽  
Tcr Activation

AbstractWe investigate the structural and orientational variability of the membrane-embedded T cell receptor (TCR) – CD3 complex in extensive atomistic molecular dynamics simulations based on the recent cryo-EM structure determined by Dong et al. (2019). We find that the TCR extracellular (EC) domain is highly variable in its orientation by attaining tilt angles relative to the membrane normal that range from 15° to 55°. The tilt angle of the TCR EC domain is both coupled to a rotation of the domain and to characteristic changes throughout the TCR – CD3 complex, in particular in the EC interactions of the Cβ FG loop of the TCR, as well as in the orientation of transmembrane helices. The concerted motions of the membrane-embedded TCR – CD3 complex revealed in our simulations provide atomistic insights for force-based models of TCR activation, which involve such structural changes in response to tilt-inducing forces on antigen-bound TCRs.

Reduction of water-mediated repulsion drives poly(N-vinylcaprolactam) collapse upon heating

2020 ◽  
Vol 22 (3) ◽  
pp. 1053-1060
Author(s):  
Kenji Mochizuki
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structural Changes ◽  
Driving Forces ◽  
Dynamics Simulations

Thermo-sensitive aqueous polymers undergo a coil-to-globule transition on heating, with drastic chemical and structural changes. We performed molecular dynamics simulations for PVCL in water to study the driving forces for the polymer's collapse.

scholarly journals Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations

2016 ◽  
Vol 144 (20) ◽  
pp. 205102 ◽  
Author(s):  
Suzette A. Pabit ◽  
Andrea M. Katz ◽  
Igor S. Tolokh ◽  
Aleksander Drozdetski ◽  
Nathan Baker ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Nucleic Acid ◽  
Molecular Dynamics Simulations ◽  
Structural Changes ◽  
Wide Angle ◽  
X Ray ◽  
X Ray Scattering ◽  
Dynamics Simulations ◽  
Ray Scattering

scholarly journals Twisting DNA by Salt

2021 ◽  
Author(s):  
Sergio Cruz-Le&oacuten ◽  
Willem Vanderlinden ◽  
Peter Müller ◽  
Tobias Forster ◽  
Georgina Staudt ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Charge Density ◽  
Molecular Dynamics Simulations ◽  
Structural Changes ◽  
Dna Nanotechnology ◽  
Metal Cations ◽  
Ion Concentration ◽  
Preferential Binding ◽  
Dynamics Simulations ◽  
Dna Twist

DNA structure and properties sensitively depend on its environment, in particular on the ion atmosphere. One of the most fundamental properties of DNA is its helicity and here we investigate how it changes with concentration and identity of the surrounding ions. To resolve how metal cations influence the helical twist, we have combined magnetic tweezer experiments and extensive all-atom molecular dynamics simulations. Two interconnected trends are observed for monovalent alkali and divalent alkaline earth cations. First, DNA twist increases with increasing ion concentration. Secondly, for a given salt concentration, DNA twist strongly depends on cation identity. Metal cations with high charge density (such as Li+ or Ca2+) are most efficient at inducing DNA twist and lead to overwinding. By contrast, metals with intermediate charge density (such as Na+ or Ba2+) reduce the twist and underwind the helix compared to higher density ions. Our molecular dynamics simulations reveal that preferential binding of the metals to the DNA backbone and the nucleobases has opposing effects on DNA twist and provide a microscopic explanation of the observed ion specificity. The comprehensive view gained from our combined approach provides a foundation to understand and predict metal-induced structural changes in nature or in DNA nanotechnology.

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