Activation helix orientation of the estrogen receptor is mediated by receptor dimerization: evidence from molecular dynamics simulations

2015 ◽  
Vol 17 (20) ◽  
pp. 13403-13420 ◽  
Author(s):  
Filip Fratev
Keyword(s):  
Molecular Dynamics ◽  
Estrogen Receptor ◽  
Molecular Dynamics Simulations ◽  
Dimer Formation ◽  
Receptor Dimerization ◽  
Helix 12 ◽  
Conformational Landscape ◽  
Helix Conformation ◽  
Helix Orientation ◽  
Dynamics Simulations

ERα dimer formation reshapes the helix 12 conformational landscape and is a leading factor for the activation helix conformation.

Molecular dynamics study of lignin constituents in water

Holzforschung ◽  
2005 ◽  
Vol 59 (3) ◽  
pp. 253-262 ◽  
Author(s):  
Xiao Yi Li ◽  
Leif A. Eriksson
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulations ◽  
Methoxy Group ◽  
Bond Formation ◽  
Coniferyl Alcohol ◽  
Dimer Formation ◽  
Mechanism Of Reaction ◽  
Centers Of Mass ◽  
Dynamics Simulations

Abstract Molecular dynamics simulations were used to explore the distribution of linkages in coumaryl alcohol and coniferyl alcohol systems, including monomeric systems and monomers interacting with β-O4 dimers, respectively. Studying the interactions of two monolignols and the corresponding dimers sheds light on the preferred mechanism of reaction of the growing lignin polymer from the view of kinetic factors. The energy change upon association was quantified, and the distances between the centers of mass of different molecules, and the relative orientations between the phenol groups were calculated for all the systems. Using a cut-off threshold of 4 Å to indicate association leading to bond formation, it is concluded that the presence of the additional methoxy group on coniferyl alcohol assists in promoting interaction of the O4 group with the second moiety. Based on the computed data it is furthermore concluded that in aqueous solution, the most likely model of polymerization is that involving initial dimer formation, followed by dimer-dimer association.

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