MD simulations of bound complex formation.

2012-07-26T00:41:05Z (GMT) by Craig N. Lumb Mark S. P. Sansom
<p><b>A</b> An optimal configuration for subsequent membrane-binding extracted from the ensemble of BD simulations conducted using an uncharged, zwitterionic lipid bilayer containing PI(3,4,5)P<sub>3</sub>. In this case <i>r</i> = 9 Å, <i>d</i> = 18 Å and <i>θ</i> = 27°. <b>B</b> A snapshot at the end of a subsequent 100 ns MD simulation. <b>C, D</b> Fingerprint plots showing the location of PH domain residues contacting the phosphorus atoms of PI(3,4,5)P<sub>3</sub> in <b>C</b> the X-ray structure (PDB 1FGY) and <b>D</b> the 100 ns snapshot from the MD simulation shown in <b>B</b>. In each plot the minimum distances between each residue and each phosphorus atom are shown.</p>

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