The evolving 3D model of dimer Super Mini-B (dimer S-MB) in SDS/water at the starting (“0 nsec”) and ending (“10 nsec”) times of the MD simulation.

Abstract

<p><u>Plate A</u>: Snapshot of dimer S-MB at “0 nsec” (see text). DSSP analysis indicated helical regions (residues in parentheses) for S-MB molecules <i>A</i> (14–17, 30–37) and <i>B</i> (14–18, 31–39). The local 2-fold axis relating the two monomers in the dimer is shown by an arrow. <u>Plate B</u>: Snapshot of S-MB at “10 nsec”. DSSP analysis indicated helical regions for S-MB molecules <i>A</i> (8–10, 17–21, 30–37) and <i>B</i> (11–16, 31–38). In Plates A and B, MD simulations were performed in the GROMACS version 3.3.3 environment (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0008672#s2" target="_blank"><u>Methods</u></a>). The protein backbone structure is shown with color-coded ribbons denoting the following domains: N-terminal insertion sequence (green), N-terminal helix (red), turn-loop (green), and C-terminal helix (red) rendered with Rasmol 2.7.4.2. Appropriately colored side-chains are shown as stick figures attached to the N-terminal insertion sequence (green), helix (red) or loop (green) ribbon backbones. Disulfide linkages between the N-terminal helix in the foreground and C-terminal helix in the background are highlighted in yellow. The helices are predominately α-helical, with additional minor contributions from 3₁₀ - and 5-helices. The side-chains and backbones for the two N-terminal phenylalanines are colored purple. The N-terminal sequences (residues 1–7) adopt extended conformations that are centered just over the N- and C-terminal helices, with each having its N-terminal Phe-1 near the loop region (Gly-25 and Gly-26). The 30 bound SDS detergent molecules are shown as wireframe molecules that are colored according to the cpk convention. The “0 nsec” dimer S-MB structure in Plate A is similar to the initial ZDOCK and Rosetta input structures (see text).</p