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. Author manuscript; available in PMC: 2012 Mar 29.
Published in final edited form as: Biochemistry. 2011 Mar 4;50(12):2249–2263. doi: 10.1021/bi101301g

FIGURE 4. Structural features of one example each of the four MDSA and four 500 K MD T-jump simulations of the 160:24:2 (R2-2) particle.

FIGURE 4

A. Final structure of one example from the ensemble of four MDSA simulations (R2-24) of the R2-2 particle. B. Final structure of one example from the ensemble of four 500 K MD T-jump simulations (X2-24) of the R2-2 particle. (Upper panel) Cross-eyed stereo image of spacefilling models, including hydrogens, viewed from the face of the particles with the central domain (helix 5) at the top. (Middle panel) Spacefilling models, excluding hydrogens, viewed from the terminal overlap domain side of the particles. Each particle has been rotated 90° from the upper row view as indicated by the arrows. The white arrowheads indicate areas of exposure of acyl chains to solvent. Protein: Skyblue except proline (yellow). POPC: Phosphorous atoms (gold), phosphate oxygen atoms (red), choline nitrogens and methyls (blue), acyl chains (black), hydrogens (white). UC: (cpk). (Lower panels) Same view as middle panel showing protein only. Protein: Silver blue except proline (yellow), N-terminal G* domain, residues 1-43 (blue), C-terminal helix 10, residues 220-243 (red), helix 5, residues 121-142 (green. The yellow arrowheads indicate clustering of the N-terminal proline-rich pairs. C. Cross-eyed stereo images of all the final structures from the ensembles of all four MDSA (R2-24, upper panel) and 500 K MD T-jump (X2-24, lower panel) simulations aligned from residues 77 to 188. POPC and UC are represented in line format (cyan). The protein is represented as a Cα backbone tube model except prolines that are spacefilling. The structures are viewed from the terminal overlap domain side of the ensemble particle. N-terminal G* domains, residues 1-43 (blue); C-terminal helix 10 domains, residues 220-243, (red); and remainder of protein (gray). D. Cross-eyed stereo images of average final structures of FL-apoA-I double belt for the four MDSA (R2-24, upper panel) and 500 K MD T-jump (X2-24, lower panel) simulations of the 160:24:2 particle created from calculated average coordinates. The apoA-I double belts are viewed from the helix 5 domain. The protein is represented as a Cα backbone tube model except Cα proline (spacefilling yellow). Helix 5 (green), C-terminal helix 10 domains, residues 220-243 (red), N-terminal G* domains, residues 1-43 (blue), and remainder of protein (gray). The N-terminal (proline-rich) domains are indicated by red arrowheads.