A model of human APOA2 on HDL

Figures

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  Fig. 1. Comparison of the amphipathicity of human APOA1 and APOA2 measured with the LOCATE algorithm (25) using two different helical pitches: the idealized α-helical pitch (18/5 in black) and the proposed pitch (11/3 in red) for the APOA1 double belt structure in discoidal HDL (26). Amphipathic α-helixes are the most important surface lipid-associating motifs in exchangeable plasma lipoproteins. The sequence extent of each amphipathic helix is denoted on the y-axis by a vertical bar whose Λ4 lipid affinity corresponds to its position on the x-axis. A: LOCATE analysis of human APOA1. B: LOCATE analysis of human APOA2.

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  Fig. 2. Analyses of the amphipathicity of human APOA2 with the program LOCATE. A, B: Helical wheel domains of the first (residues 5–31) and last (residues 51–73) amphipathic helical domains, respectively, identified by the program LOCATE in Figure 1 are plotted with the WHEEL subroutine. A, B: The helix in panel A is constructed with an α11/3 pitch since that gives a higher Λ4 lipid affinity than the standard α18/5 algorithm (25, 26); the panel B helix is constructed with the idealized 18/5 pitch. In each representation, the helix is oriented so that the N-termini points out of the page (yellow arrows). By definition, that defines the left (L) and right (R) amphipathic helical edges. The Λ4 lipid affinity calculated for each domain is indicated within each helical wheel. The four aromatic residues involved in the proposed π-cup (see Fig. 4B) are indicated by red circles. Residue C6 is indicated by a green diamond in panel A. C, D: Cartoon views of the two helical orientations allowing formation of a disulfide bond, creating, respectively, antiparallel and parallel helical pairings. Note that parallel pairing places hydrophobic faces (H) in opposite directions. Here, (P) denotes the polar…

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  Fig. 3. Mapping of chemical crosslinks onto two possible antiparallel disulfide-bond orientations denoted by cartoon representations. Since the parallel disulfide bond configuration forces the hydrophobic faces to face in opposite directions, the disulfide bond in human APOA2 restricts lipid-associated dimeric APOA2 to the antiparallel conformation. There are three possible conformations for the antiparallel alignment: A: An extended disulfide-linked dimer. B: An open disulfide-linked double hairpin belt. C: A closed disulfide-linked double hairpin belt. Intramolecular crosslinks determined by two different chemical methods are plotted onto the schematic diagrams (BS3 in rHDL and zero-order in UC-HDL onto opposite ends of each diagram) in panels A–C. Only representative crosslinks from Table 1 are shown for clarity. Charged residue positions are denoted by circles (basic, blue; acidic, pink). Crosslinks are denoted by solid blue lines (acceptable) and dotted blue lines (unacceptable); thick lines indicate definite crosslinks, thin lines uncertain crosslinks. Key linear dimensions are indicated for structures in panels A and C. Small filled circles colored in blue and pink indicate lysine…

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  Fig. 4. Detailed HDL-associated structures of two orientations of disulfide-linked double hairpin model of human APOA2. A: Open double hairpin model in an antiparallel arrangement shown in cartoon representation. The four proline residues are displayed as yellow space-filling spheres. The two Cys6 residues (space-filling, colored by atom type) are located on opposite sides of the model and therefore cannot form a disulfide bond. B: Energy-minimized model of the closed disulfide-linked double hairpin belt structure shown in cartoon representation. Curved red arrows mark the two hairpin loops. Red arrowheads indicate van der Waals contacts between N- and C-termini created in construction of the model. The location of the disulfide crosslink (space-filling green) and the 4 prolines (space-filling yellow) are denoted. Note the bilateral clustering of antiparallel prolines. The π−cup (Y21 nestled cross hairpin into the F63, Y66, and F67 “cup”) is marked in the upper half, as are the proposed salt bridges (residues D24, K28, K55 and E59) in the lower half. C: Structure in panel B in space-filling mode rotated 180° around the y-axis to expose the hydrophobic face. Hydrophobic residues, orange;…

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  Fig. 5. Docked model of APOA2 onto the surface of the 80 Å small spherical APOA1 particle. The APOA1 structure was taken from the all-atom model converted from the final frame of a 200 μs coarse-grained simulation reported in our previous work (31). Two potential APOA2 docking sites were identified on the small spherical APOA1 particle, and APOA2 was positioned at the site that maximized the number of satisfied experimental cross-links. The APOA2 model was then bent to accommodate the curved surface of the spherical HDL particle. A: APOA1 is shown in green, and APOA2 in cyan. The N- and C-termini of APOA1 are colored blue and red, respectively. The distances between the Cα atoms of each cross-linked residue are indicated by blue dotted lines. B: Surface representation of the model shown in panel A. APOA1 and APOA2 are colored black and cyan, respectively. Panel A was rotated to provide an improved view of the APOA1–APOA2 docking interface.