(a) Overview of a GNNQQNY amyloid spine (PDB entry 1yjp
; Nelson et al., 2005). Four β-strands from each of the two spinal β-sheets are shown. β-Strands are depicted in gray as cartoons. One β-strand from each β-sheet is also shown as sticks with N- and C-termini labeled. All strands of a given sheet in this spine run in the same direction from the N-terminus to the C-terminus. The spine axis is shown as a gray arrow running through the center of the spine. Here, the spine axis is oblique to the viewer. (b) View down the GNNQQNY spine axis showing one pair of β-strands, each from a different β-sheet. The arrow representing the spine axis in (a) points towards the viewer here (gray circle with dot). The N- and C- termini of the two β-strands are labeled. The magenta laminae are faces of boxes that represent the two β-strands and indicate the orientation of the β-strands, as described for (d). Here, the magenta faces are orthogonal to the spine axis. (c) A view of the GNNQQNY spine looking perpendicular to the spine axis. This vantage point is similar to that in (e), but slightly rotated around the spine axis. The x, y and z axes of the coordinate system for this GNNQQNY spine are shown in blue, green and red, respectively. The y axis is parallel to the spine axis. One β-sheet of the spine is outlined by a dashed parallelogram. One β-strand from each β-sheet is labeled at the N- and C-termini. Open triangles indicate two β-strands that are also indicated in (d). (d) The GNNQQNY spine is represented as stacks of boxes with colored faces, seen from the same vantage point as in (c). Each box represents a different β-strand. Colors indicate orientation such that various landmarks of the β-strands point towards the different colored faces of a representative box. For this GNNQQNY example, landmark features and the faces to which they point are as follows: N-terminus of each β-strand, cyan face; C-terminus, blue face; side chain of the first Q, amber face; backbone carbonyl of the first Q, magenta face; side chain of the second Q, green face; backbone carbonyl of the second Q, yellow face. (e) A view down the z axis of the GNNQQNY spine, showing only two β-strands, one from each sheet. The two β-strands are depicted as both sticks and colored boxes. Here, the blue and cyan faces of the boxes are in the xy plane, which is also the plane of the figure, so the other faces of the boxes are not visible. The spine axis is shown as a gray arrow. This vantage point, similar to those in (c) and (d), is created from the vantage point of (b) by a 90° rotation around the x axis, where the now hidden magenta faces point towards the top of the figure. (f) The homosteric zipper lattice (gray grid) is made from half-unit translations along the x and y axes at z = 0. The grey arrow represents the spine axis, which is defined to be at x = ¼ and z = 0. (g, h, i) The rotations E3 (identity), I3 (180° rotation around x), J3 (180° around y) and K3 (180° around z) on a single β-strand are illustrated using the colored box. This box is set into the zipper lattice to schematize homosteric zippers, as in (d) and (i) and in Fig. 2. β-Strands run from the N-terminus to the C-terminus parallel to the z axis (from the cyan side of the box to the blue side). The y axis is perpendicular to the magenta and yellow sides. The x axis, which is perpendicular to the green and amber sides, runs through the interface of the two spinal β-sheets. (g) The exterior surface of the box is shown as if the box were unfolded. (h) The box is shown in four orientations representing the four rotations on the reference (labeled with the identity operation, E). The subscripts have been dropped from the rotation labels E, I, J and K. (i) The GNNQQNY homosteric zipper (zipper group 1b) is depicted as two stacks of colored boxes. Two repeats (unit cells) are shown. The two β-sheets are staggered along the y axis as dictated by the zipper group 1b generators (E and Jxy), producing 21 symmetry along the spine axis. (j) The atomic resolution crystal structure of mcLVFFA (Liu et al., 2011) contains a parallel, face=back β-sheet. The structure of one dimer of a macrocycle tetramer is shown as a ball-and-stick model with the β-strands (LVFFA) represented as cartoons. In the top macrocycle (amber), the residues Leu1, Phe3 and Ala5 project toward the viewer, given the numbering 1–5. In the bottom macrocycle (green), the residues Val2 and Phe4 project toward the viewer.