Biology of Amyloid: Structure, Function, and Regulation Jason Greenwald, Roland Riek  Structure  Volume 18, Issue 10, Pages 1244-1260 (October 2010) DOI: 10.1016/j.str.2010.08.009 Copyright © 2010 Elsevier Ltd Terms and Conditions

Structure 2010 18, 1244-1260DOI: (10.1016/j.str.2010.08.009) Copyright © 2010 Elsevier Ltd Terms and Conditions

Figure 1 Underlying Structure of Amyloids (A) Amyloid fibrils are composed of long filaments that are visible in negatively stained transmission electron micrographs. (B) The schematic diagram of the cross-β sheets in a fibril, with the backbone hydrogen bonds represented by dashed lines, indicates the repetitive spacings that give rise to (C) the typical fiber diffraction pattern with a meridional reflection at ∼4.7 Å (black dashed box) and an equatorial reflection at ∼6–11 Å (white dashed box). Structure 2010 18, 1244-1260DOI: (10.1016/j.str.2010.08.009) Copyright © 2010 Elsevier Ltd Terms and Conditions

Figure 2 Steric Zippers, Hydrogen Bonding, and van der Waals Packing in Atomic Resolution Amyloid Crystal Structures The interactions found in cross-β fibrils are exemplified by the structures of two peptides (A) NNQNTF (Protein Data Bank code: 3FVA) and (B) NVGSNTY (Protein Data Bank code: 3FTL). The left panels are the views looking down the axes of the microcrystal “fibrils” with the neighboring dry interfaces depicted as a solvent-accessible surface (gray) to show the tight interdigitation of the side chains. The intersheet hydrogen bonds are shown as yellow dashed lines (only a unique set are shown, not symmetry equivalent bonds). The coloring scheme is white for main-chain carbon, yellow for side chain carbon, blue for nitrogen, and red for oxygen. The position of the two-fold screw axes that relate the individual molecules in the fibril are indicated with black hurricane symbols. The right panels are the view from the side of the fibrils showing only the β sheet corresponding to the colored strand from the left panel. The intrasheet hydrogen-bonds are shown (black for main-chain only bonds and yellow for any side chain interactions) and the coloring of the main-chain carbons of individual strands alternates blue and white. The front face of the sheet in (A) has two Asn ladders and a Phe ladder. The peptide in (B) is actually comprised of two short β strands with a kink between them. The kink allows the Asn in the ladder to make a hydrogen bond to the main-chain oxygen of residue three (Gly) within the same molecule. In (A) the spacing between the repetitive structures is indicated (the left panel has only the average spacing between main-chain atoms because the intersheet distances are not related by crystallographic translations along unit cells). Structure 2010 18, 1244-1260DOI: (10.1016/j.str.2010.08.009) Copyright © 2010 Elsevier Ltd Terms and Conditions

Figure 3 The β-Solenoid Motif in HET-s The left view is a ribbon representation of the HET-s PFD fibril with the peptide chains alternating blue and white and a ball on the N-termini (residue 225). The four β strands are numbered and with “a” and “b” designations for the codirectional strands that are broken by a short kink and “–” and “+” designations for the strands from the molecule below and above the central white one. In both views, it is clear the side chain interactions between the two sheets occur between strands 1 and 4 of the same molecule and between strands 2 and 3 of neighboring subunits. The right view is 90° rotated from the left and is showing only the Cα trace of the cross-β core and the four Asn side chains in the interior of the core that form a double Asn ladder. The absence of the visible hydrogen-bond network in the Asn ladder reflects the limitations of the technique and refinement method rather than the actual conformation of the Asn side chains (see main text). Structure 2010 18, 1244-1260DOI: (10.1016/j.str.2010.08.009) Copyright © 2010 Elsevier Ltd Terms and Conditions

Figure 4 Polymorphism in Amyloids (A) The effect of packing polymorphism (left panel) and side chain polymorphism (right panel) on the surface features of amyloids. The left panel compares the packing polymorphic structures of the peptide NVGSNTY (PDB 3FTK top and 3FTL bottom) with three orthogonal views. The right panel shows a single view of the peptide LVEALYL (PDB 3HYD) in the true crystal structure conformation on the left and with the Glu side chain rotated to its most favored conformation while maintaining its hydrogen bond network on the right. The solvent-accessible surfaces are colored by atom with yellow for carbon, blue for nitrogen and red for oxygen. (B) The HET-s PFD surface showing a complete 360° twist of the fibril (broken into two panels). The amino acid residues are colored yellow for nonpolar (F,W,Y,P,V,A,I,L,C,M,G) green for polar (S,T,N,Q,H) and blue (R,K) and red (D,E) for charged. The alternating surface charges on the amyloid core are more visible in the top view whereas the long loop connecting strands 2 and 3 is the largely yellow and green stripe of less ordered features visible in the bottom view. Structure 2010 18, 1244-1260DOI: (10.1016/j.str.2010.08.009) Copyright © 2010 Elsevier Ltd Terms and Conditions