The Relation between α-Helical Conformation and Amyloidogenicity Boris Haimov, Simcha Srebnik  Biophysical Journal  Volume 114, Issue 8, Pages 1869-1877 (April 2018) DOI: 10.1016/j.bpj.2018.03.019 Copyright © 2018 Biophysical Society Terms and Conditions

Figure 1 (a) Distribution of the lengths of α-helices in the PDB (a total of ∼1.96e6). (b) A distribution of α-helices with unique AA sequences (∼0.44e6) is shown. From the ratio 0.44/1.96, we find that only 22.4% of PDB α-helical sequences are unique or that 77.6% are redundant. The figures demonstrate that despite the strong redundancy, the distributions remain similar, with hexapeptide (6 AA-long) helices as the most abundant. To see this figure in color, go online. Biophysical Journal 2018 114, 1869-1877DOI: (10.1016/j.bpj.2018.03.019) Copyright © 2018 Biophysical Society Terms and Conditions

Figure 2 (a) Illustration of (φ,ψ) Ramachandran dihedrals for a given AA transition (pair). Black circles represent carbon atoms, blue circles represent nitrogen atoms, red circles represent oxygen atoms, and purple circles represent side chains. (b) A distribution of PDB α-helical conformations is shown using Ramachandran dihedrals. (c) A distribution of PDB α-helical conformations is shown using (θ,ρ) pairs. The shades represent the abundance of the α-helical conformations: the darkest shade for least abundant and the brightest shade for most abundant conformations. The dark-blue shade in the background represents zero abundance. A total of ∼15.9e6 conformational pairs were sampled from the PDB with ∼15.8e6 pairs within the presented (φ,ψ) and (θ,ρ) ranges. To see this figure in color, go online. Biophysical Journal 2018 114, 1869-1877DOI: (10.1016/j.bpj.2018.03.019) Copyright © 2018 Biophysical Society Terms and Conditions

Figure 3 Dependency of amyloidogenicity on θ and ρ for the three data sets: α-helices with conformations sampled directly from PDB (filled circles), PDB helices broken into hexapeptide α-helices with α-helical conformations estimated from the mean of the strongly peaked (θ, ρ) distribution (open circles), and randomly generated hexapeptide α-helices with estimated α-helical conformations (pentacles). The SEM of every bin is smaller than the marked symbol. To see this figure in color, go online. Biophysical Journal 2018 114, 1869-1877DOI: (10.1016/j.bpj.2018.03.019) Copyright © 2018 Biophysical Society Terms and Conditions

Figure 4 Dependence of the average amyloidogenicity on peptide length for PDB helices. The mean amyloidogenicity value A = 0.55 represents the 50% threshold of hexapeptide sequences. To see this figure in color, go online. Biophysical Journal 2018 114, 1869-1877DOI: (10.1016/j.bpj.2018.03.019) Copyright © 2018 Biophysical Society Terms and Conditions

Figure 5 (a) α-Helical backbone with nonbifurcated hydrogen bonds and with low θ results in exposed backbone and higher amyloidogenicity. (b) α-Helical backbone with bifurcated hydrogen bonds and with high θ results in a shielded backbone and lower amyloidogenicity. Dashed lines represent hydrogen bonds between carbonyl oxygen and amide hydrogen. Enlarged black spheres represent surrounding water molecules or neighboring side-chains that can establish hydrogen bonds with the backbone carbonyls. Residues are not shown, for clarity. Illustrations were prepared with visual molecular dynamics (48). (c) A schematic view of the α-helix basin on the Ramachandran map is shown. The α-helix basin is found near the Oi−1-Ni+1 sterically inaccessible region which is due to interactions between i + 1 amide nitrogen atoms (N) and i − 1 carbonyl oxygen atoms (O) along the α-helix backbone, where i represents the index of backbone amino acid residues. The tangent line between the sterically inaccessible region and the α-helix basin dictates the negative proportionality between ρ and θ for θ > 0. To see this figure in color, go online. Biophysical Journal 2018 114, 1869-1877DOI: (10.1016/j.bpj.2018.03.019) Copyright © 2018 Biophysical Society Terms and Conditions

Figure 6 Distribution of estimated (θ,ρ) pairs of experimentally verified nonamyloidogenic sequences (triangles) and experimentally verified amyloidogenic sequences (squares). The average conformations of the nonamyloidogenic sequences and amyloidogenic sequences are shown by “−“ and “+,” respectively. A total of 1480 sequences was acquired from the AMYLOAD web server (15), with 1037 nonamyloidogenic and 443 amyloidogenic sequences. The distribution confirms that, on average, amyloidogenic sequences have lower θ and higher ρ than nonamyloidogenic sequences. To see this figure in color, go online. Biophysical Journal 2018 114, 1869-1877DOI: (10.1016/j.bpj.2018.03.019) Copyright © 2018 Biophysical Society Terms and Conditions

Figure 7 Distribution of the homogeneous transitions of α-helical conformations. Single-letter amino acid (AA) codes are placed on the mean-calculated conformation. Letters correspond to AAs: uncharged polar (NQST), acidic (ED), basic (KRH), hydrophobic (AFILMVWY), and special (CGP). Dashed horizontal and vertical lines divide the conformational space into four quadrants, where the upper-left quadrant is the least amyloidogenic whereas the lower-right quadrant is the most amyloidogenic. Threshold values of θT ≈ 12.8° and ρT ≈ 3.61 [res/turn] correspond to an amyloidogenicity score of 0.55. To see this figure in color, go online. Biophysical Journal 2018 114, 1869-1877DOI: (10.1016/j.bpj.2018.03.019) Copyright © 2018 Biophysical Society Terms and Conditions