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. 2002 Nov 27;99(25):16052–16057. doi: 10.1073/pnas.252340199

Table 1.

Designed sequences and self-assembly behavior as a function of the molecule net charge

Sequence
Net charge of the molecule
+1 Neutral −1 >1
No. 1 KTVIIE Ac—K+TVIIE—Am Ac—K+TVIIE—am Ac—KTVIIE—Am N+—K+TVIIE—C
pH 2.6, 98%; β pH 7.4, 100%; β pH 12.5, 100%; rc + β pH 2.6, 92%, +2; rc
No. 3 STVIIE N+STVIIE—C Ac—STVIIE—Am Ac—STVIIE—am
pH 2.6, 92%; β pH 2.6, 98%; rc pH 7.4, 100%; rc + β
No. 4 KTVIIT Ac—K+TVIIT—Am Ac—KTVIIT—Am N—KTVIIT—C N+—K+TVIIT—C
pH 2.6, 100%; rc pH 12.5, 100%; rc pH 12.5, 100%; rc pH 2.6, 97%, +2; rc
No. 5 STVIIT N+STVIIT—C Ac—STVIIT—Am Ac—STVIIT—C
pH 2.6, 97%; β pH 2.6, 100%; β pH 7.4, 100%; rc + β
N+STVIIT—C
pH 6.0, 96%; β
No. 6 KTVLIE Ac—K+TVLIE—Am Ac—K+TVLIE—Am Ac—KTVLIE—Am N+—K+TVLIE—C
pH 2.6, 98%; rc pH 7.4, 100%; β pH 12.5, 100%; rc pH 2.6, 92%, +2; rc
No. 7 KTVIVE Ac—K+TVIVE—Am Ac—K+TVIVE—Am Ac—KTVIVE—Am N+—K+TVIVE—C
pH 2.6, 98%; rc pH 7.4, 100%; β pH 12.5, 100%; rc pH 2.6, 92%, +2; rc
No. 8 KTVIYE Ac—K+TVIYE—Am Ac—K+TVIYE—Am Ac—KTVIYE—Am N+—K+TVIYE—C
pH 2.6, 98%; rc pH 7.4, 100%; rc pH 12.5, 100%; rc pH 2.6, 92%, +2; rc
No. 9 STVIYE N+STVIYE—C Ac—STVIYE—Am Ac—STVIYE—Am
pH 2.6, 92%; rc + β pH 2.6, 98%; rc pH 7.4, 100%; rc + β

rc and β annotations refer to the CD signature of the peptide at the pH given. “rc” indicates random coil CD spectrum, “β” stands for β-sheet CD spectrum, and “rc + β” indicates the presence of both β-structure and unfolded conformations in solution. Bold annotations correspond to sequences and conditions that showed amyloid fibril formation as indicated by EM and x-ray diffraction data.

*

Sequences are given using the one-letter code for amino acid residues. Amino acids modelled for the six-residue β-strands of the six-stranded polymeric β-sheet are: at positions 1 and 6, K, E, T, and S; at positions 2 and 5, K, E, T, S, V, I, L, Y and W; and at positions 3 and 4, V, I, L, Y and W. The predicted sequence stability is No. 1 > 3 > 6 > 7 > 8 > 9 > 5 > 4.

Superscripts “+” and “−” stand for a formal positive and negative charge, respectively. “Ac” stands for an N terminus protected with an acetyl group, “Am” for a C terminus protected with an amide group, “N” for a free N terminus, and “C” for a free C terminus. pH and percentage of molecules with a given net charge at that pH are given below each peptide sequence. This percentage has been calculated by using the Arrhenius equation (pH = pK + log([acceptor]/[donor])) and the following pKa values (31): free N terminus, pKa(S) = 7.34; pKa(K) = 7.10. Free C terminus, pKa(T) = 4.07; pKa(E) = 3.65. Charged side chains, pKa(K) = 10.60; pKa(E) = 4.25.

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