Fig. 2. Designing sequences with varied compaction.
(A) Pie chart of the sequence composition of αSyn, A1-LCD, LAF-1-RGG, and FUS-PLD. Amino acids are grouped as negative (D and E), positive (R and K), aromatic (Y, W, and F), polar (S, T, N, Q, H, and C), aliphatic (A, V, I, L, M, and P), and glycine. (B) Design of compact (green lines) and expanded (orange lines) variants for αSyn, A1-LCD, LAF-1-RGG, and FUS-PLD. Each accepted Monte Carlo step thus gives rise to a sequence that differs from the previous by the position of the two swapped residues. Each Monte Carlo step therefore corresponds to a different sequence, whose ensemble averaged Rg is evaluated by either MD simulations or alchemical free-energy calculations. The gray horizontal line indicates the Rg of the WT sequence.