Fig 5. Properties and dynamics of the isolated E domain of hGBP1.

(A) The sequence of the E domain and preceding helix α11 of the M domain is shown and colored according to the physicochemical properties of the amino acids. The start and end of helix α12 at residues L482 and F565 are indicated by vertical arrows. (B) The structure of the E domain and its interactions with the LG domain (red transparent) and the helix α11 of the M domain (green transparent) are highlighted for the crystal structure of hGBP1 (PDB 1DG3). The residues of α11 and the E domain are colored according to the physicochemical properties of the amino acids: white, hydrophobic; green, polar; blue, positively charged; red, negatively charged. Salt bridges (K228–E575, E458–K504, D479–K487) are indicated with orange dashes and hydrogen bonds (L476/D479–K487) with black dashes. The interacting residues are shown as sticks and labeled. This includes K582 and K587, which form salt bridges with various residues of loop L1 (in yellow) of the LG domain. (C) The two most populated cluster conformations with their occurrence obtained from the MD simulations of the isolated E domain (top) and of α11 plus E domain (bottom). The cluster structures were aligned to the crystal structure of full-length hGBP1 (shown as transparent cartoon) using residues 482–484 for the alignment of the isolated E domain and α11 for alignment of α11 plus E domain. The red points indicate the turns that formed at the different positions of the E domain along with the turn at F565 separating α12 and α13 from each other.