Figure 3

Modeling. (A) Alignment of the amino acid sequences of Pv D₁r and VrD2, a defensin isolated from Vigna radiata. The lines below the cysteines of VrD2 indicate the disulfide bound formation and paring among the cysteine residues. The three different amino acid residues between the two sequences are indicated by asterisks. (B) Three-dimensional structure of Pv D₁r, modeled with the Modeller program and based on the structure of the V. radiate defensin VrD2 (pdb CODE 2GL1). Dark gray represents the β-sheets; gray represents the α-helix; and light gray lines represent the unstructured elements. A methionine residue (purple) was added as a requirement for cloning proteins into the pET-32 EK/LIC vector. The four disulfide bridges are shown by the interconnection of the cysteines residues shown in yellow. The sulfur is shown in green, the nitrogen in blue and the oxygen in red. (C) Overlap of the three-dimensional structures of Pv D₁r (light gray) and Vigna radiata defensin 2 (VrD2) (code pdb 2GL1; in dark gray. (D and E) Three-dimensional structure of Pv D₁r with a surface charge; the negative surface charge is shown in red, and the positive surface charge is shown in blue. In E the structure is rotated 180º in relation to D. For an additional explanation of the color usage in this figure, please refer to the web version of the article.