Toward full-sequence de novo protein design with flexible templates for human beta-defensin-2

Abstract

In this article, we introduce and apply our de novo protein design framework, which observes true backbone flexibility, to the redesign of human beta-defensin-2, a 41-residue cationic antimicrobial peptide of the innate immune system. The flexible design templates are generated using molecular dynamics simulations with both Generalized Born implicit solvation and explicit water molecules. These backbone templates were employed in addition to the x-ray crystal structure for designing human beta-defensin-2. The computational efficiency of our framework was demonstrated with the full-sequence design of the peptide with flexible backbone templates, corresponding to the mutation of all positions except the native cysteines.

FIGURE 1

Workflow for the new method for fold specificity.

FIGURE 2

Illustration of upper bounds on RMSD and AMBER energy. Lines indicate upper bounds. Data points in the shaded regions are not considered in further calculations.

FIGURE 3

Structure of human β-defensin-2 (chain A) as elucidated by Hoover et al. (60). Its secondary structure consists of a β-sheet made up of three β-strands and an α-helix.

FIGURE 4

Overlay of the 10 structures of human β-defensin-2 used for the flexible design template from MD simulations with the GB implicit solvation model. The structures are snapshots with 1-ns increment.

FIGURE 5

Overlay of the 10 structures of human β-defensin-2 for the flexible design template from MD simulations with explicit water molecules. The structures are snapshots with 0.2-ns increment.

FIGURE 6

Structural alignment of the crystal structure of human β-defensin-2 (chain A) by Hoover et al. (60) (rainbow color), the 5-ns MD-GB structure (light gray), and the 1-ns explicit MD structure (dark gray).

FIGURE 7

Clustering and optimal reordering of the 4266 sequences predicted from all sequence selection models with the flexible templates. Dotted lines indicate cluster boundaries. Different amino acids at the 41 positions are illustrated with different colors.