FIGURE 6.

Comparison of secondary and three dimensional structures of KR-12 and retro KR-12. Secondary chemical shift (Δδ) was calculated by subtracting random coil αH chemical shift from the experimental αH chemical shift. Stretches of negative values (<0.1) represent alpha-helical structure. (A) KR-12 (B) retro-KR12; white bars represent the peptide in H₂O:D₂O (90:10 v/v) and black bars represents the peptide H₂O:D₂O (90:10 v/v) together with deuterized SDS (1:40, peptide:SDS). The corresponding three dimensional structures are represented by superimposition of the 15 lowest-energy structures (Ribbon and Line structures). (C) Ribbon structure with the lowest energy and surface representation of the structure; hydrophobic residues are highlighted in gray, polar residues in green and positively charged in red. The left view has similar orientation as the ribbon model and the right view is from the back. In the current paper, the KR-12 structure was calculated with higher number of distant constrains, i.e., 245 distant constrains (81 sequential restrains, 54 medium range restrains, 16 H bond restrains) in comparison to 86 distant restrains (37 sequential, 32 medium range, no H bonds) used in a previous study. The RMS deviation from mean coordinate structure for backbone atoms is similar for KR-12 in SDS (0.2 ± 0.05) and KR-12 in D8PG (0.24). Stereochemical quality of the KR-12 structure in SDS is 94 ± 6.11% residues in the most favored Ramachandran region in contrary to 90% residues reported for KR-12 in D8PG (Wang, 2008).