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Figure 6.
Schematic Presentation of Helicase Motion. (A) Schematic view
of conformational changes between NS3h subdomains. The NS3h
complexes are simplified as spherical modules (NS3h) and black
lines (ssDNA). The two DNA-binding surfaces (NABS1 and NABS2)
are noted. The yellow dots represent the sites involved in the
coordination of phosphate groups of ssDNA. The W501 side chain
is simplified as a black line. Nucleotides are noted as red
letters. (B) Schematic view of ssDNA in the substrate-binding
groove. Individual DNA residues are presented. The deoxyribose
groups in C2′-endo pucker are labeled B, whereas the others in
C3′-endo pucker are labeled A. The solid-black DNA bases are
in syn orientation. The two DNA-binding surfaces are simplified
as blue and pink modules. The black dashed lines represent
hydrogen bonds between NS3h and the phosphodiester backbone of
DNA, whereas the gray dashed lines are water-mediated
interactions. (C) Fluorescence anisotropy titration in the
absence and presence of ATP mimics. Data were fit to a quadratic
equation to obtain dissociation constants (Kd).
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