Funneled angle landscapes for helical proteins

Abstract

We use crystallographic data for four helical iron proteins (cytochrome c-b₅₆₂, cytochrome c', sperm whale myoglobin, human cytoglobin) to calculate radial and angular signatures as each unfolds from the native state stepwise though four unfolded states. From these data we construct an angle phase diagram to display the evolution of each protein from its native state; and, in turn, the phase diagram is used to construct a funneled angle landscape for comparison with the topography of its folding energy landscape. We quantify the departure of individual helical and turning regions from the areal, angular profile of corresponding regions of the native state. This procedure allows us to identify the similarities and differences among individual helical and turning regions in the early stages of unfolding of the four helical heme proteins.

Keywords: Cytochromes; Myoglobin; Protein folding.

Figure 1:

Specification of the geometrical model for a five-residue segment in cytochrome c-b₅₆₂.

Figure 2.

Ratio vs residue number for cyt c-b₅₆₂: left: ratio T(i)⁄R(i − 3) to R(i + 3) and right: ratio T(i)⁄R(i − 5) to R(i + 5)

Figure 3.

Angle phase diagrams for cyt c-b₅₆₂, (top): {γ vs α} and {β vs α} native states, (bottom) : {γ vs α} and {β vs α} sixth extended states.

Figure 4.

Angle phase diagrams for h-Cygb, (top): {γ vs α} and {β vs α} native states and (bottom) : {γ vs α} and {β vs α} sixth extended states.

Figure 5.

Top: Funneled angle landscape for cyt c-b₅₆₂ (left: [γ, α] vs unfolding stage, right: [β, α] vs unfolding stage. Bottom: Funneled angle landscape for h-Cygb; [β, α] vs unfolding stage.