Background: Rop is an RNA binding, dimeric, four-helix bundle protein with
a well-defined, regular hydrophobic core ideally suited for redesign studie
s. A family of Rop variants in which the hydrophobic core was systematicall
y redesigned has previously been created and characterized.
Results: We present a structural and thermodynamic analysis of Ala(2)lle(2)
-6, a variant of Rop with an extensively redesigned hydrophobic core. The s
tructure of Ala(2)lle(2)-6 reveals a completely new fold formed by a confor
mational "flip" of the two protomers around the dimeric interface. The free
-energy profile of Ala(2)lle(2)-6 is also very different from that of wild-
type Rop. Ala(2)lle(2)-6 has a higher melting temperature than Rep, but und
ergoes a slightly smaller free-energy change on unfolding.
Conclusions: The structure of Ala(2)lle(2)-6, along with molecular modeling
results, demonstrate the importance of tight packing of core residues and
the adoption of favorable core side chain rotamer values in determining hel
ix-helix interactions in the four-helix bundle fold. Structural disorder at
the N and C termini of Ala(2)lle(2)-6 provides a basis for the large diffe
rences in the enthalpy and entropy of Ala(2)lle(2)-6 folding compared with
wildtype Rep.