Dramatic structural and thermodynamic consequences of repacking a protein's hydrophobic core.
BACKGROUND
Rop is an RNA binding, dimeric, four-helix bundle protein with a well-defined, regular hydrophobic core ideally suited for redesign studies. A family of Rop variants in which the hydrophobic core was systematically redesigned has previously been created and characterized.


RESULTS
We present a structural and thermodynamic analysis of Ala2Ile2-6, a variant of Rop with an extensively redesigned hydrophobic core. The structure of Ala2Ile2-6 reveals a completely new fold formed by a conformational "flip" of the two protomers around the dimeric interface. The free-energy profile of Ala2Ile2-6 is also very different from that of wild-type Rop. Ala2Ile2-6 has a higher melting temperature than Rop, but undergoes a slightly smaller free-energy change on unfolding.


CONCLUSIONS
The structure of Ala2Ile2-6, 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 helix-helix interactions in the four-helix bundle fold. Structural disorder at the N and C termini of Ala2Ile2-6 provides a basis for the large differences in the enthalpy and entropy of Ala2Ile2-6 folding compared with wildtype Rop.
Willis
M A
MA
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.
Bishop
B
B
Regan
L
L
Brunger
A T
AT
D000595:Amino Acid Sequence; D019943:Amino Acid Substitution / Q000235:genetics; D001426:Bacterial Proteins / Q000138:chemical synthesis / Q000737:chemistry* / Q000235:genetics; D003086:Bacteriocin Plasmids / Q000737:chemistry / Q000235:genetics; D002942:Circular Dichroism; D003460:Crystallization; D018360:Crystallography, X-Ray; D019281:Dimerization; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D015202:Protein Engineering; D017510:Protein Folding; D020033:Protein Isoforms / Q000138:chemical synthesis / Q000737:chemistry / Q000235:genetics; D017433:Protein Structure, Secondary; D016601:RNA-Binding Proteins / Q000138:chemical synthesis / Q000737:chemistry* / Q000235:genetics; D011994:Recombinant Proteins / Q000138:chemical synthesis; D013816:Thermodynamics
D001426:Bacterial Proteins; D020033:Protein Isoforms; D016601:RNA-Binding Proteins; D011994:Recombinant Proteins; C054243:Rop protein, ColE1 plasmid