M A Willis1, B Bishop, L Regan, A T Brunger. 1. Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.
Abstract
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.
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.
Authors: Yaakov Levy; Samuel S Cho; Tongye Shen; José N Onuchic; Peter G Wolynes Journal: Proc Natl Acad Sci U S A Date: 2005-02-08 Impact factor: 11.205
Authors: Yann Gambin; Alexander Schug; Edward A Lemke; Jason J Lavinder; Allan Chris M Ferreon; Thomas J Magliery; José N Onuchic; Ashok A Deniz Journal: Proc Natl Acad Sci U S A Date: 2009-06-08 Impact factor: 11.205
Authors: Krisna C Duong-Ly; Sandra B Gabelli; Wenlian Xu; Christopher A Dunn; Andrew J Schoeffield; Maurice J Bessman; L Mario Amzel Journal: J Bacteriol Date: 2011-04-29 Impact factor: 3.490