helix-turn-helix motif as an ultrafast independently folding domain: The pathway of folding of Engrailed homeodomain

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 104; no. 22; pp. 9272 - 9277
• Main Authors: Religa, Tomasz L, Johnson, Christopher M, Vu, Dung M, Brewer, Scott H, Dyer, R. Brian, Fersht, Alan R
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 29.05.2007; National Acad Sciences
• Subjects: Biochemistry; Biological Sciences; Chemical equilibrium; Crystal structure; Crystallography, X-Ray; Dihedral angle; Fluorescence; Helix-Turn-Helix Motifs; Kinetics; Leucine - genetics; Leucine - metabolism; Mayors; Models, Molecular; Mutation - genetics; Nuclear Magnetic Resonance, Biomolecular; Osmolar Concentration; Protein Folding; Protein Structure, Tertiary; Proteins; Proteins - chemistry; Proteins - genetics; Proteins - metabolism; Salts; Spectrometry, Fluorescence; Spectrophotometry, Infrared; Table salt; Temperature dependence; Temperature effects; Time Factors
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.0703434104

Helices 2 and 3 of Engrailed homeodomain (EnHD) form a helix-turn-helix (HTH) motif. This common motif is believed not to fold independently, which is the characteristic feature of a motif rather than a domain. But we found that the EnHD HTH motif is monomeric and folded in solution, having essentially the same structure as in full-length protein. It had a sigmoidal thermal denaturation transition. Both native backbone and local tertiary interactions were formed concurrently at 4 x 10⁵ s⁻¹ at 25°C, monitored by IR and fluorescence T-jump kinetics, respectively, the same rate constant as for the fast phase in the folding of EnHD. The HTH motif, thus, is an ultrafast-folding, natural protein domain. Its independent stability and appropriate folding kinetics account for the stepwise folding of EnHD, satisfy fully the criteria for an on-pathway intermediate, and explain the changes in mechanism of folding across the homeodomain family. Experiments on mutated and engineered fragments of the parent protein with different probes allowed the assignment of the observed kinetic phases to specific events to show that EnHD is not an example of one-state downhill folding.