Protein folding of the SAP domain, a naturally occurring two-helix bundle.
Bottom Line: The SAP domain from the Saccharomyces cerevisiae Tho1 protein is comprised of just two helices and a hydrophobic core and is one of the smallest proteins whose folding has been characterised.Φ-value analysis revealed that Tho1 SAP folds through a transition state where helix 1 is the most extensively formed element of secondary structure and flickering native-like core contacts from Leu35 are also present.The contacts that contribute most to native state stability of Tho1 SAP are not formed in the transition state.
Affiliation: MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, UK; Molecular Medicine, National Heart & Lung Institute, Imperial College London, SAF Building, London SW7 2AZ, UK. Electronic address: email@example.com.Show MeSH
Mentions: As an additional check on data fitting, we observed that the measured rate constant for R20A in 0 M urea is at, or is a little above, the midpoint of the transition (visual inspection of Fig. 2d). This places an upper bound of 1500 s−1 on kf (half the measured observed rate constant), consistent with the values in Supplementary Table SI. As a final check on our estimate of Φ, we recalculated this parameter using a ΔΔGN-D of 2.1 kcal mol−1. This is the most destabilised transition we have been able to fit (D39N) and represents the minimum value of ΔΔGN-D (maximum value of Φ) for this mutant. We are thus confident in an estimate of Φ for R20A as <0.3.
Affiliation: MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, UK; Molecular Medicine, National Heart & Lung Institute, Imperial College London, SAF Building, London SW7 2AZ, UK. Electronic address: firstname.lastname@example.org.