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: firstname.lastname@example.org.Show MeSH
Related in: MedlinePlus
Mentions: As an alternative method of determining the extent of structure formation in the Tho1 SAP transition state, we plotted ΔΔG‡-D against ΔΔGD-N for each of our Φ-value mutants (Fig. 4). By comparison with Brønsted analysis  and Leffler α-values  of organic chemistry, linearity among residues present in the same region of the protein (e.g. within an element of secondary structure) indicates that this region is equally formed in the transition state. The gradient of the line gives the extent of formation of this region on a reaction coordinate of free energy . Outliers in this analysis can indicate long-range contacts. Depending on the position of the outlier (i.e. above or below the trend line), a point may indicate long-range contacts formed in the transition state, or may indicate contacts formed in the native state but not present 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.