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Protein folding of the SAP domain, a naturally occurring two-helix bundle.

Dodson CA, Arbely E - FEBS Lett. (2015)

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.

View Article: PubMed Central - PubMed

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: c.dodson@imperial.ac.uk.

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Brønsted plot for Tho1 SAP. Mutations colour-coded by position as Leu8/Thr9 (black), helix 1 (red), connecting loop (green), helix 2 (blue), N-terminus (orange). Dashed line indicates linear regression line for helix 1 and Leu8/Thr9. Filled circles indicate mutants where ΔΔGD-N < 2.6 kcal mol−1; open circles indicate mutants where ΔΔGD-N > 2.6 kcal mol−1. Error bars show error from Tables 1 and 2. A minimum error of 10% has been applied to ΔΔG‡-D.
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f0020: Brønsted plot for Tho1 SAP. Mutations colour-coded by position as Leu8/Thr9 (black), helix 1 (red), connecting loop (green), helix 2 (blue), N-terminus (orange). Dashed line indicates linear regression line for helix 1 and Leu8/Thr9. Filled circles indicate mutants where ΔΔGD-N < 2.6 kcal mol−1; open circles indicate mutants where ΔΔGD-N > 2.6 kcal mol−1. Error bars show error from Tables 1 and 2. A minimum error of 10% has been applied to ΔΔG‡-D.

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 [27] and Leffler α-values [28] 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 [29]. 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.


Protein folding of the SAP domain, a naturally occurring two-helix bundle.

Dodson CA, Arbely E - FEBS Lett. (2015)

Brønsted plot for Tho1 SAP. Mutations colour-coded by position as Leu8/Thr9 (black), helix 1 (red), connecting loop (green), helix 2 (blue), N-terminus (orange). Dashed line indicates linear regression line for helix 1 and Leu8/Thr9. Filled circles indicate mutants where ΔΔGD-N < 2.6 kcal mol−1; open circles indicate mutants where ΔΔGD-N > 2.6 kcal mol−1. Error bars show error from Tables 1 and 2. A minimum error of 10% has been applied to ΔΔG‡-D.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4509717&req=5

f0020: Brønsted plot for Tho1 SAP. Mutations colour-coded by position as Leu8/Thr9 (black), helix 1 (red), connecting loop (green), helix 2 (blue), N-terminus (orange). Dashed line indicates linear regression line for helix 1 and Leu8/Thr9. Filled circles indicate mutants where ΔΔGD-N < 2.6 kcal mol−1; open circles indicate mutants where ΔΔGD-N > 2.6 kcal mol−1. Error bars show error from Tables 1 and 2. A minimum error of 10% has been applied to ΔΔG‡-D.
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 [27] and Leffler α-values [28] 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 [29]. 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.

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.

View Article: PubMed Central - PubMed

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: c.dodson@imperial.ac.uk.

Show MeSH
Related in: MedlinePlus