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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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Chevron plots for L31W mutants. (a) pseudo-wildtype (black), Y5F (red), Q12A (orange), L13A (green), K14A (light blue), K14G (dark blue). (b) pseudo-wildtype (black), S23A (red), I36A (orange), I36V (green), D39A (light blue), D39N (dark blue). (c) pseudo- wildtype (black), L8A (red), T9A (orange), V10G (green), Q12G (light blue), L16A (dark blue). (d) pseudo-wildtype (black), V24A (red), R34A (orange), L17A (dark green), R20A (light blue), L35A (dark blue). No fit shown for very destabilised mutants.
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f0010: Chevron plots for L31W mutants. (a) pseudo-wildtype (black), Y5F (red), Q12A (orange), L13A (green), K14A (light blue), K14G (dark blue). (b) pseudo-wildtype (black), S23A (red), I36A (orange), I36V (green), D39A (light blue), D39N (dark blue). (c) pseudo- wildtype (black), L8A (red), T9A (orange), V10G (green), Q12G (light blue), L16A (dark blue). (d) pseudo-wildtype (black), V24A (red), R34A (orange), L17A (dark green), R20A (light blue), L35A (dark blue). No fit shown for very destabilised mutants.

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.


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

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

Chevron plots for L31W mutants. (a) pseudo-wildtype (black), Y5F (red), Q12A (orange), L13A (green), K14A (light blue), K14G (dark blue). (b) pseudo-wildtype (black), S23A (red), I36A (orange), I36V (green), D39A (light blue), D39N (dark blue). (c) pseudo- wildtype (black), L8A (red), T9A (orange), V10G (green), Q12G (light blue), L16A (dark blue). (d) pseudo-wildtype (black), V24A (red), R34A (orange), L17A (dark green), R20A (light blue), L35A (dark blue). No fit shown for very destabilised mutants.
© Copyright Policy - CC BY
Related In: Results  -  Collection

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

f0010: Chevron plots for L31W mutants. (a) pseudo-wildtype (black), Y5F (red), Q12A (orange), L13A (green), K14A (light blue), K14G (dark blue). (b) pseudo-wildtype (black), S23A (red), I36A (orange), I36V (green), D39A (light blue), D39N (dark blue). (c) pseudo- wildtype (black), L8A (red), T9A (orange), V10G (green), Q12G (light blue), L16A (dark blue). (d) pseudo-wildtype (black), V24A (red), R34A (orange), L17A (dark green), R20A (light blue), L35A (dark blue). No fit shown for very destabilised mutants.
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.

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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