Unspecific hydrophobic stabilization of folding transition states.


Here we present a method for determining the inference of non-native conformations in the folding of a small domain, alpha-spectrin Src homology 3 domain. This method relies on the preservation of all native interactions after Tyr/Phe exchanges in solvent-exposed, contact-free positions. Minor changes in solvent exposure and free energy of the denatured ensemble are in agreement with the reverse hydrophobic effect, as the Tyr/Phe mutations slightly change the polypeptide hydrophilic/hydrophobic balance. Interestingly, more important Gibbs energy variations are observed in the transition state ensemble (TSE). Considering the small changes induced by the H/OH replacements, the observed energy variations in the TSE are rather notable, but of a magnitude that would remain undetected under regular mutations that alter the folded structure free energy. Hydrophobic residues outside of the folding nucleus contribute to the stability of the TSE in an unspecific nonlinear manner, producing a significant acceleration of both unfolding and refolding rates, with little effect on stability. These results suggest that sectors of the protein transiently reside in non-native areas of the landscape during folding, with implications in the reading of phi values from protein engineering experiments. Contrary to previous proposals, the principle that emerges is that non-native contacts, or conformations, could be beneficial in evolution and design of some fast folding proteins. Study holds ProTherm entries: 14807, 14808, 14809, 14810, 14811, 14812, 14813, 14814, 14815, 14816, 14817, 14818, 14819, 14820, 14821, 14822, 14823, 14824, 14825, 14826, 14827, 14828, 14829, 14830, 14831, 14832 Extra Details: Length calculated from PIR of SH3 domain solvent-exposed; Trp/Phe mutations; hydrophilic/hydrophobic balance; folding nucleus; phi values

Submission Details

ID: bGAuiNHd

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:45 p.m.

Version: 1

Publication Details
Viguera AR;Vega C;Serrano L,Proc. Natl. Acad. Sci. U.S.A. (2002) Unspecific hydrophobic stabilization of folding transition states. PMID:11959988
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Spectrin alpha chain, non-erythrocytic 1 P07751 SPTN1_CHICK
100.0 Spectrin alpha chain, non-erythrocytic 1 Q13813 SPTN1_HUMAN
100.0 Spectrin alpha chain, non-erythrocytic 1 P16546 SPTN1_MOUSE
100.0 Spectrin alpha chain, non-erythrocytic 1 P16086 SPTN1_RAT