Aromatic residues engineered into the beta-turn nucleation site of ubiquitin lead to a complex folding landscape, non-native side-chain interactions, and kinetic traps

Rea, Anita M., Simpson, Emma R., Meldrum, Jill K., Williams, Huw E. L. and Searle, Mark S. (2008) Aromatic residues engineered into the beta-turn nucleation site of ubiquitin lead to a complex folding landscape, non-native side-chain interactions, and kinetic traps. Biochemistry, 47 48: 12910-12922.


Author Rea, Anita M.
Simpson, Emma R.
Meldrum, Jill K.
Williams, Huw E. L.
Searle, Mark S.
Title Aromatic residues engineered into the beta-turn nucleation site of ubiquitin lead to a complex folding landscape, non-native side-chain interactions, and kinetic traps
Journal name Biochemistry  (ERA 2012 Listed)    (ERA 2010 Rank A)   Check publisher's open access policy
Publication date 2008
Sub-type Article
DOI 10.1021/bi801330r
Volume number 47
Issue number 48
ISSN 0006-2960
Start page 12910
End page 12922
Total pages 13
Place of publication Washington, D.C. USA
Publisher American Chemical Society
Language eng
Subject 1007 Nanotechnology
Abstract The fast folding of small proteins is likely to be the product of evolutionary pressures that balance the search for native-like contacts in the transition state with the minimum number of stable non-native interactions that could lead to partially folded states prone to aggregation and amyloid formation. We have investigated the effects of non-native interactions on the folding landscape of yeast ubiquitin by introducing aromatic substitutions into the β-turn region of the N-terminal β-hairpin, using both the native G-bulged type I turn sequence (TXTGK) as well as an engineered 2:2 XNGK type I′ turn sequence. The N-terminal β-hairpin is a recognized folding nucleation site in ubiquitin. The folding kinetics for wt-Ub (TLTGK) and the type I′ turn mutant (TNGK) reveal only a weakly populated intermediate, however, substitution with X = Phe or Trp in either context results in a high propensity to form a stable compact intermediate where the initial U→I collapse is visible as a distinct kinetic phase. The introduction of Trp into either of the two host turn sequences results in either complex multiphase kinetics with the possibility of parallel folding pathways, or formation of a highly compact I-state stabilized by non-native interactions that must unfold before refolding. Sequence substitutions with aromatic residues within a localized β-turn capable of forming non-native hydrophobic contacts in both the native state and partially folded states has the undesirable consequence that folding is frustrated by the formation of stable compact intermediates that evolutionary pressures at the sequence level may have largely eliminated.
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Created: Wed, 06 Jan 2010, 08:23:32 EST by Ms Lynette Adams on behalf of Aust Institute for Bioengineering & Nanotechnology