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Stabilization of secondary structure elements by NLIs. The interplay between local secondary structure
elements and hydrophobic NLIs
Most nucleation models of folding assume that secondary structure elements that form the nucleus (or
other sub-domain structures) are formed first and then stabilized by NLIs while in other models (e.g. the
loop hypothesis) this stabilization is not the cause for the addition of the NLIs but rather a consequence of
the formation of NLIs between disordered segments. Here we review some experiments where this
question was addressed. Wright et al. studied the refolding of sperm whale apomyoglobin (Cavagnero,
Dyson et al. 1999; Cavagnero, Nishimura et al. 2001) (Kay and Baldwin 1996; Kay, Ramos et al. 1999).
It was shown that for the fast intermediate state, even when the local structure is destabilized by
mutations, the (hydrophobic) NLIs within the core of the protein are effective. In a complementary study,
a polar to hydrophobic substitution that was introduced (in helix E, H64F) (Garcia, Nishimura et al. 2000)
resulted in enhanced helix stability due to an enhanced non-local interaction.
Redford studied folding of the small (87 residues) four helix bundle protein, Im7 (Knowling,
Bartlett et al. ; Knowling, Figueiredo et al. 2009). It was shown that the interaction of the fourth helix is
not dependent on its helicity but rather on the presence of non-polar residues that contribute NLIs with
the previously formed triple helix bundle of the folding intermediate. These examples suggest that NLIs
can be effective even without pre ordering of local elements. Serrano and coworkers studied the relative
contribution of LIs vs. NLIs in the folding rate and stability of proteins by engineering enhanced
interactions. (Munoz, Cronet et al. 1996; Munoz and Serrano 1996) they concluded that secondary
structure elements have low specificity for the native state, also stabilizing alternative conformations
which gives a clue as to why natural proteins have such low helical propensities, as compared to what is
attainable with synthetic peptides. In another study(Prieto, Wilmans et al. 1997) Serrano group
demonstrated that NLIs can overcome strong non-native secondary structure propensities and, more
important, that optimisation of folding speed and co-operativity requires the latter to be relatively small.
Several other examples were reported where stabilization of LIs increased and sometimes decreased the
folding rate.(Bofill, Simpson et al. 2005) Niggemann and Steipe (Niggemann and Steipe 2000) used
structural motifs’ engineering and suggest that LIs contribut to stability of the folded molecules while the
NLIs are responsible for the cooperativity of the folding transition. . In a theoretical study Baker and
coworkers examined the balance between LIs and NLIs using extension of Zwanzig’s (Zwanzig
1995)model and also concluded that both types are enriched during the folding transition. (Doyle, Simons
et al. 1997)
References
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Cavagnero, S., C. Nishimura, et al. (2001). "Conformational and dynamic characterization of the
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