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PDBsum entry 2kbu
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References listed in PDB file
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Key reference
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Title
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Evaluating beta-Turn mimics as beta-Sheet folding nucleators.
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Authors
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A.A.Fuller,
D.Du,
F.Liu,
J.E.Davoren,
G.Bhabha,
G.Kroon,
D.A.Case,
H.J.Dyson,
E.T.Powers,
P.Wipf,
M.Gruebele,
J.W.Kelly.
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Ref.
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Proc Natl Acad Sci U S A, 2009,
106,
11067-11072.
[DOI no: ]
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PubMed id
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Abstract
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Beta-turns are common conformations that enable proteins to adopt globular
structures, and their formation is often rate limiting for folding. Beta-turn
mimics, molecules that replace the i + 1 and i + 2 amino acid residues of a
beta-turn, are envisioned to act as folding nucleators by preorganizing the
pendant polypeptide chains, thereby lowering the activation barrier for
beta-sheet formation. However, the crucial kinetic experiments to demonstrate
that beta-turn mimics can act as strong nucleators in the context of a
cooperatively folding protein have not been reported. We have incorporated 6
beta-turn mimics simulating varied beta-turn types in place of 2 residues in an
engineered beta-turn 1 or beta-bulge turn 1 of the Pin 1 WW domain, a
three-stranded beta-sheet protein. We present 2 lines of kinetic evidence that
the inclusion of beta-turn mimics alters beta-sheet folding rates, enabling us
to classify beta-turn mimics into 3 categories: those that are weak nucleators
but permit Pin WW folding, native-like nucleators, and strong nucleators. Strong
nucleators accelerate folding relative to WW domains incorporating all
alpha-amino acid sequences. A solution NMR structure reveals that the native Pin
WW beta-sheet structure is retained upon incorporating a strong E-olefin
nucleator. These beta-turn mimics can now be used to interrogate protein folding
transition state structures and the 2 kinetic analyses presented can be used to
assess the nucleation capacity of other beta-turn mimics.
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Figure 1.
β-Turn mimics studied.
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Figure 2.
Comparison of the solution structures of the Pin1 WW domain.
(A) Superposition of 12 structures of the WT protein (36; PDB ID
code 2kcf) (B) Superposition of 15 structures of variant C-4
(PDB ID code 2kbu). (C) Superposition of a low-energy structure
from each of the ensembles in (A) and (B). The inset shows the
structure of dipeptide replacement 4 in loop 1.
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