 |
PDBsum entry 1zcn
|
|
|
|
References listed in PDB file
|
 |
|
Key reference
|
|
|
Title
|
|
Structure-Function-Folding relationship in a ww domain.
|
|
|
Authors
|
|
M.Jäger,
Y.Zhang,
J.Bieschke,
H.Nguyen,
M.Dendle,
M.E.Bowman,
J.P.Noel,
M.Gruebele,
J.W.Kelly.
|
|
|
Ref.
|
|
Proc Natl Acad Sci U S A, 2006,
103,
10648-10653.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Abstract
|
|
|
Protein folding barriers result from a combination of factors including
unavoidable energetic frustration from nonnative interactions, natural variation
and selection of the amino acid sequence for function, and/or selection pressure
against aggregation. The rate-limiting step for human Pin1 WW domain folding is
the formation of the loop 1 substructure. The native conformation of this
six-residue loop positions side chains that are important for mediating
protein-protein interactions through the binding of Pro-rich sequences.
Replacement of the wild-type loop 1 primary structure by shorter sequences with
a high propensity to fold into a type-I' beta-turn conformation or the
statistically preferred type-I G1 bulge conformation accelerates WW domain
folding by almost an order of magnitude and increases thermodynamic stability.
However, loop engineering to optimize folding energetics has a significant
downside: it effectively eliminates WW domain function according to
ligand-binding studies. The energetic contribution of loop 1 to ligand binding
appears to have evolved at the expense of fast folding and additional protein
stability. Thus, the two-state barrier exhibited by the wild-type human Pin1 WW
domain principally results from functional requirements, rather than from
physical constraints inherent to even the most efficient loop formation process.
|
|
|
|
|
|
|
|
Figure 1.
Fig. 1. Loop structures and sequences of WW domains. (a)
Backbone diagram of the loop 1 substructure in WT Pin WW
(residues S16–R21) [Protein Data Bank (PDB) ID code 1PIN]. (b)
Backbone diagram of the loop 1 substructure in WT FBP WW
(residues T13–K17) (PDB ID code 1E01). Backbone H-bonds are
indicated by black dotted lines. (c) Aligned sequences of the WT
Pin WW domain (variant 1) and loop 1 redesigned variants 2–9
and the redesigned and sequence-minimized FBP WW variants (10
and 11).  -strand residues are
colored blue, residues that were mutated or deleted upon loop 1
redesign are in red, and all other residues are in gray.
|
|
Figure 3.
Fig. 3. Effect of loop 1 redesign on WW domain stability.
(a) Normalized equilibrium unfolding transitions for Pin WW
(variant 1) and variants 2–6 with either a confirmed (2) or
predicted (3–6) (3:5) type-I bulge turn. (b) Normalized
equilibrium unfolding transitions for variants 1 and 7–9 with
either a confirmed (7) or predicted (8, 9) (2:2) type-I' -hairpin
turn. (c) Normalized equilibrium unfolding transitions for FBP
(WW variant 10) with a confirmed (3:5) type-I G1 bulge turn and
variant 11 with a predicted (4:6) loop.
|
|
|
|
|
|
|
|
|
|
