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PDBsum entry 2f2w
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Signaling protein
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PDB id
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2f2w
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References listed in PDB file
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Key reference
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Title
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Cooperative propagation of local stability changes from low-Stability and high-Stability regions in a sh3 domain.
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Authors
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S.Casares,
O.López-Mayorga,
M.C.Vega,
A.Cámara-Artigas,
F.Conejero-Lara.
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Ref.
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Proteins, 2007,
67,
531-547.
[DOI no: ]
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PubMed id
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Abstract
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Site-directed mutagenesis has been used to produce local stability changes at
two regions of the binding site surface of the alpha-spectrin SH3 domain
(Spc-SH3) differing in their intrinsic stability. Mutations were made at residue
56, located at the solvent-exposed side of the short 3(10) helix, and at residue
21 in the tip of the flexible RT-loop. NMR chemical-shift analysis and X-ray
crystallography indicated negligible changes produced by the mutations in the
native structure limited to subtle rearrangements near the mutated residue and
at flexible loops. Additionally, mutations do not alter importantly the SH3
binding site structure, although produce significant changes in its affinity for
a proline-rich decapeptide. The changes in global stability measured by
differential scanning calorimetry are consistent the local energy changes
predicted by theoretical models, with the most significant effects observed for
the Ala-Gly mutations. Propagation of the local stability changes throughout the
domain structure has been studied at a per-residue level of resolution by
NMR-detected amide hydrogen-deuterium exchange (HX). Stability propagation is
remarkably efficient in this small domain, apparently due to its intrinsically
low stability. Nevertheless, the HX-core of the domain is not fully cooperative,
indicating the existence of co-operative subunits within the core, which is
markedly polarized. An equilibrium phi-analysis of the changes in the apparent
Gibbs energies of HX per residue produced by the mutations has allowed us to
characterize structurally the conformational states leading to HX. Some of these
states resemble notably the folding transition state of the Spc-SH3 domain,
suggesting a great potential of this approach to explore the folding energy
landscape of proteins. An energy perturbation propagates more effectively from a
flexible region to the core than in the opposite direction, because the former
affects a broader region of the energy landscape than the latter. This might be
of importance in understanding the special thermodynamic signature of the
SH3-peptide interaction and the relevance of the dual character of SH3 binding
sites.
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Figure 3.
Figure 3. Stereo-view of the 2F[o]-F[c] electron density map of
the R21G  -spectrin
SH3 mutant. The type I  -turn
is shown in green and the type II -turn
is shown in yellow. The figure was created with PyMOL (DeLano,
W.L. The PyMOL Molecular Graphics System, DeLano Scientific, San
Carlos, CA).
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Figure 7.
Figure 7. Ribbon representations of the Spc-SH3 domain
structure showing in color codes the probabilities of
HX-competent states for each residue that are either cooperative
(right-hand side panels) or noncooperative (left-hand side
panels) with the interaction probed by each mutation. The color
bar at the bottom of the figure indicates the relative scale of
probabilities.
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2007,
67,
531-547)
copyright 2007.
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