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PDBsum entry 3v1e
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De novo protein, metal binding protein
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PDB id
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3v1e
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References listed in PDB file
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Key reference
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Title
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Metal-Mediated affinity and orientation specificity in a computationally designed protein homodimer.
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Authors
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B.S.Der,
M.Machius,
M.J.Miley,
J.L.Mills,
T.Szyperski,
B.Kuhlman.
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Ref.
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J Am Chem Soc, 2012,
134,
375-385.
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PubMed id
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Abstract
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Computationally designing protein-protein interactions with high affinity and
desired orientation is a challenging task. Incorporating metal-binding sites at
the target interface may be one approach for increasing affinity and specifying
the binding mode, thereby improving robustness of designed interactions for use
as tools in basic research as well as in applications from biotechnology to
medicine. Here we describe a Rosetta-based approach for the rational design of a
protein monomer to form a zinc-mediated, symmetric homodimer. Our metal
interface design, named MID1 (NESG target ID OR37), forms a tight dimer in the
presence of zinc (MID1-zinc) with a dissociation constant <30 nM. Without
zinc the dissociation constant is 4 μM. The crystal structure of MID1-zinc
shows good overall agreement with the computational model, but only three out of
four designed histidines coordinate zinc. However, a histidine-to-glutamate
point mutation resulted in four-coordination of zinc, and the resulting metal
binding site and dimer orientation closely matches the computational model (Cα
rmsd = 1.4 Å).
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