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Figure 1.
The concept of directed domain interface evolution and
building blocks used in this work. (A and B) Comparison of
domain interface engineering with conventional protein
engineering. In the conventional engineering that mimics gene
duplication and sequence divergence (A), the interface
predefined in the starting scaffold is altered/refined, which
tends to produce incremental changes in function. In contrast,
domain interface engineering that mimics gene combination and
sequence divergence (B) produces a new functional site at the
interface between two domains, which can result in a major leap
in protein function. (C) The structure of the Erbin PDZ bound to
a peptide (PDB entry 1MFG). The N and C termini are indicated.
The positions for the new termini of the circularly permutated
PDZ (cpPDZ) are shown with a triangle and residue numbers. Right
shows the surface of the PDZ domain with the peptide as a stick
model, illustrating the shallow binding pocket. (D) The
structure of FN3 (PDB entry 1FNF). The loops that are
diversified to construct combinatorial libraries are labeled.
The termini are also labeled. Note that the N terminus and the
recognition loops are located on the same side of the FN3
protein.
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