The potential for engineering stable proteins with
multiple amino acid substitutions was explored. Eleven
lysine, five methionine, two tryptophan, one glycine, and
three threonine substitutions were simultaneously made
in barley chymotrypsin inhibitor-2 (CI-2) to substantially
improve the essential amino acid content of the protein.
These substitutions were chosen based on the three-dimensional
structure of CI-2 and an alignment of homologous sequences.
The initial engineered protein folded into a wild-type-like
structure, but had a free energy of unfolding of only 2.2
kcal/mol, considerably less than the wild-type value of
7.5 kcal/mol. Restoration of the lysine mutation at position
67 to the wild-type arginine increased the free energy
of unfolding to 3.1 kcal/mol. Subsequent cysteine substitutions
at positions 22 and 82 resulted in disulfide bond formation
and a protein with nearly wild-type thermodynamic stability
(7.0 kcal/mol). None of the engineered proteins retained
inhibitory activity against chymotrypsin or elastase, and
all had substantially reduced inhibitory activity against
subtilisin. The proteolytic stabilities of the proteins
correlated with their thermodynamic stabilities. Reduction
of the disulfide bond resulted in substantial loss of both
thermodynamic and proteolytic stabilities, confirming that
the disulfide bond, and not merely the cysteine substitutions,
was responsible for the increased stability. We conclude
that it is possible to replace over a third of the residues
in CI-2 with minimal disruption of stability and structural
integrity.