The first fully automated design and experimental validation of a
novel sequence for an entire protein is described. A
computational design algorithm based on physical chemical
potential functions and stereochemical constraints was used
to screen a combinatorial library of
1.9 × 1027 possible amino acid sequences for
compatibility with the design target, a beta-beta-alpha
protein motif based on the polypeptide backbone structure
of a zinc finger domain. A BLAST search shows that the
designed sequence, full sequence design 1 (FSD-1), has very
low identity to any known protein sequence. The solution
structure of FSD-1 was solved by nuclear magnetic resonance
spectroscopy and indicates that FSD-1 forms a compact
well-ordered structure, which is in excellent agreement
with the design target structure. This result demonstrates
that computational methods can perform the immense
combinatorial search required for protein design, and it
suggests that an unbiased and quantitative algorithm can be
used in various structural contexts.
B I. Dahiyat, Division of Chemistry and Chemical Engineering,
California Institute of Technology, mail code 147-75, Pasadena, CA
91125, USA.
S. L. Mayo, Howard Hughes Medical institute and Division of
Biology, California Institute of Technology, mail code 147-75, Pasadena, CA 91125, USA.