A new computer program (CORE) is described that predicts
core hydrophobic sequences of predetermined target protein
structures. A novel scoring function is employed, which for
the first time incorporates parameters directly correlated
to free energies of unfolding (ΔGu),
melting temperatures (Tm), and cooperativity.
Metropolis-driven simulated annealing and low-temperature
Monte Carlo sampling are used to optimize this score, generating
sequences predicted to yield uniquely folded, stable proteins
with cooperative unfolding transitions. The hydrophobic
core residues of four natural proteins were predicted using
CORE with the backbone structure and solvent exposed residues
as input. In the two smaller proteins tested (Gβ1,
11 core amino acids; 434 cro, 10 core amino acids), the
native sequence was regenerated as well as the sequence
of known thermally stable variants that exhibit cooperative
denaturation transitions. Previously designed sequences
of variants with lower thermal stability and weaker cooperativity
were not predicted. In the two larger proteins tested (myoglobin,
32 core amino acids; methionine aminopeptidase, 63 core
amino acids), sequences with corresponding side-chain conformations
remarkably similar to that of native were predicted.