Abstract
The results of minimal model calculations indicate that the stability and the kinetic accessibility of the native
state of small globular proteins are controlled by few “hot” sites. By means of molecular dynamics
simulations around the native conformation, which describe the protein and the surrounding solvent at the
all-atom level, an accurate and compact energetic map of the native state of the protein is generated. This
map is further simplified by means of an eigenvalue decomposition. The components of the eigenvector
associated with the lowest eigenvalue indicate which hot sites are likely to be responsible for the stability
and for the rapid folding of the protein. The comparison of the results of the model with the findings of
mutagenesis experiments performed for four small proteins show that the eigenvalue decomposition method
is able to identify between 60% and 80% of these (hot) sites.
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