Prediction of folding rates and transition-state placement from native-state geometry
Proteins, 51, 74-84 (2003).
Link to online article.
A variety of experimental and theoretical studies have established
that the folding process of monomeric proteins is strongly influenced
by the topology of the native state. In particular, folding times have
been shown to correlate well with the contact order, a measure of
contact locality. Our investigation focuses on identifying additional
topologic properties that correlate with experimentally measurable
quantities, such as folding rates and transition state placement, for
both two- and three-state folders. The validation against data from
forty experiments shows that a particular topologic property which
measures the interdepedence of contacts, termed cliquishness or
clustering coefficient, can account with statistically significant
accuracy both for the transition state placement and especially for
folding rates. The observed correlations can be further improved by
optimally combining the distinct topologic information captured by
cliquishness and contact order.