Folding simulation experiments

I. Comparison with two-body potentials

-(total Energy) of 6 pre-transition, 20 post-transition and the native structure of CI2 using Miyazawa-Jernigan (MJ) potentials

Though the native structure is clearly distinguished from all the pre- and post-transition conformations, the MJ potentials could not clearly differentiate the pre-transition structures from the post-transition structures. Also, conformation #5 is known to have a higher probability of folding (0.15) as compared to the other five pre-transition structures (which all have near zero probabilities of folding correctly). This is not captured by the MJ potentials either (in fact, conformation #1 has a better score than conformation #5).

II. Four-body potentials applied to pre-transition, post-transition and native structures of sh3

(preliminary results)

W-20L5T total log-likelihood scores for 9 pre-transition, 12 post-transition conformations and the

native structure of sh3 are shown above. As with the case of CI2, pre- and post-transition conformations are clearly distinguished from the native structure. The first pre-transition structure (UU01) was found to have a 0.10 probability of folding correctly.

W-20L5T profiles for a typical pre-transition (brown line), post-transition (broken blue line) and

the native structure of SH3 (cyan line). The core tetrahedra are formed by the residues

Y8, L16,F18, A37, I48 and Y52.