Free energy landscapes and thermodynamic features from Protein to DNA based on computational chemistry

Eunae Kim (Chosun Univ.)

I will introduce the general protein folding mechanisms and the results of ab initio folding simulations which were performed for various mini-proteins with a modified all-atom force field using the Generalized Born solvation model (param99MOD5/GBSA). Starting from a fully extended conformation, we were able to locate the native-like structures of the mixed folds with a ββα motif in the global free minimum region at 280 K. The current approach, which combines the more balanced force field with the efficient sampling scheme, demonstrates a clear advantage in free energy based ab-initio predictions of the native structures of mixed folds at all-atom level. In addition, transition state of DNA helical structure was elucidated by structurally mechanical model. Various features of DNA structure will be addressed in this seminar.