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Bulletin of the Korean Chemical Society (BKCS)

ISSN 0253-2964(Print)
ISSN 1229-5949(Online)
Volume 35, Number 6
BKCSDE 35(6)
June 20, 2014 

Probing α/β Balances in Modified Amber Force Fields from a Molecular Dynamics Study on a ββα Model Protein (1FSD)
Changwon Yang, Eunae Kim, Youngshang Pak*
ββα motif, 1FSD, Amber force field, Biased exchange meta-dynamics (BEMD) simulation, Protein folding pathway
1FSD is a 28-residue designed protein with a ββα motif. Since this protein displays most essential features of protein structures in such a small size, this model protein can be an outstanding system for evaluating the balance in the propensity of the secondary structures and the quality of all-atom protein force fields. Particularly, this protein would be difficult to fold to its correct native structure without establishing proper balances between the secondary structure elements in all-atom energy functions. In this work, a series of the recently optimized five amber protein force fields [ff03*, ff99sb*-ildn, ff99sb-φ'-ildn, ff99sb-nmr1-ildn, ff99sb-ΦΨ(G24, CS)-ildn] were investigated for the simulations of 1FSD using a conventional molecular dynamics (MD) and a biased-exchange meta-dynamics (BEMD) methods. Among those tested force fields, we found that ff99sb-nmr1-ildn and ff99sb-ΦΨ(G24, CS)-ildn are promising in that both force fields can locate the native state of 1FSD with a high accuracy (backbone rmsd ≤ 1.7 Å) in the global free energy minimum basin with a reasonable energetics conforming to a previous circular dichroism (CD) experiment. Furthermore, both force fields led to a common set of two distinct folding pathways with a heterogeneous nature of the transition state to the folding. We anticipate that these force fields are reasonably well balanced, thereby transferable to many other protein folds.
1713 - 1719
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