Browsing by Author "Le, Khanh"

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Investigating explicit coupling between local and non-local interactions in protein folding forcefiields
(2018-10-18) Le, Khanh
Cooperativity is a nearly universal property of the folding of small globular proteins. However, this feature is not always well captured by coarse-grained protein folding forcefields. One characteristic of coarse-grained forcefields that may lead to lack of the experimentally observed degree of cooperativity is insufficient coupling between the local- and non-local-in-sequence interactions. Here we investigate the influence of introducing explicit coupling of local and non-local interactions on the folding landscapes of several proteins. In this explicit coupling, we have made an energetic restraint such that the local energy term is only active when at least one of the two residues participating in a local interaction must also have 1 non-local interaction. In the case of a ????-helical protein, introduction of coupling results in an increase in the free energy barrier between folded and unfolded states. This means coupling does improve cooperativity of the folding of the ????-helical protein. However, for ????/???? and ????-sheet proteins, the height of the free energy barrier is largely unchanged by the introduction of coupling. Also, when local and non-local interactions are coupled, non-native interactions may have been created between residues that are non-local in sequence, which results in a more compact and collapsed structure.