| The study of all-atom protein folding dynamics is usually restricted to conformations close to the native state as it requires significant computational efforts and its force fields may not be accurate for unfolded structures. Coarse-grained models are therefore of great interest to capture essential features of the free energy landscape. We employ the tube model, describing a protein as a chain of uniform thickness with bending rigidity, and a bias towards the native structure to investigate protein folding dynamics from completely unfolded to folded native structure. The structural bias is based on a one-dimensional representation of the structure (structure profile) which is conceptually very different from the use of the contact map (Go-models). Unlike Go-models which favour the formation of contacts between specific residues our approach mediates `connectivity' of residues, that, much like hydrophobicity, describes a residue's propensity to have many contacts. We show that the `effective connectivity' profile constitutes a suitable bias towards the native structure and explore the free energy landscape and folding dynamics of this model. |
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