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  • Title: Characterizing folding funnels with replica exchange Wang-Landau simulation of lattice proteins.
    Author: Shi G, Wüst T, Landau DP.
    Journal: Phys Rev E; 2016 Nov; 94(5-1):050402. PubMed ID: 27967143.
    Abstract:
    We have studied the folding of ribonuclease A by mapping it onto coarse-grained lattice protein models. With replica exchange Wang-Landau sampling, we calculated the free energy vs end-to-end distance as a function of temperature. A mapping to the famous hydrophobic-polar (HP) model shows a relatively shallow folding funnel and flat free energy minimum, reflecting the high degeneracy of the ground state. In contrast, extending the HP model with an additional "neutral" monomer type (i.e., a mapping to the three-letter H0P model) has a well developed, rough free energy funnel with a low degeneracy ground state. In both cases, folding funnels are asymmetric with temperature dependent shape.
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