Replica Exchange Wang - Landau Simulation of Lattice Protein Folding Funnels
Landau, David P.
- Conference Paper
Rights / licenseCreative Commons Attribution 3.0 Unported
The resolution of Levinthal's paradox concerning the ability of proteins to fold rapidly postulates the existence of a rough "folding funnel" in free energy space that guides the protein to its lowest free energy, native state. To study the folding of the protein ribonuclease A we have mapped it onto a 124 monomer, coarse-grained HP lattice model and onto an H0P model that also includes "neutral" 0-mers in addition to the hydrophobic H-mers and polar P-mers. Using Replica Exchange Wang-Landau sampling, we determined the density of states, g(E), which we then used to calculate the free energy of the protein vs end-to-end distance as a function of temperature. At low temperature the HP model shows a rather shallow and at free energy minimum, while the H0P model maintains a rough free energy funnel. Unlike the common, schematic figures, we find an asymmetric folding funnel that also changes shape substantially as the temperature decreases. Even the location of the free energy minimum shifts as the temperature decreases Show more
Journal / seriesJournal of Physics. Conference Series
Pages / Article No.
PublisherInstitute of Physics
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