title: Characterizing folding funnels with replica exchange Wang-Landau simulation of lattice proteins.
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.
authors.affiliation: Center for Simulational Physics, The University of Georgia, Athens, Georgia 30602, USA.
authors.forename: Guangjie
authors.initials: G
authors.lastname: Shi
authors.affiliation: Scientific IT Services, ETH Zürich, 8092 Zürich, Switzerland.
authors.forename: Thomas
authors.initials: T
authors.lastname: Wüst
authors.affiliation: Center for Simulational Physics, The University of Georgia, Athens, Georgia 30602, USA.
authors.forename: David P
authors.initials: DP
authors.lastname: Landau
mesh_terms: D003198:Computer Simulation; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013696:Temperature; D013816:Thermodynamics
chemical_list: D011506:Proteins