title: Wang-Landau density of states based study of the folding-unfolding transition in the mini-protein Trp-cage (TC5b).
abstract: We present the results of a high-statistics equilibrium study of the folding/unfolding transition for the 20-residue mini-protein Trp-cage (TC5b) in water. The ECEPP/3 force field is used and the interaction with water is treated by a solvent-accessible surface area method. A Wang-Landau type simulation is used to calculate the density of states and the conditional probabilities for the various values of the radius of gyration and the number of native contacts at fixed values of energy--along with a systematic check on their convergence. All thermodynamic quantities of interest are calculated from this information. The folding-unfolding transition corresponds to a peak in the temperature dependence of the computed specific heat. This is corroborated further by the structural signatures of folding in the distributions for radius of gyration and the number of native contacts as a function of temperature. The potentials of mean force are also calculated for these variables, both separately and jointly. A local free energy minimum, in addition to the global minimum, is found in a temperature range substantially below the folding temperature. The free energy at this second minimum is approximately 5 k(B)T higher than the value at the global minimum.
authors.affiliation: School of Physical Sciences, Jawaharlal Nehru University, New Delhi - 110 067, India.
authors.forename: Priya
authors.initials: P
authors.lastname: Singh
authors.affiliation: School of Physical Sciences, Jawaharlal Nehru University, New Delhi - 110 067, India.
authors.forename: Subir K
authors.initials: SK
authors.lastname: Sarkar
authors.affiliation: School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi - 110 067, India.
authors.forename: Pradipta
authors.initials: P
authors.lastname: Bandyopadhyay
mesh_terms: D007700:Kinetics; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D058767:Protein Unfolding; D011994:Recombinant Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry*; D013696:Temperature; D013816:Thermodynamics
chemical_list: D010455:Peptides; D011994:Recombinant Proteins; D012997:Solvents; C476389:TC5b protein, synthetic