title: Multicanonical Monte Carlo simulations of a de novo designed protein with end-to-end β-sheet.
abstract: One of the smallest proteins with end-to-end β-sheet is the designed 36-residue protein DS119. We recently suggested that the rate-limiting step in the folding of the βαβ protein is the formation of the central helix that then provides a scaffold for the parallel β-sheet formed by the two chain ends. In the present report we investigate whether and how this folding mechanism depends on the energy function, and compare the efficiency of molecular dynamics and Monte Carlo implementations of multicanonical sampling. While we find the native structure with similar frequency as in our previous simulations, we observe that the folding mechanism differs for both force fields.
authors: Faculty of Applied Sciences, Istanbul Commerce University, 34843 Istanbul, Turkey.
authors: Sahin
authors: S
authors: Uyaver
authors: Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019-5251, USA.
authors: Ulrich H E
authors: UH
authors: Hansmann
mesh_terms: D000595:Amino Acid Sequence; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D011506:Proteins