Folding in a semi-flexible lattice model for Crambin

8th Brazilian Meeting on Simulational Physics

Shi, Guangjie^1 ; Farris, Alfred C.K.^1 ; Wüst, Thomas^2 ; Landau, David P.^1

Center for Simulational Physics, University of Georgia, Athens

GA

30602, United States^1

ID Scientific IT Services, ETH Zürich, Zürich

8092, Switzerland^2

关键词: Ground-state structures;    Hydrophobic protein;    Lattice modeling;    Lattice protein model;    Native structures;    Orders of magnitude;    Replica exchange;    Wang-Landau sampling;   

Others  :  https://iopscience.iop.org/article/10.1088/1742-6596/686/1/012001/pdf
DOI  :  10.1088/1742-6596/686/1/012001

来源: IOP

【 摘 要 】

Using the Replica-Exchange Wang-Landau sampling method, we investigated and compared three different coarse-grained lattice protein models for the small, hydrophobic protein Crambin. We show that slight extensions of the HP lattice protein model, including the stiffness of bonds can lead to a significant decrease in ground-state degeneracies (up to 5 orders of magnitudes). Moreover, the ground-state structures begin to bear resemblance to native structures observed in real Crambin.