Using Monte Carlo simulations, we investigate simple, physically motivated extensions to the hydrophobic-polar lattice protein model for the small (46 amino acid) protein Crambin. We use two-dimensional replica-exchange Wang-Landau sampling to study the effects of a bond angle stiffness parameter on the folding and uncover a new step in the collapse process for particular values of this stiffness parameter. A physical interpretation of the folding is developed by analysis of changes in structural quantities, and the free energy landscape is explored. For these special values of stiffness, we find non-degenerate ground states, a property that is consistent with behavior of real proteins, and we use these unique ground states to elucidate the formation of native contacts during the folding process. Through this analysis, we conclude that chain-stiffness is particularly influential in the low energy, low temperature regime of the folding process once the lattice protein has partially collapsed.
Skip Nav Destination
Article navigation
28 September 2018
Research Article|
September 28 2018
The role of chain-stiffness in lattice protein models: A replica-exchange Wang-Landau study
Alfred C.K. Farris
;
Alfred C.K. Farris
a)
1
Center for Simulational Physics, Department of Physics and Astronomy, The University of Georgia
, Athens, Georgia 30602, USA
Search for other works by this author on:
Guangjie Shi;
Guangjie Shi
1
Center for Simulational Physics, Department of Physics and Astronomy, The University of Georgia
, Athens, Georgia 30602, USA
Search for other works by this author on:
Thomas Wüst;
Thomas Wüst
2
Scientific IT Services, ETH Zürich
, 8092 Zürich, Switzerland
Search for other works by this author on:
David P. Landau
David P. Landau
1
Center for Simulational Physics, Department of Physics and Astronomy, The University of Georgia
, Athens, Georgia 30602, USA
Search for other works by this author on:
J. Chem. Phys. 149, 125101 (2018)
Article history
Received:
June 20 2018
Accepted:
September 10 2018
Citation
Alfred C.K. Farris, Guangjie Shi, Thomas Wüst, David P. Landau; The role of chain-stiffness in lattice protein models: A replica-exchange Wang-Landau study. J. Chem. Phys. 28 September 2018; 149 (12): 125101. https://doi.org/10.1063/1.5045482
Download citation file:
Sign in
Don't already have an account? Register
Sign In
You could not be signed in. Please check your credentials and make sure you have an active account and try again.
Pay-Per-View Access
$40.00
Citing articles via
A theory of pitch for the hydrodynamic properties of molecules, helices, and achiral swimmers at low Reynolds number
Anderson D. S. Duraes, J. Daniel Gezelter
DeePMD-kit v2: A software package for deep potential models
Jinzhe Zeng, Duo Zhang, et al.
Electronic structure simulations in the cloud computing environment
Eric J. Bylaska, Ajay Panyala, et al.
Related Content
Effects of lattice constraints in coarse-grained protein models
J. Chem. Phys. (February 2021)
Elucidating thermal behavior, native contacts, and folding funnels of simple lattice proteins using replica exchange Wang-Landau sampling
J. Chem. Phys. (October 2018)
Examining the phase transition behavior of amphiphilic lipids in solution using statistical temperature molecular dynamics and replica-exchange Wang-Landau methods
J. Chem. Phys. (August 2013)
Enhanced Wang Landau sampling of adsorbed protein conformations
J. Chem. Phys. (March 2012)
Configurational entropy, transition rates, and optimal interactions for rapid folding in coarse-grained model proteins
J. Chem. Phys. (September 2022)