The role of chain-stiffness in lattice protein models: A replica-exchange Wang-Landau study
| Autor: | Guangjie Shi, Thomas Wüst, Alfred C.K. Farris, David P. Landau |
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| Rok vydání: | 2018 |
| Předmět: |
Models
Molecular Protein Folding animal structures Protein Conformation Monte Carlo method General Physics and Astronomy Brassica 01 natural sciences Protein structure 0103 physical sciences Lattice protein medicine Statistical physics Amino Acids Physical and Theoretical Chemistry 010306 general physics Plant Proteins Physics Quantitative Biology::Biomolecules 010304 chemical physics Crambin Energy landscape Stiffness Folding (chemistry) Thermodynamics Protein folding medicine.symptom Hydrophobic and Hydrophilic Interactions Monte Carlo Method |
| Zdroj: | The Journal of Chemical Physics. 149:125101 |
| ISSN: | 1089-7690 0021-9606 |
| DOI: | 10.1063/1.5045482 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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