Effects of lattice constraints in coarse-grained protein models
| Autor: | Daniel T. Seaton, David P. Landau, Alfred C.K. Farris |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
Physics
Models Molecular Quantitative Biology::Biomolecules Protein Folding 010304 chemical physics Protein Conformation Monte Carlo method Crambin General Physics and Astronomy Sampling (statistics) Context (language use) 010402 general chemistry 01 natural sciences 0104 chemical sciences Folding (chemistry) Lattice (module) 0103 physical sciences Protein model Thermodynamics Grain Proteins Statistical physics Physical and Theoretical Chemistry Hydrophobic and Hydrophilic Interactions Monte Carlo Method |
| Zdroj: | The Journal of chemical physics. 154(8) |
| ISSN: | 1089-7690 |
| Popis: | We compare and contrast folding behavior in several coarse-grained protein models, both on- and off-lattice, in an attempt to uncover the effect of lattice constraints in these kinds of models. Using modern, extended ensemble Monte Carlo methods—Wang–Landau sampling, multicanonical sampling, replica-exchange Wang–Landau sampling, and replica-exchange multicanonical sampling, we investigate the thermodynamic and structural behavior of the protein Crambin within the context of the hydrophobic-polar, hydrophobic-“neutral”-polar (H0P), and semi-flexible H0P model frameworks. We uncover the folding process in all cases; all models undergo, at least, the two major structural transitions observed in nature—the coil–globule collapse and the folding transition. As the complexity of the model increases, these two major transitions begin to split into multi-step processes, wherein the lattice coarse-graining has a significant impact on the details of these processes. The results show that the level of structural coarse-graining is coupled to the level of interaction coarse-graining. |
| Databáze: | OpenAIRE |
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