Solvation enhances folding cooperativity and the topology dependence of folding rates in a lattice protein model
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arXiv
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| Autori principali: | , , , , |
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| Natura: | Preprint |
| Pubblicazione: |
2025
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| _version_ | 1866913766408454144 |
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| author | Nguyen, Nhung T. T. Phong, Pham Nam Le, Duy Manh Tran, Minh-Tien Hoang, Trinh Xuan |
| author_facet | Nguyen, Nhung T. T. Phong, Pham Nam Le, Duy Manh Tran, Minh-Tien Hoang, Trinh Xuan |
| contents | The aqueous solvent profoundly influences protein folding, yet its effects are relatively poorly understood. In this study, we investigate the impact of solvation on the folding of lattice proteins by using Monte Carlo simulations. The proteins are modelled as self-avoiding 27-mer chains on a cubic lattice, with compact native states and structure-based Gō potentials. Each residue that makes no contacts with other residues in a given protein conformation is assigned a solvation energy ε_s , representing its full exposure to the solvent. We find that a negative ε_s , indicating a favorable solvation, increases the cooperativity of the folding transition by lowering the free energy of the unfolded state, increasing the folding free energy barrier, and narrowing the folding routes. This favorable solvation also significantly improves the correlation between folding rates and the native topology, measured by the relative contact order. Our results suggest that Gō model may overestimate the importance of native interactions and a solvation potential countering the native bias can play a significant role. The solvation energy in our model can be related to the polar interaction between water and peptide groups in the protein backbone. It is therefore suggested that the solvation of peptide groups may significantly contribute to the exceptional folding cooperativity and the pronounced topology-dependence of folding rates observed in two-state proteins. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2503_23280 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Solvation enhances folding cooperativity and the topology dependence of folding rates in a lattice protein model Nguyen, Nhung T. T. Phong, Pham Nam Le, Duy Manh Tran, Minh-Tien Hoang, Trinh Xuan Soft Condensed Matter Biomolecules The aqueous solvent profoundly influences protein folding, yet its effects are relatively poorly understood. In this study, we investigate the impact of solvation on the folding of lattice proteins by using Monte Carlo simulations. The proteins are modelled as self-avoiding 27-mer chains on a cubic lattice, with compact native states and structure-based Gō potentials. Each residue that makes no contacts with other residues in a given protein conformation is assigned a solvation energy ε_s , representing its full exposure to the solvent. We find that a negative ε_s , indicating a favorable solvation, increases the cooperativity of the folding transition by lowering the free energy of the unfolded state, increasing the folding free energy barrier, and narrowing the folding routes. This favorable solvation also significantly improves the correlation between folding rates and the native topology, measured by the relative contact order. Our results suggest that Gō model may overestimate the importance of native interactions and a solvation potential countering the native bias can play a significant role. The solvation energy in our model can be related to the polar interaction between water and peptide groups in the protein backbone. It is therefore suggested that the solvation of peptide groups may significantly contribute to the exceptional folding cooperativity and the pronounced topology-dependence of folding rates observed in two-state proteins. |
| title | Solvation enhances folding cooperativity and the topology dependence of folding rates in a lattice protein model |
| topic | Soft Condensed Matter Biomolecules |
| url | https://arxiv.org/abs/2503.23280 |