dorsal/arxiv
View SchemaGeometric and Statistical Properties of the Mean-Field HP Model, the LS Model and Real Protein Sequences
| Authors | C. T. Shih, Z. Y. Su, J. F. Gwan, B. L. Hao, C. H. Hsieh, J. L. Lo., H. C. Lee |
|---|---|
| Categories | |
| ArXiv ID | physics/0104015 |
| URL | https://arxiv.org/abs/physics/0104015 |
| DOI | 10.1103/PhysRevE.65.041923 |
Abstract
Lattice models, for their coarse-grained nature, are best suited for the study of the ``designability problem'', the phenomenon in which most of the about 16,000 proteins of known structure have their native conformations concentrated in a relatively small number of about 500 topological classes of conformations. Here it is shown that on a lattice the most highly designable simulated protein structures are those that have the largest number of surface-core switchbacks. A combination of physical, mathematical and biological reasons that causes the phenomenon is given. By comparing the most foldable model peptides with protein sequences in the Protein Data Bank, it is shown that whereas different models may yield similar designabilities, predicted foldable peptides will simulate natural proteins only when the model incorporates the correct physics and biology, in this case if the main folding force arises from the differing hydrophobicity of the residues, but does not originate, say, from the steric hindrance effect caused by the differing sizes of the residues.
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"abstract": "Lattice models, for their coarse-grained nature, are best suited for the\nstudy of the ``designability problem\u0027\u0027, the phenomenon in which most of the\nabout 16,000 proteins of known structure have their native conformations\nconcentrated in a relatively small number of about 500 topological classes of\nconformations. Here it is shown that on a lattice the most highly designable\nsimulated protein structures are those that have the largest number of\nsurface-core switchbacks. A combination of physical, mathematical and\nbiological reasons that causes the phenomenon is given. By comparing the most\nfoldable model peptides with protein sequences in the Protein Data Bank, it is\nshown that whereas different models may yield similar designabilities,\npredicted foldable peptides will simulate natural proteins only when the model\nincorporates the correct physics and biology, in this case if the main folding\nforce arises from the differing hydrophobicity of the residues, but does not\noriginate, say, from the steric hindrance effect caused by the differing sizes\nof the residues.",
"arxiv_id": "physics/0104015",
"authors": [
"C. T. Shih",
"Z. Y. Su",
"J. F. Gwan",
"B. L. Hao",
"C. H. Hsieh",
"J. L. Lo.",
"H. C. Lee"
],
"categories": [
"physics.bio-ph",
"physics.comp-ph",
"q-bio"
],
"doi": "10.1103/PhysRevE.65.041923",
"title": "Geometric and Statistical Properties of the Mean-Field HP Model, the LS Model and Real Protein Sequences",
"url": "https://arxiv.org/abs/physics/0104015"
},
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