dorsal/arxiv
View SchemaGeometric and physical considerations for realistic protein models
| Authors | Isaac A. Hubner, Eugene I. Shakhnovich |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0504033 |
| URL | https://arxiv.org/abs/q-bio/0504033 |
| DOI | 10.1103/PhysRevE.72.022901 |
Abstract
Protein structure is generally conceptualized as the global arrangement or of smaller, local motifs of helices, sheets, and loops. These regular, recurring secondary structural elements have well-understood and standardized definitions in terms of amino acid backbone geometry and the manner in which hydrogen bonding requirements are satisfied. Recently, "tube" models have been proposed to explain protein secondary structure in terms of the geometrically optimal packing of a featureless cylinder. However, atomically detailed simulations demonstrate that such packing considerations alone are insufficient for defining secondary structure; both excluded volume and hydrogen bonding must be explicitly modeled for helix formation. These results have fundamental implications for the construction and interpretation of realistic and meaningful biomacromolecular models.
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"abstract": "Protein structure is generally conceptualized as the global arrangement or of\nsmaller, local motifs of helices, sheets, and loops. These regular, recurring\nsecondary structural elements have well-understood and standardized definitions\nin terms of amino acid backbone geometry and the manner in which hydrogen\nbonding requirements are satisfied. Recently, \"tube\" models have been proposed\nto explain protein secondary structure in terms of the geometrically optimal\npacking of a featureless cylinder. However, atomically detailed simulations\ndemonstrate that such packing considerations alone are insufficient for\ndefining secondary structure; both excluded volume and hydrogen bonding must be\nexplicitly modeled for helix formation. These results have fundamental\nimplications for the construction and interpretation of realistic and\nmeaningful biomacromolecular models.",
"arxiv_id": "q-bio/0504033",
"authors": [
"Isaac A. Hubner",
"Eugene I. Shakhnovich"
],
"categories": [
"q-bio.BM"
],
"doi": "10.1103/PhysRevE.72.022901",
"title": "Geometric and physical considerations for realistic protein models",
"url": "https://arxiv.org/abs/q-bio/0504033"
},
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