Geometric and physical considerations for realistic protein models

Details Geometric and physical considerations for realistic protein models Geometric and physical considerations for realistic protein models

2005-04-29

arxiv.org/abs/q-bio/0504033v1

Biology

Quantitative Biology

Biomolecules

Scientific paper

10.1103/PhysRevE.72.022901

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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