Topological thermal instability and length of proteins

Details Topological thermal instability and length of proteins Topological thermal instability and length of proteins

2004-05-14

arxiv.org/abs/q-bio/0405010v1

Proteins 55:529-535 (2004)

Biology

Quantitative Biology

Biomolecules

15 pages, 6 eps figures, 2 tables

Scientific paper

We present an analysis of the effects of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we computed the harmonic spectrum within the Gaussian Network Model (GNM) and determined the spectral dimension, a parameter describing the low frequency behaviour of the density of modes. We find a surprisingly strong correlation between the spectral dimension and the number of amino acids of the protein. Considering that larger spectral dimension value relate to more topologically compact folded state, our results indicate that for a given temperature and length of the protein, the folded structure corresponds to the less compact folding compatible with thermodynamic stability.

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