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Topological thermal instability and length of proteins
Author(s) -
Burioni Raffaella,
Cassi Davide,
Cecconi Fabio,
Vulpiani Angelo
Publication year - 2004
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20072
Subject(s) - topology (electrical circuits) , protein folding , physics , dimension (graph theory) , folding (dsp implementation) , harmonic , instability , gaussian , statistical physics , stability (learning theory) , spectral density , mathematics , quantum mechanics , pure mathematics , computer science , combinatorics , nuclear magnetic resonance , machine learning , electrical engineering , engineering , statistics
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 their spectral dimension, a parameter describing the low frequency behavior of the density of modes. We found a surprisingly strong correlation between the spectral dimension and the number of amino acids in the protein. Considering that larger spectral dimension values relate to more topologically compact folded states, our results indicate that, for a given temperature and length of protein, the folded structure corresponds to a less compact folding, one compatible with thermodynamic stability. Proteins 2004. © 2004 Wiley‐Liss, Inc.