Topological thermal instability and length of proteins.
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.
Burioni
Raffaella
R
Dipartimento di Fisica and INFM, Università di Parma, Parco Area delle Scienze 7A, 43100 Parma, Italy.
Cassi
Davide
D
Cecconi
Fabio
F
Vulpiani
Angelo
A
D000596:Amino Acids / Q000737:chemistry; D008956:Models, Chemical; D015394:Molecular Structure; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry; D013696:Temperature
D000596:Amino Acids; D011506:Proteins