TY - JOUR
T1 - Coexistence of flexibility and stability of proteins
T2 - An equation of state
AU - de Leeuw, Marina
AU - Reuveni, Shlomi
AU - Klafter, Joseph
AU - Granek, Rony
PY - 2009/10/9
Y1 - 2009/10/9
N2 - We consider a recently suggested "equation of state" for natively folded proteins, and verify its validity for a set of about 5800 proteins. The equation is based on a fractal viewpoint of proteins, on a generalization of the Landau-Peierls instability, and on a marginal stability criterion. The latter allows for coexistence of stability and flexibility of proteins, which is required for their proper function. The equation of state relates the protein fractal dimension df, its spectral dimension ds, and the number of amino acids N. Using structural data from the protein data bank (PDB) and the Gaussian network model (GNM), we compute df and ds for the entire set and demonstrate that the equation of state is well obeyed. Addressing the fractal properties and making use of the equation of state may help to engineer biologically inspired catalysts.
AB - We consider a recently suggested "equation of state" for natively folded proteins, and verify its validity for a set of about 5800 proteins. The equation is based on a fractal viewpoint of proteins, on a generalization of the Landau-Peierls instability, and on a marginal stability criterion. The latter allows for coexistence of stability and flexibility of proteins, which is required for their proper function. The equation of state relates the protein fractal dimension df, its spectral dimension ds, and the number of amino acids N. Using structural data from the protein data bank (PDB) and the Gaussian network model (GNM), we compute df and ds for the entire set and demonstrate that the equation of state is well obeyed. Addressing the fractal properties and making use of the equation of state may help to engineer biologically inspired catalysts.
UR - http://www.scopus.com/inward/record.url?scp=70350536555&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0007296
DO - 10.1371/journal.pone.0007296
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AN - SCOPUS:70350536555
SN - 1932-6203
VL - 4
JO - PLoS ONE
JF - PLoS ONE
IS - 10
M1 - e7296
ER -