Thermodynamically important contacts in folding of model proteins.
We introduce a quantity, the entropic susceptibility, that measures the thermodynamic importance-for the folding transition-of the contacts between amino acids in model proteins. Using this quantity, we find that only one equilibrium run of a computer simulation of a model protein is sufficient to select a subset of contacts that give rise to the peak in the specific heat observed at the folding transition. To illustrate the method, we identify thermodynamically important contacts in a model 46-mer. We show that only about 50% of all contacts present in the protein native state are responsible for the sharp peak in the specific heat at the folding transition temperature, while the remaining 50% of contacts do not affect the specific heat.
Scala
A
A
Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215, USA.
Dokholyan
N V
NV
Buldyrev
S V
SV
Stanley
H E
HE
D000596:Amino Acids / Q000737:chemistry*; D001665:Binding Sites; D003198:Computer Simulation; D019277:Entropy; D008958:Models, Molecular; D015233:Models, Statistical; D009038:Motion; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013329:Structure-Activity Relationship; D013816:Thermodynamics
D000596:Amino Acids; D011506:Proteins