Abstract
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.
| Original language | English (US) |
|---|---|
| Journal | Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics |
| Volume | 63 |
| Issue number | 3 |
| DOIs | |
| State | Published - Jan 1 2001 |
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All Science Journal Classification (ASJC) codes
- Statistical and Nonlinear Physics
- Mathematical Physics
- Condensed Matter Physics
- Physics and Astronomy(all)
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Thermodynamically important contacts in folding of model proteins. / Scala, Antonio; Dokholyan, Nikolay N.; Buldyrev, Sergey S.; Stanley, Eugene E.
In: Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, Vol. 63, No. 3, 01.01.2001.Research output: Contribution to journal › Article
TY - JOUR
T1 - Thermodynamically important contacts in folding of model proteins
AU - Scala, Antonio
AU - Dokholyan, Nikolay N.
AU - Buldyrev, Sergey S.
AU - Stanley, Eugene E.
PY - 2001/1/1
Y1 - 2001/1/1
N2 - 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.
AB - 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.
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U2 - 10.1103/PhysRevE.63.032901
DO - 10.1103/PhysRevE.63.032901
M3 - Article
C2 - 11308693
AN - SCOPUS:0035278121
VL - 63
JO - Physical Review E
JF - Physical Review E
SN - 2470-0045
IS - 3
ER -