Thermodynamically important contacts in folding of model proteins

Antonio Scala, Nikolay N. Dokholyan, Sergey S. Buldyrev, Eugene E. Stanley

Research output: Contribution to journalArticle

6 Citations (Scopus)

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.

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Folding
folding
specific heat
Contact
proteins
Protein
Specific Heat
set theory
amino acids
computerized simulation
transition temperature
Model
magnetic permeability
thermodynamics
Susceptibility
Amino Acids
Thermodynamics
Computer Simulation
Sufficient
Subset

All Science Journal Classification (ASJC) codes

  • Statistical and Nonlinear Physics
  • Mathematical Physics
  • Condensed Matter Physics
  • Physics and Astronomy(all)

Cite this

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title = "Thermodynamically important contacts in folding of model proteins",
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.",
author = "Antonio Scala and Dokholyan, {Nikolay N.} and Buldyrev, {Sergey S.} and Stanley, {Eugene E.}",
year = "2001",
month = "1",
day = "1",
doi = "10.1103/PhysRevE.63.032901",
language = "English (US)",
volume = "63",
journal = "Physical Review E",
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publisher = "American Physical Society",
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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 journalArticle

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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