The protein folding transition state: insights from kinetics and thermodynamics.

J Chem Phys

Departamento de Física, Centro de Física Computacional, Universidade de Coimbra, Coimbra 3004-516, Portugal.

Published: September 2010

AI Article Synopsis

  • The study uses lattice Monte Carlo simulations to analyze protein folding and compares the transition state ensembles from both equilibrium and kinetic perspectives for a model protein with two-state kinetics.
  • The kinetic transition state is defined using a folding probability analysis (0.4 < P(fold) < 0.6), while the equilibrium transition state involves conformations at the maximum of free energy concerning various reaction coordinates.
  • Results indicate structural similarities between the two transition state ensembles, but the equilibrium transition state's folding probability distribution is broader (0.2 < P(fold) < 0.8) compared to the more restrictive kinetic transition state's distribution.

Article Abstract

We perform extensive lattice Monte Carlo simulations of protein folding to construct and compare the equilibrium and the kinetic transition state ensembles of a model protein that folds to the native state with two-state kinetics. The kinetic definition of the transition state is based on the folding probability analysis method, and therefore on the selection of conformations with 0.4

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http://dx.doi.org/10.1063/1.3485286DOI Listing

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