Zamparo Marco, Pelizzola Alessandro
Dipartimento di Fisica and CNISM, Politecnico di Torino, corso Duca degli Abruzzi 24, Torino, Italy.
Phys Rev Lett. 2006 Aug 11;97(6):068106. doi: 10.1103/PhysRevLett.97.068106. Epub 2006 Aug 10.
We consider a simplified model of protein folding, with binary degrees of freedom, whose equilibrium thermodynamics is exactly solvable. Based on this exact solution, the kinetics is studied in the framework of a local equilibrium approach, for which we prove that (i) the free energy decreases with time, (ii) the exact equilibrium is recovered in the infinite time limit, and (iii) the equilibration rate is an upper bound of the exact one. The kinetics is compared to the exact one for a small peptide and to Monte Carlo simulations for a longer protein; then rates are studied for a real protein and a model structure.
我们考虑一个具有二元自由度的蛋白质折叠简化模型，其平衡热力学是完全可解的。基于这个精确解，在局部平衡方法的框架内研究动力学，我们证明：（i）自由能随时间降低；（ii）在无限时间极限下恢复到精确平衡；（iii）平衡速率是精确速率的一个上限。将该动力学与一个小肽的精确动力学以及一个更长蛋白质的蒙特卡罗模拟进行比较；然后研究了一个真实蛋白质和一个模型结构的速率。
