Abstract
We consider a simplified model of protein folding, with binary degrees
of freedom, whose equilibrium thermodynamics is exactly solvable 1,2.
The kinetics is studied by means of computer simulations and a local
equilibrium approach 3,4. Equilibration rates show good agreement
with the experimental ones for both wild type proteins and their
mutants 5. The relationship between the logarithm of the
equilibration rate and the absolute contact order is studied for model
structures and is found to be almost perfectly linear within definite
classes 6.
The model is then generalized with the inclusion of an external force,
and the mechanical unfolding and refolding of protein domains and RNA
fragments is studied 7. Considering both dynamic loading and force
clamp protocols, we verify theoretical expectations for unfolding
forces and times and obtain unfolding lengths which compare very well
with the experimental values. We also show that the generalized
Jarzynski equality is satisfied. Finally, we compute the unfolding and
refolding work distributions for RNA fragments, which show a good
qualitative agreement with experimental results and satisfy Crooks'
theorem.
1) P. Bruscolini and A. Pelizzola, Phys. Rev. Lett. 88, 258101 (2002).\\
2) A. Pelizzola, J. Stat. Mech. P11010 (2005).\\
3) M. Zamparo and A. Pelizzola, Phys. Rev. Lett. 97, 068106 (2006).\\
4) M. Zamparo and A. Pelizzola, J. Stat. Mech. P12009 (2006).\\
5) M. Zamparo and A. Pelizzola, in preparation.\\
6) P. Bruscolini, A. Pelizzola and M. Zamparo, submitted to Phys. Rev. Lett.\\
7) A. Imparato, A. Pelizzola and M. Zamparo, arXiv:cond-mat/0611003,
to appear in Phys. Rev. Lett.
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