%0 Book Section %1 statphys23_0415 %A Pelizzola, A. %B Abstract Book of the XXIII IUPAP International Conference on Statistical Physics %C Genova, Italy %D 2007 %E Pietronero, Luciano %E Loreto, Vittorio %E Zapperi, Stefano %K fluctuations folding ising-like mechanical model nonequilibrium protein rna statphys23 topic-10 unfolding %T Ising-Like Model of Protein Folding: Kinetics, Mutations, Mechanical Unfolding %U http://st23.statphys23.org/webservices/abstract/preview_pop.php?ID_PAPER=415 %X 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.

@incollection{statphys23_0415, 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.}, added-at = {2007-06-20T10:16:09.000+0200}, address = {Genova, Italy}, author = {Pelizzola, A.}, biburl = {https://www.bibsonomy.org/bibtex/2574410e1eb03a9594258a904a0bdaa7f/statphys23}, booktitle = {Abstract Book of the XXIII IUPAP International Conference on Statistical Physics}, editor = {Pietronero, Luciano and Loreto, Vittorio and Zapperi, Stefano}, interhash = {2d7ee1b0c1431ca10927e6c5a905fdd5}, intrahash = {574410e1eb03a9594258a904a0bdaa7f}, keywords = {fluctuations folding ising-like mechanical model nonequilibrium protein rna statphys23 topic-10 unfolding}, month = {9-13 July}, timestamp = {2007-06-20T10:16:19.000+0200}, title = {Ising-Like Model of Protein Folding: Kinetics, Mutations, Mechanical Unfolding}, url = {http://st23.statphys23.org/webservices/abstract/preview_pop.php?ID_PAPER=415}, year = 2007 }