Issue
EPL
Volume 87, Number 1, July 2009
Article Number 18002
Number of page(s) 5
Section Interdisciplinary Physics and Related Areas of Science and Technology
DOI http://dx.doi.org/10.1209/0295-5075/87/18002
Published online 17 July 2009
EPL, 87 (2009) 18002
DOI: 10.1209/0295-5075/87/18002

Saddles of the energy landscape and folding of model proteins

L. Angelani1 and G. Ruocco2, 3

1   Research center SMC INFM-CNR, c/o Università di Roma “Sapienza” - I-00185, Roma, Italy, EU
2   Research center Soft INFM-CNR, c/o Università di Roma “Sapienza” - I-00185, Roma, Italy, EU
3   Dipartimento di Fisica, Università di Roma “Sapienza” - I-00185, Roma, Italy, EU

luca.angelani@phys.uniroma1.it

received 18 March 2009; accepted in final form 15 June 2009; published July 2009
published online 17 July 2009

Abstract
We numerically investigate the Potential Energy Landscape of an off-lattice $\beta $-sheet model protein, looking at saddles and minima probed by the system during the folding process. ${\rm G} {\bar {\rm o}} $- like (with native-state-dependent force field and funnel-like landscape) and non- ${\rm G} {\bar {\rm o}} $-like models are considered. In the ${\rm G} {\bar {\rm o}} $-like case, on varying the temperature, we observe: i) a pronounced peak at the collapse/folding temperature $T_{\theta}\simeq T_{f}$ in the energy elevation of visited saddles from underlying minima, ii) a crossover at the same point of the saddle order. Saddles-based quantities seem then to be good candidates as indicators of the funneled shape of the landscape in protein models.

PACS
87.15.Cc - Folding: thermodynamics, statistical mechanics, models, and pathways.
05.10.-a - Computational methods in statistical physics and nonlinear dynamics.
87.15.A- - Theory, modeling, and computer simulation.

© EPLA 2009