Saddles of the energy landscape and folding of model proteinsL. 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
received 18 March 2009; accepted in final form 15 June 2009; published July 2009
published online 17 July 2009
We numerically investigate the Potential Energy Landscape of an off-lattice -sheet model protein, looking at saddles and minima probed by the system during the folding process. - like (with native-state-dependent force field and funnel-like landscape) and non- -like models are considered. In the -like case, on varying the temperature, we observe: i) a pronounced peak at the collapse/folding temperature 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.
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