Saddles of the energy landscape and folding of model proteins

L. Angelani; G. Ruocco

doi:10.1209/0295-5075/87/18002

All issues

Volume 87 / No 1 (July 2009)

EPL, 87 1 (2009) 18002

Abstract

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		https://doi.org/10.1209/0295-5075/87/18002
Published online		17 July 2009

EPL, 87 (2009) 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

Corresponding author: luca.angelani@phys.uniroma1.it

Received: 18 March 2009
Accepted: 15 June 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

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