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What thermodynamic features characterize good and bad folders? Results from a simplified off-lattice protein model

A. Amatori·J. Ferkinghoff-Borg·G. Tiana·R. A. Broglia
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Abstract

The thermodynamics of the small SH3 protein domain is studied by means of a simplified model where each bead-like amino acid interacts with the others through a contact potential controlled by a 20x20 random matrix. Good folding sequences, characterized by a low native energy, display three main thermodynamical phases, namely a coil-like phase, an unfolded globule and a folded phase (plus other two phases, namely frozen and random coil, populated only at extremes temperatures). Interestingly, the unfolded globule has some regions already structured. Poorly designed sequences, on the other hand, display a wide transition from the random coil to a frozen state. The comparison with the analytic theory of heteropolymers is discussed.

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A. Amatori, J. Ferkinghoff-Borg, G. Tiana, R. A. Broglia. 2005-12-12. What thermodynamic features characterize good and bad folders? Results from a simplified off-lattice protein model. https://doi.org/10.1103/physreve.73.061905

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