Structural, thermodynamic, and kinetic properties of Gramicidin analogue GS6 studied by molecular dynamics simulations and statistical mechanics

Laura Zanetti-Polzi 1, Massimiliano Anselmi 1, Maira D'Alessandro 1 2, Andrea Amadei 2 *, Alfredo Di Nola 1

1Department of Chemistry, University of Rome La Sapienza, Rome, Italy 2Department of Chemical Sciences and Technology, University of Rome Tor Vergata, Rome, Italy

email: Andrea Amadei (andrea.amadei@uniroma2.it)

^*Correspondence to Andrea Amadei, Department of Chemistry, University of Rome La Sapienza, Rome, Italy

In honor of Professor Lelio Mazzarella.

Funded by:
 Italian FIRB Structure, function, dynamics and folding of proteins founded by MIUR

Gramicidin S (GS) analogues belong to an important class of cyclic peptides, characterized by an antiparallel double-stranded -sheet structure with Type II -turns. Such compounds can be used as model systems to understand the folding/unfolding process of -hairpins and more in general of -structures. In the present study, we specifically investigate the folding/unfolding behavior of the hexameric Gramicidin S analogue GS6 by using all-atoms molecular dynamics (MD) simulations at different temperatures, coupled to a statistical mechanical model based on the Quasi Gaussian Entropy theory. Such an approach permits to describe the structural, thermodynamic, and kinetic properties of the peptide and to quantitatively characterize its folding/unfolding transitions. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 1154-1160, 2009.

This article was originally published online as an accepted preprint. The Published Online date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

Received: 20 November 2008; Revised: 16 April 2009; Accepted: 17 April 2009