Molecular dynamics study of structural properties of beta-sheet assemblies formed by synthetic de novo oligopeptides

Bellesia, Giovanni and Fedorov, Maxim V. and Timoshenko, Edward G. (2007) Molecular dynamics study of structural properties of beta-sheet assemblies formed by synthetic de novo oligopeptides. Physica A: Statistical Mechanics and its Applications, 373. pp. 455-476. ISSN 0378-4371

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Abstract

We study, by means of molecular dynamics (MD) simulations with explicit water, the structure and stability of beta-sheet tapes, ribbons and double ribbons formed by rationally designed oligopeptides P-11-I and P-11-II in aqueous solutions. Two different methods for the treatment of the electrostatic interactions were considered: a smoothly shifted spherical cutoff approach under spherical harmonic conditions, and the particle mesh Ewald technique. We investigate the transfer of chirality from single L-aminoacids to the molecular scale of oligopeptides and from the latter to the supramolecular scale of peptide clusters. Furthermore, we obtain structural data for the representative conformations of these clusters, as well as study various average properties of their geometry.