Paper Citing NAMD - Abstract
Lopez-Perez, Daniel E.; Revilla-Lopez, Guillermo; Jacquemin, Denis; Zanuy, David; Palys, Barbara; Sek, Slawomir; Aleman, Carlos
Intermolecular interactions in electron transfer through stretched helical peptides
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:10332-10344, 2012
The helical peptide Cys-Ala-Lys-(Glu-Ala-Ala-Ala-Lys)(2)-Ala-NH-(CH2)(2)-SH has been organized forming a self-assembled monolayer on gold (0.602 peptides per nm(2)), its conductance behavior under stretching conditions being studied using scanning tunnelling microscopy and current sensing atomic force microscopy. The helical conformation of the peptide has been found to play a fundamental role in the conductance. Moreover, variation of the current upon molecular stretching indicates that peptides can be significantly elongated before the conductance drops to zero, the critical elongation being 1.22 +/- 0.47 nm. Molecular dynamics simulations of a single peptide in the free state and of a variable number of peptides tethered to a gold surface (i.e. densities ranging from 0.026 to 1.295 peptides per nm(2)) have indicated that the helical conformation is intrinsically favored in solvated environments while in desolvated environments it is retained because of the fundamental role played by peptide-peptide intermolecular interactions. The structure obtained for the system with 24 tethered peptides, with a density of 0.634 peptides per nm(2) closest to the experimental one, is in excellent agreement with experimental observations. On the other hand, simulations in which a single molecule is submitted to different compression and stretching processes while the rest remain in the equilibrium have been used to mimic the variation of the tip-substrate distance in experimental measures. Results allowed us to identify the existence, and in some cases coexistence, of intermolecular and intramolecular ionic ladders, suggesting that peptide-mediated electron transfer occurs through the hopping mechanism. Finally, quantum mechanical calculations have been used to investigate the variation of the electronic structure upon compression and stretching deformations.
