Molecular Dynamics Modeling of the first self-organisation events of oligopeptides on surfaces

The self organization of the oligopeptide EAK 16-II1 onto hydrophilic surfaces into well-defined fibrils has been studied by means of molecular dynamic calculations. Both a fully silanolic charged quartz suface and a fully methylated quartz surface were considered; initial oligopetides configuration were chosen considering several orientations of the backbones with respect to the surfaces. We propose that the fibrils growth may occur, only onto hydrophilic surface, according to a mechanism which explicitly encompasses a head-to-head configuration with a double interaction, respectively involving an electrostatic and a hydrogen bond linkages. This arrangement produces a peculiar complementary sequence. In this mechanism fibril grows longitudinally from the initial “seeds”, keeping alternate hydrophobic and hydrophilic interactions and maintaining a constant width of 11.4 nm, in nice agreement with the experimental finding (Figure 1). Since the growth is related to the high mobility of EAK onto the hydrophilic surface it was shown that the fibrils do not grow onto the surface, but, instead, onto a disordered layer of or oligopeptides which interacts directly with the surface. Molecular MD simulation performed on the system schematically reported in Figure 2 - with two oligopeptides (P1 and P2) placed, with their backbone parallel to the surface, at a distance of about 1.5 nm each other - and about 0.3 nm from the surface (S1), while a third oligopeptide (P3) placed, still with its backbone parallel to the surface, at about 0.3 nm from the first two, suggest such hypothesis. The time evolution point out a fluctuation of the distance P3 – S1 somewhere about 0.75 nm, (Figure 3), therefore during the simulation P1 and P2 act like a shield maintaining anchored P3.