Paper Citing NAMD - Abstract
Kang, Seung-gu; Li, Hai; Tien Huynh; Zhang, Fuchun; Xia, Zhen; Zhang, Yi; Zhou, Ruhong
Molecular Mechanism of Surface-Assisted Epitaxial Self-Assembly of Amyloid-like Peptides
ACS NANO, 6:9276-9282, OCT 2012
A surprising "upright" fibrilar conformation (with a height of similar to 2.6 nm) was observed with in situ atomic force microscopy (AFM) for an amyloid-like peptide (NH2-VGGAVVAV-COHN2) on mica surface, which is very different from its "flat" conformation (with a much smaller height of similar to 0.9 nm) on the HOPG surface. Our all-atom molecular dynamics (MD) simulations reveal that it is the strong electrostatic interactions between the N-terminus of the peptide and the mica surface that result in an upright conformation and a highly ordered beta-stranded structure on mica, with a height of 2.5 +/- 0.1 nm, consistent with the AFM experiment. Similarly, our MD simulations show that the same peptides adopt a flat conformation on HOPG surfaces due to the favorable hydrophobic interactions with HOPG. Our simulations also indicate that epitaxial patterns found in mica are preferentially controlled by anisotropic binding sites commer surate with the inherent crystallographic unit cell of the basal substrate.
