Paper Citing NAMD - Abstract
Lockhart, Christopher; Klimov, Dmitri K.
Revealing Hidden Helix Propensity in A beta Peptides by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 117:12030-12038, OCT 10 2013
Using all-atom explicit solvent model and exhaustive replica exchange molecular dynamics simulations we studied the conformational ensembles of several amino-truncated A beta peptides. In our simulations we specifically monitored the formation of helix structure in the C-terminals of various A beta fragments. We show that the equilibrium distributions of structures adopted by A beta 23-40 and A beta 10-40 are similar, but sharply distinct from the conformational ensemble of A beta 29-40. The latter features a stable helical structure not present in longer fragments. Because the lambda-expansion method applied to A beta 23-40 identified Lys28 as the residue producing the strongest impact on the C-terminal helix structure, we hypothesized that addition of a single Lys28 to A beta 29-40 would change the peptide's conformational ensemble. REMD simulations of A beta 28-40 confirmed this expectation by showing that in this peptide the helix conformation is destabilized and it adopts structures similar to those of A beta 23-40 and A beta 10-40. Therefore, a major conformational switch in the A beta C-terminal occurs by truncating A beta peptide after the position Lys28. By comparing our findings with previous studies we argue that A beta C-terminal harbors helical propensity, which can be revealed by various factors, including environment, ligand binding, or sequence truncation.
