Paper Citing NAMD - Abstract
Bellesia, Giovanni; Shea, Joan-Emma
What Determines the Structure and Stability of KFFE Monomers, Dimers, and Protofibrils?
BIOPHYSICAL JOURNAL, 96:875-886, FEB 4 2009
The self-assembly of the KFFE peptide was studied using replica exchange molecular dynamics simulations with a fully atomic description of the peptide and explicit solvent. The relative roles of the aromatic residues and oppositely charged end groups in stabilizing the earliest oligomers and the end-products of aggregation were investigated. beta and non-beta-peptide conformations compete in the monomeric state as a result of a balancing between the high beta-sheet propensity of the phenylalanine residues and charge-charge interactions that favor non-beta-conformations. Dinners are present in beta- and non-beta-sheet conformations and are stabilized primarily by direct and water-mediated charge-charge interactions between oppositely charged side chains and between oppositely charged termini, with forces between aromatic residues playing a minor role. Dimerization to a beta-sheet, fibril-competent state, is seen to be a cooperative process, with the association process inducing beta-structure in otherwise non-beta-monomers. We propose a model for the KFFE fibril, with mixed interface and antiparallel sheet and strand arrangements, which is consistent with experimental electron microscopy measurements. Both aromatic and charge-charge interactions contribute to the fibril stability, although the dominant contribution arises from electrostatic interactions.
