Paper Citing NAMD - Abstract
GhattyVenkataKrishna, Pavan K.; Uberbacher, Edward C.; Cheng, Xiaolin
Effect of the amyloid beta hairpin's structure on the handedness of helices formed by its aggregates
FEBS LETTERS, 587:2649-2655, AUG 19 2013
Various structural models for amyloid beta fibrils have been derived from a variety of experimental techniques. However, these models cannot differentiate between the relative position of the two arms of the beta hairpin called the stagger. Amyloid fibrils of various hierarchical levels form left-handed helices composed of beta sheets. However it is unclear if positive, negative and zero staggers all form the macroscopic left-handed helices. To address this issue we have conducted extensive molecular dynamics simulations of amyloid beta sheets of various staggers and shown that only negative staggers lead to the experimentally observed left-handed helices while positive staggers generate the incorrect right-handed helices. This result suggests that the negative staggers are physiologically relevant structure of the amyloid beta fibrils. (C) 2013 The Authors. Published by Elsevier B.V. All rights reserved.
