Paper Citing NAMD - Abstract
Vanschouwen, Bryan M. B.; Oblinsky, Daniel G.; Gordon, Heather L.; Rothstein, Stuart M.
Structure Propensities in Mutated Polyglutamine Peptides
INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES, 3:1-16, MAR 2011
Polyglutamine is a naturally occurring peptide found within several proteins in neuronal cells of the brain, and its aggregation has been implicated in several neurodegenerative diseases, including Huntington's disease. The resulting aggregates have been demonstrated to possess beta-sheet structure, and experimental evidence has demonstrated that aggregation begins with a nucleus composed of a single peptide. In this paper, we computationally examined the structural tendencies of mutant polyglutamine peptides that were studied experimentally, and found to aggregate with varying efficiencies. Low-energy structures were generated for each peptide by simulated annealing molecular dynamics, and were analyzed quantitatively by various geometry-based methods. In all simulations, the carboxy-terminal end of each peptide was constrained to a beta-turn-beta-strand structure to simulate a situation in which beta-structure formation has initiated due to interaction with a seed or a growing oligomer/aggregate. Our results suggest the experimentally-observed inhibition of aggregation to be due to localized conformational restraint on the peptide backbone, which in turn confines the peptide to native coil structure, discouraging transition towards the beta-sheet structure required for aggregation.
