Paper Citing NAMD - Abstract
Xu, Jun; Zhang, John Z. H.; Xiang, Yun
Molecular Dynamics Simulation and Computational Two-Dimensional Infrared Spectroscopic Study of Model Amyloid beta-Peptide Oligomers
JOURNAL OF PHYSICAL CHEMISTRY A, 117:6373-6379, JUL 25 2013
Molecular dynamics simulations were carried out to study the structure stability of model amyloid beta 40 (A beta 40) peptide oligomers, from monomer to hexamer, in aqueous solution at room temperature. The initial oligomer models were built by using the parallel in-register beta-sheet fibril structure and then allowed to relax in the simulations. Our simulation results indicated that the stable A beta 40 monomer was a random coil, while the oligomer structures became more fibril-like with the increase of the peptide strands. Linear absorption and two-dimensional infrared spectra of the isotope-labeled oligomers were calculated and analyzed in detail, which revealed the differential secondary structural features characteristic of A beta 40 aggregation. A quantitative relation was established to make connection between the calculated spectra and experimental ensemble measurements.
