Paper Citing NAMD - Abstract
da Silva, Luis Pinto; Esteves da Silva, Joaquim C. G.
TD-DFT/Molecular Mechanics Study of the Photinus pyralis Bioluminescence System
JOURNAL OF PHYSICAL CHEMISTRY B, 116:2008-2013, FEB 16 2012
This is the first report of a computational study of the bioluminescence of ligand-bound Photinus pyralis luciferase. A time-dependent PBEO/molecular mechanics approach was used to study the interaction between excited-state oxyluciferin (Keto-(-1)) and. neighboring active site molecules. The results of these calculations demonstrated that the most important intermolecular interactions are: blue-shifting ionic interactions, red-shifting pi-pi stacking, and red/blue shifting hydrogen bonding. Subsequent molecular dynamics simulations further supported these conclusions.
