Paper Citing NAMD - Abstract
Zou, Hongling; Strzalka, Joseph; Xu, Ting; Tronin, Andrey; Blasie, J. Kent
Three-dimensional structure and dynamics of a de novo designed, amphiphilic, metallo-porphyrin-binding protein maquette at soft interfaces by molecular dynamics simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 111:1823-1833, FEB 22 2007
The three-dimensional structure and dynamics of de novo designed, amphiphilic four-helix bundle peptides (or "maquettes"), capable of binding metallo-porphyrin cofactors at selected locations along the length of the core of the bundle, are investigated via molecular dynamics simulations. The rapid evolution of the initial design to stable three-dimensional structures in the absence (apo-form) and presence (holo-form) of bound cofactors is described for the maquettes at two different soft interfaces between polar and nonpolar media. This comparison of the apo- versus holo-forms allows the investigation of the effects of cofactor incorporation on the structure of the four-helix bundle. The simulation results are in qualitative agreement with available experimental data describing the structures at lower resolution and limited dimension.
