Paper Citing NAMD - Abstract
Abramavicius, Darius; Jiang, Jun; Bulheller, Benjamin M.; Hirst, Jonathan D.; Mukamel, Shaul
Simulation Study of Chiral Two-Dimensional Ultraviolet Spectroscopy of the Protein Backbone
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:7769-7775, JUN 9 2010
Amide n-pi* and pi-pi* excitations around 200 nm are prominent spectroscopic signatures of the protein backbone, which are routinely used in ultraviolet (UV) circular dichroism for structure characterization. Recently developed ultrafast laser sources may be used to extend these studies to two dimensions. We apply a new algorithm for modeling protein electronic transitions to simulate two-dimensional UV photon echo signals in this regime and to identify signatures of protein backbone secondary (and tertiary) structure. Simulated signals for a set of globular and fibrillar proteins and their specific regions reveal characteristic patterns of helical and sheet secondary structures. We investigate how these patterns vary and converge with the size of the structural motif. Specific chiral polarization configurations of the UV pulses are found to be sensitive to aspects of the protein structure. This information significantly augments that available from linear circular dichroism.
