Paper Citing NAMD - Abstract
Elgabarty, Hossam; Schmieder, Peter; Sebastiani, Daniel
Unraveling the existence of dynamic water channels in light-harvesting proteins: alpha-C-phycocyanobilin in vitro
CHEMICAL SCIENCE, 4:755-763, 2013
We present hybrid ab initio QM/MM MD simulations and theoretical NMR chemical shift calculations of the bilin chromophore phycocyanobilin (PCB) in the binding pocket of the alpha-subunit of C-phycocyanin (alpha-C-PC). The good overall agreement between the computed NMR chemical shifts and the experimental values confirm the overall structural picture. A particular discrepancy is observed for the pyrrole nitrogen and hydrogen on ring A, which points to a disagreement between the reported X-ray structure and the experimental solution-state NMR spectrum. Our results suggest that in the solution-state, the binding pocket of alpha-C-PC slightly opens up allowing one water molecule to form a stable bridge between ring A in PCB and the protein backbone at the ASN73 residue. With this modified solution-state structure, the computed NMR chemical shifts are in excellent agreement with experimental values. For proteins still lacking a fully-resolved solution-state NMR-based structure, this approach of combining ab initio MD/NMR provides a very sensitive probe for local geometries at the sub-angstrom ngstrom range that can be utilized to compare/reconcile simple experimental one-and two-dimensional NMR data with X-ray structures.
