Paper Citing NAMD - Abstract
Mroginski, Maria A.; Kaminski, Steve; Hildebrandt, Peter
Raman Spectra of the Phycoviolobilin Cofactor in Phycoerythrocyanin Calculated by QM/MM Methods
CHEMPHYSCHEM, 11:1265-1274, APR 26 2010
The Raman spectrum of the phycoviolobilin cofactor of the alpha-subunit of phycoerythrocyanin was computed using a hybrid quantum mechanical/molecular mechanics (QM/MM) method in order to evaluate the performance of the QM/MM approach for calculating the vibrational spectra of protein-bound tetrapyrroles as found in phytochrome photoreceptors. A good overall agreement between the experimental and the calculated spectra was achieved. In addition, calculation of the vibrational properties of several snapshots extracted from a molecular dynamics simulation allowed us to investigate in detail the effect of the protein environment on the vibrational spectra. Heterogeneous broadening of most of the experimental bands could be reproduced in a satisfactory manner as the sum of individual spectra obtained by normal-mode-analysis (NMA). An exception is the bandwidth of the peak at 1646 cm(-1), which is underestimated by the NMA sum as well as by the instantaneous normal mode analysis (INMA) approach.
