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Biophys. J. BioFAST: First Published May 18, 2007. doi:10.1529/biophysj.107.108878
© 2007 by the Biophysical Society.

A more recent version of this article appeared on September 15, 2007.
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BIOPHYSICAL THEORY AND MODELING

QM/MM calculation of the Raman spectra of the phycocyanobilin chromophore in {alpha}-C-phycocyanin

Maria-Andrea Mroginski 1*, Franz Mark 2, Walter Thiel 3 and Peter Hildebrandt 1

1 Technische Universität Berlin
2 Max-Planck-Institut fär Bioanorganische Chemie
3 Max-Planck-Institut fär Kohlenforschung

* To whom correspondence should be addressed. E-mail: andrea.mroginski{at}tu-berlin.de.

Submitted on March 14, 2007
Revised on April 10, 2007
Accepted on 9 May 2007


  Abstract
We have established a quantum-mechanics (QM) / molecular mechanics (MM) hybrid method for calculating the Raman spectra of protein-bound cofactors using the {alpha}-subunit of C-phycocyanin containing a phycocyanobilin (PCB) chromophore as a test case. The PCB cofactor was described with density functional theory (DFT) whereas the protein matrix was treated with the CHARMM force field. The Hessian matrix of the QM region was built by taking into account bonded and non-bonded interactions with the protein environment, and projected onto the internal coordinate space. Force constants were scaled with a global set of scaling factors and the Raman intensities were computed using a finite-field method combined with a fourth-order differentiation algorithm for the calculation of the polarizability derivatives. In general, the QM/MM results provided a substantially improved description of the experimental resonance Raman (RR) spectra of the protein-bound cofactor compared to QM calculations of isolated PCB models in vacuo. The results allow assessing the effect of the protein-cofactor interactions on the RR spectra and reveal the potential and limitations of QM calculations on isolated tetrapyrroles for determining the chromophore structures in the various species and states of phytochromes for which three-dimensional structures are not available.

Key Words: density functional theory, hybrid methods, molecular mechanics, phycocyanin, phytochrome, resonance Raman spectroscopy




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P. Schwinte, H. Foerstendorf, Z. Hussain, W. Gartner, M.-A. Mroginski, P. Hildebrandt, and F. Siebert
FTIR Study of the Photoinduced Processes of Plant Phytochrome Phya using Isotope-Labeled Bilins and Density Functional Theory Calculations
Biophys. J., August 1, 2008; 95(3): 1256 - 1267.
[Abstract] [Full Text] [PDF]


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Copyright © 2007 by the Biophysical Society.