Quantum mechanics/molecular mechanics calculation of the Raman spectra of the phycocyanobilin chromophore in alpha-C-phycocyanin.

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, 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 nonbonded 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 derivat

SUBMITTER: Mroginski MA 

PROVIDER: S-EPMC1959556 | biostudies-literature | 2007 Sep

REPOSITORIES: biostudies-literature