Interpretation of Nuclear Resonant Vibrational Spectra of Rubredoxin Using a Combined Quantum Mechanics and Molecular Mechanics Approach

Abstract

Nuclear resonant vibrational spectra of the reduced and oxidized form of a mutant of rubredoxin from Pyrococcus abyssii were measured and are compared with simulated spectra that were calculated by a combined quantum mechanics (QM) and molecular mechanics (MM) method. Density functional theory was used for the QM level. Calculations were performed for different models of rubredoxin. Realistic spectra were simulated with reduced models that include at least the iron center, the four cysteins coordinating it, and the residues connected to the cysteins together with a QM layer that comprises the first two coordination shells of the iron center. Larger QM layers did not lead to significant changes of the simulated spectra.

Nickel(ii), copper(ii) and zinc(ii) metallo-intercalators: structural details of the DNA-binding by a combined experimental and computational investigation

“…In this context, quantum mechanics/molecular mechanics (QM/MM) calculations provide reliable structural information on a local region of biomolecular systems, such as the active site of metalloproteins. [29][30][31] We have recently shown that molecular dynamics (MD) simulations, followed by QM/MM calculations, with the QM part described by density functional theory (DFT), provided a detailed structure of the intercalation complexes of dodecanucleotide double-helices with a copper(II) metallointercalator, and formation energy data in good agreement with the experimental DNA-binding constant. 32 On the other hand, detailed local structural information can be experimentally obtained by X-ray crystallography or by NMR spectroscopy only of drug-DNA supramolecular complexes involving small synthetic DNA oligonucleotides, typically in the range 2-12-mer oligonucleotides.…”