Interpretation of nuclear resonant vibrational spectra of rubredoxin using a combined quantum mechanics and molecular mechanics approach.
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.
Institut für Physik, Universität zu Lübeck, 23562 Lübeck, Germany. paulsen@physik.uni-luebeck.de
Hauke
H
Paulsen
Alfred X
AX
Trautwein
Patrick
P
Wegner
Christian
C
Schmidt
Aleksandr I
AI
Chumakov
Volker
V
Schünemann
D007501:Iron / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D043903:Pyrococcus abyssi / Q000378:metabolism; D011789:Quantum Theory; D012416:Rubredoxins / Q000737:chemistry*; D013455:Sulfur / Q000737:chemistry; D014732:Vibration
D012416:Rubredoxins; D013455:Sulfur; D007501:Iron