Resonance Raman Active Vibrations of Rubredoxin. Normal Coordinate Analysis of a 423-Atom Model

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Abstract
Normal coordinate analyses were performed on three molecular models of the rubredoxin of Desulfovibrio vulgaris, Desulfovibrio gigas, and Clostridium pasteurianum. The total 1081, 1093, and 1148 internal coordinates were specified by the X-ray analyzed coordinates of the 390, 399, and 423 atoms, respectively, in a mass-group approximation. The appropriately assumed values of Urey–Bradley force constants as well as some diagonal values of out-of-plane bending and torsional forces gave 146, 146, and 148 normal modes, respectively, in 250–450 cm−1 region. These are the deformational vibrations within the peptide skeleton of the protein molecules. The Fe–S stretching displacements of the FeS4 core contribute to a limited number of these vibrations. The modes having a totally symmetric Fe–S stretching contribution confined within a frequency region of 290–330 cm−1 in which the principal resonance Raman band of rubredoxin has been reported, and the several minor resonance Raman bands reported in the higher frequency region of 330–420 cm−1 were assigned to noraml modes having a non-totally symmetric Fe–S stretching character. The PED values indicated that all of these modes are constructed mostly by the deformational displacements in the peptide skeleton widely spread into the molecule around the FeS4 core. This feature is very similar to the case of the blue-copper protein studied previously.