Dynamics of iron active sites in heme proteins and model compounds

Brajesh Kumar Rai, Purdue University

Abstract

Vibrational dynamics of iron active sites in heme proteins and model compounds have been studied by refining theoretical calculations to nuclear resonance vibrational spectroscopy (NRVS) data. The NRVS measurements give quantitative information on the frequencies and iron amplitudes of all modes having significant Fe vibrational motion. Normal mode analysis is used to identify and characterize the iron vibrational modes of the heme models, (Nitrosyl)iron (II)tetraphenylporphyrin, [Fe(TPP)(NO)], (2-methylimidazole)(tetraphenylporphinato)iron (II). [Fe(TPP)(2-McHIm)], and six-coordinate [Fe(TPP)(1-MeIm)(CO)]. Modes having large overlaps with in-plane ν42, ν50, and ν53 vibrations of the porphyrin core are identified, as well as several modes with large stretch and bend components of axial ligands. The out-of-plane Fe modes with significant doming of the porphyrin core are found near 75 cm−1, but the largest Fe doming motion arises from the coupling of the phenyls near 30 cm−1. Significantly, the normal mode analysis of the model compounds, in conjunction with NRVS data, provides a good set of refined force constants, which is used to study the effects of protein environment on the active sites of heme proteins. The vibrational spectra of iron active sites in myoglobin and in alpha and beta subunits of hemoglobin are calculated using a Green-function approach, and the results are compared to NRVS data. The method allows us to focus on the heme active site, and gives insights into the effects of globin coupling on the functionally important heme iron modes. The most prominent vibrational feature of the iron VDOS spectra (i.e. the 250 cm−1 band) of myoglobin, as well as that from the alpha and beta subunits of hemoglobin, have been assigned to the localized ν53 modes of heme. While the high frequency modes of both rnyoglobin and hemoglobin couple weakly to the globin, the low frequency features in the vibrational spectra are significantly altered by the protein environment. The globin-driven translations of the entire heme contribute to the 25 cm−1 feature of the VDOS spectra of myoglobin and hemoglobin. The coupling of globin to the heme produces numerous weak and delocalized Fe out-of-plane modes at the intermediate frequencies (60–140 cm−1) that overlap with the doming coordinate of the porphyrin core. We find that the iron out-of-plane motion at different active sites in hemoglobin is most strongly correlated for a couple modes at ∼93 cm−1, suggesting that the biologically significant cooperative motions of hemoglobin occur at intermediate frequencies.

Degree

Ph.D.

Advisors

Prohofsky, Purdue University.

Subject Area

Biophysics

COinS