Determination of CO orientation in myoglobin by single-crystal infrared linear dichroism

Ivanov, Dmitri; Sage, J. Timothy; Keim, M.; Powell, J. Robert; Asher, Sanford A.; Champion, P. M.

doi:10.1021/ja00088a084

Cited by 88 publications

(105 citation statements)

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“…1) reproduces reported structural features [42], including the almost linear FeCO unit [39,[43][44][45][46][47][48][49]. The nearest neighbors of the Fe are approximately four-fold rotationally symmetric about an axis perpendicular to the plane of the molecule, and most of the predicted vibrational features occur either as single modes with Fe motion perpendicular to the plane, or as nearly degenerate pairs of modes with Fe motion along orthogonal directions within the plane.…”

Section: One-quantum Transitionssupporting

confidence: 75%

Vibrational dynamics of biological molecules: Multi-quantum contributions

Leu

Zgierski

Wyllie

et al. 2005

Journal of Physics and Chemistry of Solids

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High-resolution X-ray measurements near a nuclear resonance reveal the complete vibrational spectrum of the probe nucleus. Because of this, nuclear resonance vibrational spectroscopy (NRVS) is a uniquely quantitative probe of the vibrational dynamics of reactive iron sites in proteins and other complex molecules. Our measurements of vibrational fundamentals have revealed both frequencies and amplitudes of 57 Fe vibrations in proteins and model compounds. Information on the direction of Fe motion has also been obtained from measurements on oriented single crystals, and provides an essential test of normal mode predictions. Here, we report the observation of weaker two-quantum vibrational excitations (overtones and combinations) for compounds that mimic the active site of heme proteins. The predicted intensities depend strongly on the direction of Fe motion. We compare the observed features with predictions based on the observed fundamentals, using information on the direction of Fe motion obtained either from DFT predictions or from single crystal measurements. Two-quantum excitations may become a useful tool to identify the directions of the Fe oscillations when single crystals are not available.

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Section: One-quantum Transitionssupporting

confidence: 75%

Vibrational dynamics of biological molecules: Multi-quantum contributions

Leu

Zgierski

Wyllie

et al. 2005

Journal of Physics and Chemistry of Solids

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“…Variations in NMR and Mössbauer parameters have been similarly explained [21]. Finally infrared polarization measurements on the CO stretching band in single crystals [22][23][24] and in picosecond photoselection experiments [25] have indicated essentially upright FeCO, within 7°of the heme normal. Arguments against significant FeCO bending have also been advanced on the basis of invariance in the FeCO bending frequency between proteins and models [26], and the excessively large energy required for FeCO bending which the high bending frequency implies [19].…”

Section: Introductionmentioning

confidence: 92%

“…The most direct estimates come from infrared polarization measurements. Independent measurements on MbCO single crystals [22][23][24] and on photoselected molecules [25] have yielded angles of 7°to the heme normal, or less, for the dipole generated by the C-O stretching mode. Since the mode involves nearly pure C-O stretching, it was natural to assume that the dipole direction measures the bond vector.…”

Section: Spectroscopic Consequences Of Feco Distortionmentioning

confidence: 99%

Steric contributions to CO binding in heme proteins: a density functional analysis of FeCO vibrations and deformability

Kozłowski

Vogel

Zgierski

et al. 2001

J. Porphyrins Phthalocyanines

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Non-local Density Functional Theory (DFT) is applied to the calculation of geometry and vibrational frequencies of Fe II (porphine)(imidazole)(CO), a model for CO adducts of heme proteins. Bond distances and angles are in agreement with crystallographic data, and frequencies are correctly calculated for C-O and Fe-C stretching and for Fe-C-O bending. This last mode is actually the out-of-phase combination of Fe-C-O bending and Fe-C tilting coordinates, which are heavily mixed because of a large bend-tilt interaction force constant. The in-phase combination is predicted at a very low frequency, 73 cm À1, and to have a low infrared intensity; attempts to detect it in far-IR spectra via 13 C 18 O isotope sensitivity have been unsuccessful. The stretch-bend interaction lowers the energy required for FeCO distortion. A soft potential may account for the wide range of crystallographically determined Fe-C-O displacements and orientations in myoglobin (Mb). The minimum energy path for displacement of the O atom from the heme normal was calculated by relaxing the structure while constraining only the O atom displacement from the heme normal. Energies of 0.2 to 3.5 kcal mol À1 are required for the range of reported displacement, 0.3-1.3 Å . However, vibrational spectroscopy limits the allowable displacement to the low end of this range. The O atom displacement is computed via DFT to be 0.6 Å for a 7°angle of the C-O stretching IR dipole relative to the heme normal, the maximum value compatible with IR polarization measurements on MbCO. FeCO distortion is predicted to diminish both n CO and n FeC , thereby producing deviations from the well-established backbonding correlation; the scatter of the data permits a maximum displacement of 0.5 Å . This displacement would cost about 1.6 kcal mol À1 of steric energy. A small distortion energy is consistent with the CO affinity changes produced by mutations of the distal histidine residue in Mb. Taking the leucine mutant as reference, we estimate the 1.6 kcal mol À1 affinity loss in the wild-type protein to be the resultant of a 0.0-1.6 kcal steric inhibition, a 0.5 kcal mol À1 attraction of the distal histidine sidechain for the bound CO [weak H-bond], and a 0.5-2.1 kcal mol À1 attraction of the same side-chain for a water molecule in the deoxy protein. The observed 2.3 kcal mol À1 O 2 affinity increase in the wild-type protein relative to the leucine mutant then implies a 2.8-4.4 kcal mol À1 attraction of the histidine sidechain for bound O 2 , consistent with a substantial H-bond interaction with the distal histidine. Thus steric inhibition can account for only a minor fraction of the discrimination factor against CO and in favor of O 2 which is produced by the heme-myoglobin interaction.

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“…These values are based on extended x-ray absorption fine structure data from Fe(II)-CO myoglobin and X-ray crystallographic data for the Fe(II)-CO complex of the Ns H-NOX domain (18,20). In the calculated structures, the Fe-C-O bonding was modeled as linear based on structures of small-molecule heme models, X-ray crystallographic data derived from the Fe(II)-CO H-NOX from Ns, and X-ray crystallographic and spectroscopic data from Fe(II)-CO myoglobin (18,(21)(22)(23)(24). Because there were no unambiguous NOE distance restraints identified between the propionates of the heme cofactor and the protein, loose (5 Å) distance restraints were used to restrain the position of the heme propionate groups so as to preserve their † Assays with the H103G mutant were carried out in the presence of 10 mM imidazole to stabilize heme binding.…”

Section: Nmrmentioning

confidence: 99%