Resonance Raman spectra of octaethylporphyrinato-Ni(II) and m
 e
 s
 o-deuterated and 15N substituted derivatives. II. A normal coordinate analysis

Abe, Mitsutomo; Kitagawa, Teizo; Kyōgoku, Yoshimasa

doi:10.1063/1.436450

Cited by 579 publications

(465 citation statements)

References 19 publications

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“…The photoproduct spectra is neither that of equilibrium 5c-His AXCP (spectrum a) nor that of its 5c-NO adduct (spectrum b), therefore confirming its assignment to the four-coordinate transient species. The frequencies of the structure-sensitive (28,29) porphyrin marker bands 3 (1482-1483 cm Ϫ1 ), 2 (ϳ1574 cm Ϫ1 ), and 10 (ϳ1624 cm Ϫ1 ) are shifted to lower frequency with respect to the ground-state 5c-NO form. On the basis of these frequencies, we have calculated (29,30) the heme core size D, which corresponds to the distance between the center of the heme and the N ⑀ nitrogen of the four pyrroles coordinating the iron and constituting the heme macrocycle (Table 1).…”

Section: Transient Absorption Changes Andmentioning

confidence: 99%

Molecular Basis for Nitric Oxide Dynamics and Affinity with Alcaligenes xylosoxidans Cytochrome c´

Kruglik

Lambry

Cianetti

et al. 2007

Journal of Biological Chemistry

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The bacterial heme protein cytochrome c from Alcaligenes xylosoxidans (AXCP) reacts with nitric oxide (NO) to form a 5-coordinate ferrous nitrosyl heme complex. The crystal structure of ferrous nitrosyl AXCP has previously revealed that NO is bound in an unprecedented manner on the proximal side of the heme. To understand how the protein structure of AXCP controls NO dynamics, we performed absorption and Raman timeresolved studies at the heme level as well as a molecular computational dynamics study at the entire protein structure level. We found that after NO dissociation from the heme iron, the structure of the proximal heme pocket of AXCP confines NO close to the iron so that an ultrafast (7 ps) and complete (99 ؎ 1%) geminate rebinding occurs, whereas the proximal histidine does not rebind to the heme iron on the timescale of NO geminate rebinding. The distal side controls the initial NO binding, whereas the proximal heme pocket controls its release. These dynamic properties allow the trapping of NO within the protein core and represent an extreme behavior observed among heme proteins.Nitric oxide (NO) acts as a second messenger in several physiological systems (1, 2), is involved in the production of several cytotoxic chemical species and nitrosative stress (3), and appears as an intermediate in the denitrification process (4). Cells have, thus, developed numerous heme proteins whose diverse functions involve nitric oxide binding and/or release. In some bacteria heme sensors were recently discovered (5) with a femtomolar affinity for NO, whereas cytochromes cЈ able to bind NO are found in many nitrogen-fixing, denitrifying, and photosynthetic bacteria (6). Although the physiological role the bacterial cytochrome cЈ from Alcaligenes xylosoxidans (AXCP) 2 is not yet established, the homologous cytochrome cЈ from Rhodobacter capsulatus has been shown to increase the resistance of this bacteria against NO toxicity (7,8). Thus, the bacterial cytochromes cЈ are inferred to disclose a particular behavior regarding NO dynamics and affinity. How heme proteins interact with NO and control its reactivity is ultimately related to their structure and the heme surroundings. A wide range of affinity and kinetic constants can be observed that correlates with the molecular dynamics of NO within the protein core. A striking example of this diversity is offered when comparing the NO dynamics governed by the enzyme NO synthase (9), the endogenous cellular source, and the NO receptorsoluble guanylate cyclase (10) (sGC) whose heme cofactor has a somewhat opposite role. Nitrosylated heme proteins usually form 6-coordinate complexes having histidine and NO as axial ligands at the proximal and distal sides of the heme, respectively (6c-NO-His), but some become 5-coordinate (5c) with NO (5c-NO) like sGC (11, 12) and AXCP (13,14). These latter proteins have an overall structure that presumably controls the strain upon the proximal histidine. Although sGC and AXCP possess different sequences and tertiary structures, they share the pro...

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Section: Transient Absorption Changes Andmentioning

confidence: 99%

Molecular Basis for Nitric Oxide Dynamics and Affinity with Alcaligenes xylosoxidans Cytochrome c´

Kruglik

Lambry

Cianetti

et al. 2007

Journal of Biological Chemistry

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“…80 Table S1 and Figs. S1 and S2 in the supplementary information 81 describe the complete set of vibrational modes of Fe(P) below 450 cm −1 .…”

Section: Computational Description Of Porphine Halide Vibrationsmentioning

confidence: 99%

Spectroscopic identification of reactive porphyrin motions

Barabanschikov

Demidov

Kubo

et al. 2011

The Journal of Chemical Physics

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Nuclear resonance vibrational spectroscopy (NRVS) reveals the vibrational dynamics of a Mössbauer probe nucleus. Here, 57 Fe NRVS measurements yield the complete spectrum of Fe vibrations in halide complexes of iron porphyrins. Iron porphine serves as a useful symmetric model for the more complex spectrum of asymmetric heme molecules that contribute to numerous essential biological processes. Quantitative comparison with the vibrational density of states (VDOS) predicted for the Fe atom by density functional theory calculations unambiguously identifies the correct sextet ground state in each case. These experimentally authenticated calculations then provide detailed normal mode descriptions for each observed vibration. All Fe-ligand vibrations are clearly identified despite the high symmetry of the Fe environment. Low frequency molecular distortions and acoustic lattice modes also contribute to the experimental signal. Correlation matrices compare vibrations between different molecules and yield a detailed picture of how heme vibrations evolve in response to (a) halide binding and (b) asymmetric placement of porphyrin side chains. The side chains strongly influence the energetics of heme doming motions that control Fe reactivity, which are easily observed in the experimental signal.

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“…Most of the Raman and IR bands appear to occur at approximately the same position ( < 20 cm-l ) as those observed for NiOEP [6][7][8]. Therefore, we use the NiOEP data [6][7][8][9][10] for band assignment. Table 1 collects the assignments of the Raman bands.…”

Section: Raman Spectroscopymentioning

confidence: 99%

An in-situ Raman study of the effect of the support for adsorbed iridium-chelates in catalysing oxygen reduction

Bouwkamp-Wijnoltz

Pałys

Visscher

et al. 1996

Journal of Electroanalytical Chemistry

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Resonance Raman spectra of octaethylporphyrinato-Ni(II) and m e s o-deuterated and 15N substituted derivatives. II. A normal coordinate analysis

Cited by 579 publications

References 19 publications

Molecular Basis for Nitric Oxide Dynamics and Affinity with Alcaligenes xylosoxidans Cytochrome c´

Molecular Basis for Nitric Oxide Dynamics and Affinity with Alcaligenes xylosoxidans Cytochrome c´

Spectroscopic identification of reactive porphyrin motions

An in-situ Raman study of the effect of the support for adsorbed iridium-chelates in catalysing oxygen reduction

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