CO Vibration as a Probe of Ligand Dissociation and Transfer in Myoglobin

Polack, Thomas; Ogilvie, Jennifer P.; Franzen, Stefan; Vos, Marten H.; Joffre, Manuel; Martin, Jean−Louis; Alexandrou, Antigoni

doi:10.1103/physrevlett.93.018102

Cited by 18 publications

(18 citation statements)

References 22 publications

(32 reference statements)

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“…[3][4][5] Furthermore,arisetimeforthedockingsite absorption signal 6 and a spectral evolution due to interconversion of the two CO orientations 7 and to conformational changes of the protein 8 were reported, while the total amount of docked CO remained constant for hundreds of picoseconds. Our group further observed a progressive change of the absorption strength after CO photolysis 9 and demonstrated coherent MIR emission in MbCO 10 and coherent vibrational climbing in HbCO. 11 Although MIR pulses can have sufficiently broad spectra, the photobleach of Fe-bound CO and the absorption of docked CO have never been recorded simultaneously with a single probe pulse.…”

Section: Section Biophysical Chemistrymentioning

confidence: 97%

Multiply Excited Vibration of Carbon Monoxide in the Primary Docking Site of Hemoglobin Following Photolysis from the Heme

Nuernberger

Lee

Bonvalet

et al. 2010

J. Phys. Chem. Lett.

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Vous avez des questions? Nous pouvons vous aider. Pour communiquer directement avec un auteur, consultez la première page de la revue dans laquelle son article a été publié afin de trouver ses coordonnées. Si vous n'arrivez pas à les repérer, communiquez avec nous à PublicationsArchive-ArchivesPublications@nrc-cnrc.gc.ca. Questions?Contact the NRC Publications Archive team at PublicationsArchive-ArchivesPublications@nrc-cnrc.gc.ca. If you wish to email the authors directly, please see the first page of the publication for their contact information. NRC Publications Archive Archives des publications du CNRCThis publication could be one of several versions: author's original, accepted manuscript or the publisher's version. / La version de cette publication peut être l'une des suivantes : la version prépublication de l'auteur, la version acceptée du manuscrit ou la version de l'éditeur. For the publisher's version, please access the DOI link below./ Pour consulter la version de l'éditeur, utilisez le lien DOI ci-dessous.http://doi.org/10.1021/jz1006324Access and use of this website and the material on it are subject to the Terms and Conditions set forth at Multiply excited vibration of carbon monoxide in the primary docking site of hemoglobin following photolysis from the heme Nuernberger, Patrick; Lee, Kevin F.; Bonvalet, Adeline; Vos, Marten H.; Joffre, Manuel http://nparc.cisti-icist.nrc-cnrc.gc.ca/fra/droits L'accès à ce site Web et l'utilisation de son contenu sont assujettis aux conditions présentées dans le site

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Section: Section Biophysical Chemistrymentioning

confidence: 97%

Multiply Excited Vibration of Carbon Monoxide in the Primary Docking Site of Hemoglobin Following Photolysis from the Heme

Nuernberger

Lee

Bonvalet

et al. 2010

J. Phys. Chem. Lett.

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“…A probe in the visible domain (2) is sensitive to the ligand arrival and departure from the heme through its effect on the heme electronic transitions, a mid-infrared (mid-IR) probe (3)(4)(5) allows the observation of the ligand trajectory via the ligand's vibrational frequency changes, whereas an x-ray probe (6) is directly sensitive to the atomic positions.…”

mentioning

confidence: 99%

Direct observation of ligand transfer and bond formation in cytochrome c oxidase by using mid-infrared chirped-pulse upconversion

Treuffet

Kubarych

Lambry

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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We have implemented the recently demonstrated technique of chirped-pulse upconversion of midinfrared femtosecond pulses into the visible in a visible pump-midinfrared probe experiment for high-resolution, high-sensitivity measurements over a broad spectral range. We have succeeded in time-resolving the CO ligand transfer process from the heme Fe to the neighboring CuB atom in the bimetallic active site of mammalian cytochrome c oxidase, which was known to proceed in <1 ps, using the full CO vibrational signature of Fe-CO bond breaking and CuB-CO bond formation. Our differential transmission results show a delayed onset of the appearance of the CuB-bound species (200 fs), followed by a 450-fs exponential rise. Trajectories calculated by using moleculardynamics simulations with a Morse potential for the CuB-C interaction display a similar behavior. Both experimental and calculated data strongly suggest a ballistic contribution to the transfer process.

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“…X-ray studies of carbon monoxide ligated HbCO show a nearly perfect square planar symmetry of the plane formed by the four nitrogen atoms of the pyrrole unit, which shows an almost linear geometry for the Fe–C–O group. , The subsystem of HbCO is composed of hexacoordinated iron–porphyrin–imidazole–CO and two distal histidines, which are used to mimic the effect of the protein (Protein Data Bank entry 1HHO) (Figure ). The distal histidine (His63) is chosen to be protonated at the N ε , which is known to influence the vibrational dynamic of the CO oscillator ,,− and the distal histidine (His92) bind to the central Fe atom. ,,− The geometry optimization and anharmonic frequency calculation of the subsystem are performed using density function theory (DFT) combination with a hybrid density functional, built up using Becke’s three parameter exchange and Lee–Yang–Parr’s correlation functional (B3LYP-D3). − Because there exists obviously a weak interaction among the active site and the distal histidines, Becke–Johnson damping (BJ-damping) is included, , as implemented in Gaussian 16 program . As in previous studies, the iron center is described by the Los Alamos effective core potential with the associated basis set double zeta, such effective core potential are used in various domains of organometallic chemistry. − The atoms of the porphyrin ring and the distal histidines are described with the standard 6-31G(d,p) basis set .…”

Section: Computational Methods and Theoriesmentioning

confidence: 99%

Quasi-Static Two-Dimensional Infrared Spectra of the Carboxyhemoglobin Subsystem under Electric Fields: A Theoretical Study

Ren

Chen

et al. 2020

J. Phys. Chem. B

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There is no doubt that electric fields of a specific frequency and intensity could excite certain vibrational modes of a macromolecule, which alters its mode coupling and conformation. Motivated by recent experiments and theories, we study the mode coupling between the Fe–CO mode and CO-stretch mode and vibration energy transfer among the active site and proteins in carboxyhemoglobin (HbCO) under different electric fields using the quasi-static two-dimensional infrared spectra. This study uses iron–porphyrin–imidazole–CO and two distal histidines in HbCO as the subsystem. The potential energy and dipole moment surfaces of the subsystem are calculated using an all-electron ab initio (B3LYP-D3(BJ)) method with the basis set Lanl2dz for the Fe atom and 6-31G(d,p) for C, H, O, and N atoms. Although the subsystem is reduced dimensionally, the anharmonic frequency and anharmonicity of the CO-stretch mode show excellent agreement with experimental values. We use the revealing noncovalent interaction method to confirm the hydrogen bond between the Hε atom of the His63 and the CO molecule. Our study confirms that the mode coupling between the Fe–CO mode and CO-stretch mode does not exist when the subsystem is free of electric field perturbation, which is coupled when the electric field is −0.5142 V/nm. In addition, with the increases of distance between the active site and the His92, there is no vibrational energy transfer between them when the electric field is 1.028 V/nm. We believe that our work could provide new ideas for increasing the dissociation efficiency of the Fe–CO bond and theoretical references for experimental research.

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CO Vibration as a Probe of Ligand Dissociation and Transfer in Myoglobin

Cited by 18 publications

References 22 publications

Multiply Excited Vibration of Carbon Monoxide in the Primary Docking Site of Hemoglobin Following Photolysis from the Heme

Multiply Excited Vibration of Carbon Monoxide in the Primary Docking Site of Hemoglobin Following Photolysis from the Heme

Direct observation of ligand transfer and bond formation in cytochrome c oxidase by using mid-infrared chirped-pulse upconversion

Quasi-Static Two-Dimensional Infrared Spectra of the Carboxyhemoglobin Subsystem under Electric Fields: A Theoretical Study

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