Distal and proximal ligand interactions in heme proteins: correlations between carbon-oxygen and iron-carbon vibrational frequencies, oxygen-17 and carbon-13 nuclear magnetic resonance chemical shifts, and oxygen-17 nuclear quadrupole coupling constants in [C17O-] and [13CO]-labeled species

Park, Ki Deok; Guo, K.; Adebodun, Foluso; Chiu, Mark L.; Sligar, Stephen G.; Oldfield, Eric

doi:10.1021/bi00223a007

Cited by 136 publications

(230 citation statements)

References 95 publications

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“…Our Raman data, in which we find only a six-coordinate low spin form in the exogenous ligand-free ferrous preparation, is consistent with the observations of Dewilde et al 2 A confirmation of histidine as the proximal ligand is revealed by the analysis of the Fe 2ϩ CO complex. It is well known that there is an inverse correlation between the frequencies of the Fe-CO stretching modes and the frequencies of the C-O stretching modes of heme proteins and heme model compounds (17)(18)(19). As a result of this relation, which arises from the -electron back-donation from the d (dxz,dyz) orbitals of Fe to the empty * orbitals of CO, the bond order between iron and CO increases as the bond order between the carbon and oxygen atoms of CO decreases and vice versa.…”

Section: Discussionmentioning

confidence: 99%

The Heme Environment of Mouse Neuroglobin

Couture¹,

Burmester²,

Hankeln³

et al. 2001

Journal of Biological Chemistry

140

112

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Neuroglobin (Ngb) is a newly discovered oxygen-binding heme protein that is primarily expressed in the brain of humans and other vertebrates. To characterize the structure/function relationships of this new heme protein, we have used resonance Raman spectroscopy to determine the structure of the heme environment in Ngb from mice. In the Fe 2؉ CO complex, two conformations of the Fe-CO unit are present, one of which arises from an open conformation of the heme pocket in which the CO is not interacting with any nearby residue, and the other arises from a closed conformation where a positively charged residue near the CO group stabilizes the complex. For the Fe 2؉ O 2 complex, we detect a single Fe-OO stretching mode at a frequency similar to that of oxymyoglobins and oxyhemoglobins of vertebrates (571 cm ؊1 ). Based on the Fe-C-O frequencies of the closed conformation of Ngb, a highly polar distal environment is indicated from which the O 2 off-rate is predicted to be lower than that of Mb. In the absence of exogenous ligands, a heme pocket residue coordinates to the heme iron, forming a six-coordinate complex, thereby predicting a low on-rate for exogenous ligands. These structural properties of the heme pocket of Ngb are discussed with respect to its proposed in vivo oxygen delivery function.

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Section: Discussionmentioning

confidence: 99%

The Heme Environment of Mouse Neuroglobin

Couture¹,

Burmester²,

Hankeln³

et al. 2001

Journal of Biological Chemistry

140

112

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“…These studies have inferred electrostatic potentials based on free energy measurements [e.g., pK a shifts of ionizable residues (9-11), reactivity differences among cysteines (12,13), equilibrium binding constants of charged ligands (14), and redox potential shifts (15)] or spectroscopic variations in probes incorporated into or bound to proteins [e.g., fluorescent dyes (16), 19 F and 13 C chemical shifts (17)(18)(19)(20)(21), and EPR-measured g-factor perturbations of nitroxides (22)]. These studies have spurred the ongoing development of electrostatic calculation methodology (6,7) and contributed greatly to our general recognition that the solvation environment within proteins is very different from water.…”

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confidence: 99%

Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase

Fafarman¹,

Sigala²,

Schwans³

et al. 2012

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

216

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Understanding the electrostatic forces and features within highly heterogeneous, anisotropic, and chemically complex enzyme active sites and their connection to biological catalysis remains a longstanding challenge, in part due to the paucity of incisive experimental probes of electrostatic properties within proteins. To quantitatively assess the landscape of electrostatic fields at discrete locations and orientations within an enzyme active site, we have incorporated site-specific thiocyanate vibrational probes into multiple positions within bacterial ketosteroid isomerase. A battery of X-ray crystallographic, vibrational Stark spectroscopy, and NMR studies revealed electrostatic field heterogeneity of 8 MV∕cm between active site probe locations and widely differing sensitivities of discrete probes to common electrostatic perturbations from mutation, ligand binding, and pH changes. Electrostatic calculations based on active site ionization states assigned by literature precedent and computational pK a prediction were unable to quantitatively account for the observed vibrational band shifts. However, electrostatic models of the D40N mutant gave qualitative agreement with the observed vibrational effects when an unusual ionization of an active site tyrosine with a pK a near 7 was included. UV-absorbance and 13 C NMR experiments confirmed the presence of a tyrosinate in the active site, in agreement with electrostatic models. This work provides the most direct measure of the heterogeneous and anisotropic nature of the electrostatic environment within an enzyme active site, and these measurements provide incisive benchmarks for further developing accurate computational models and a foundation for future tests of electrostatics in enzymatic catalysis. E xtensive structural studies of enzymes have revealed that biological catalysis occurs within sequestered active site crevices that solvate reacting substrates with an anisotropic and chemically complex constellation of charged, polar, and hydrophobic groups. But beyond visualization of the chemical composition and architecture of active sites permitted by the rich library of available protein structures, our understanding of the electrostatic nature and properties of this highly heterogeneous environment and its role in molecular recognition and catalysis is largely based on simulations. Computations using three-dimensional structures routinely provide electrostatic potentials, as in Fig. 1A. These potentials have been used to identify and characterize protein-protein and protein-ligand binding sites, and interaction energies derived from these calculations have suggested key contributions from the electrostatic environment to enzymatic rate enhancement and specificity (1-5). However, even the most sophisticated computational methods have multiple approximations and limitations (6-8) and, most importantly, have not been rigorously evaluated through cycles of nontrivial computational predictions and experimental tests. Incisive and quantitative experimental measures o...

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“…These observations show that the specific DNA binding causes the structural change around the distal heme environment, which shifts the equilibrium between A 0 and A 3 conformers to the A 3 site and the narrowing of the A 0 mode. Although some controversy exists on the interpretation of the A 3 conformer of Mb (18,32,33), it is considered that a strong hydrogen bonding would increase the back-donation and enhance the Fe-C stretching frequency to ϳ520 cm Ϫ1 (35). A side chain of the replaced axial ligand is a possible candidate that exerts hydrogen-bonding interaction to the iron-bound CO.…”

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confidence: 99%

Heme Environmental Structure of CooA Is Modulated by the Target DNA Binding

Uchida

Ishikawa

Takahashi

et al. 1998

Journal of Biological Chemistry

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In order to investigate the gene activation mechanism triggered by the CO binding to CooA, a heme-containing transcriptional activator, the heme environmental structure and the dynamics of the CO rebinding and dissociation have been examined in the absence and presence of its target DNA. In the absence of DNA, the Fe-CO and C‫؍‬O stretching Raman lines of the CO-bound CooA were observed at 487 and 1969 cm ؊1 , respectively, suggesting that a neutral histidine is an axial ligand trans to CO. The frequency of (Fe-CO) implies an open conformation of the distal heme pocket, indicating that the ligand replaced by CO is located away from the bound CO. When the target DNA was added to CO-bound CooA, an appearance of a new (Fe-CO) line at 519 cm ؊1 and narrowing of the main line at 486 cm ؊1 were observed. Although the rate of the CO dissociation was insensitive to the additions of DNA, the CO rebinding was decelerated in the presence of the target DNA, but not in the presence of nonsense DNA. These observations demonstrate the structural alterations in the heme distal site in response to binding of the target DNA and support the activation mechanism proposed for CooA, which is triggered by the movement of the heme distal ligand to modify the conformation of the DNA binding domain.

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Distal and proximal ligand interactions in heme proteins: correlations between carbon-oxygen and iron-carbon vibrational frequencies, oxygen-17 and carbon-13 nuclear magnetic resonance chemical shifts, and oxygen-17 nuclear quadrupole coupling constants in [C17O-] and [13CO]-labeled species

Cited by 136 publications

References 95 publications

The Heme Environment of Mouse Neuroglobin

The Heme Environment of Mouse Neuroglobin

Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase

Heme Environmental Structure of CooA Is Modulated by the Target DNA Binding

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