Magnetic susceptibility tensor and heme contact shifts determinations in the Rhodobacter capsulatus ferricytochrome c': NMR and magnetic susceptibility studies

Pseudocontact Shifts in Biomolecular NMR Spectroscopy

Paramagnetic centers in biomolecules, such as specific metal ions that are bound to a protein, affect the nuclei in their surrounding in various ways. One of these effects is the pseudocontact shift (PCS), which leads to strong chemical shift perturbations of nuclear spins, with a remarkably long range of 50 Å and beyond. The PCS in solution NMR is an effect originating from the anisotropic part of the dipole-dipole interaction between the magnetic momentum of unpaired electrons and nuclear spins. The PCS contains spatial information that can be exploited in multiple ways to characterize structure, function, and dynamics of biomacromolecules. It can be used to refine structures, magnify effects of dynamics, help resonance assignments, allows for an intermolecular positioning system, and gives structural information in sensitivity-limited situations where all other methods fail. Here, we review applications of the PCS in biomolecular solution NMR spectroscopy, starting from early works on natural metalloproteins, following the development of non-natural tags to chelate and attach lanthanoid ions to any biomolecular target to advanced applications on large biomolecular complexes and inside living cells. We thus hope to not only highlight past applications but also shed light on the tremendous potential the PCS has in structural biology.

Paramagnetic properties of the low- and high-spin states of yeast cytochrome c peroxidase

Here we describe paramagnetic NMR analysis of the low- and high-spin forms of yeast cytochrome c peroxidase (CcP), a 34 kDa heme enzyme involved in hydroperoxide reduction in mitochondria. Starting from the assigned NMR spectra of a low-spin CN-bound CcP and using a strategy based on paramagnetic pseudocontact shifts, we have obtained backbone resonance assignments for the diamagnetic, iron-free protein and the high-spin, resting-state enzyme. The derived chemical shifts were further used to determine low- and high-spin magnetic susceptibility tensors and the zero-field splitting constant (D) for the high-spin CcP. The D value indicates that the latter contains a hexacoordinate heme species with a weak field ligand, such as water, in the axial position. Being one of the very few high-spin heme proteins analyzed in this fashion, the resting state CcP expands our knowledge of the heme coordination chemistry in biological systems.

Stability of the heme Fe-N-terminal amino group coordination bond in denatured cytochrome c

In the denatured states of Hydrogenobacter thermophilus cytochrome c(552) (HT) and Pseudomonas aeruginosa cytochrome c(551) (PA), and their mutants, the N-terminal amino group of the polypeptide chain is coordinated to heme Fe in place of the axial Met, the His-N(term) form being formed. The coordination of the N-terminal amino group to heme Fe leads to loop formation by the N-terminal stretch preceding the first Cys residue bound to the heme, and the N-terminal stretches of HT and PA are different from each other in terms of both the sequence and the number of constituent amino acid residues. The His-N(term) form was shown to be rather stable, and hence it can influence the stability of the denatured state. We have investigated the heme Fe coordination structures and stabilities of the His-N(term) forms emerging upon guanidine hydrochloric acid-induced unfolding of the oxidized forms of the proteins. The Fe-N(term) coordination bond in the His-N(term) form with a 9-residue N-terminal stretch of HT proteins was found to be tilted to some extent away from the heme normal, as reflected by the great heme methyl proton shift spread. On the other hand, the small heme methyl proton shift spread of the His-N(term) form with an 11-residue stretch of PA proteins indicated that its Fe-N(term) bond is nearly parallel with the heme normal. The stability of the His-N(term) form was found to be affected by the structural properties of the N-terminal stretch, such as its length and the N-terminal residue. With a given N-terminal residue, the stability of the His-N(term) form is higher for a 9-residue N-terminal stretch than an 11-residue one. In addition, with a given length of the N-terminal stretch, the His-N(term) form with an N-terminal Glu is stabilized by a few kJ mol(-1) relative to that with an N-terminal Asn. These results provide a novel insight into the stabilizing interactions in the denatured cyts c that will facilitate elucidation of the folding/unfolding mechanisms of the proteins.

Solution structure of NOD1 CARD and mutational analysis of its interaction with the CARD of downstream kinase RICK

NOD1 is a cytosolic signalling host pattern-recognition receptor composed of a caspase-activating and recruitment domain (CARD), a nucleotide-binding and oligomerization domain (NOD) and leucine-rich repeats. It plays a crucial role in innate immunity by activating the NF-kappaB pathway via its downstream effector the kinase RICK (RIP2) following the recognition of a specific bacterial ligand. RICK is recruited by NOD1 through interaction of their respective CARDs. Here we present the high resolution NMR structure of the NOD1 CARD. It is generally similar to other CARDs of known structure, consisting of six tightly packed helices, although the length and orientation of the last helix is unusual. Mutations in both the NOD1 and RICK CARD domains were assayed by immuno-precipitation of cell lysates and in vivo NF-kappaB activation in order to define residues important for CARD-CARD interaction and downstream signalling. The results show that the interaction is critically dependent on three acidic residues on NOD1 CARD and three basic residues on RICK CARD and thus is likely to have a strong electrostatic component, similar to other characterised CARD-CARD interactions.

NMR paramagnetic relaxation due to the S=5∕2 complex, Fe(III)-(tetra-p-sulfonatophenyl)porphyrin: Central role of the tetragonal fourth-order zero-field splitting interaction

The metalloporphyrins, Me-TSPP [Me=Cr(III), Mn(III), Mn(II), Fe(III), and TSPP=meso-(tetra-p-sulfonatophenyl)porphyrin], which possess electron spins S=3/2, 2, 5/2, and 5/2, respectively, comprise an important series of model systems for mechanistic studies of NMR paramagnetic relaxation enhancement (NMR-PRE). For these S>1/2 spin systems, the NMR-PRE depends critically on the detailed form of the zero-field splitting (zfs) tensor. We report the results of experimental and theoretical studies of the NMR relaxation mechanism associated with Fe(III)-TSPP, a spin 5/2 complex for which the overall zfs is relatively large (D approximately = 10 cm(-1)). A comparison of experimental data with spin dynamics simulations shows that the primary determinant of the shape of the magnetic relaxation dispersion profile of the water proton R1 is the tetragonal fourth-order component of the zfs tensor. The relaxation mechanism, which has not previously been described, is a consequence of zfs-induced mixing of the spin eigenfunctions of adjacent Kramers doublets. We have also investigated the magnetic-field dependence of electron-spin relaxation for S=5/2 in the presence of a large zfs, such as occurs in Fe(III)-TSPP. Calculations show that field dependence of this kind is suppressed in the vicinity of the zfs limit, in agreement with observation.

Effects of axial methionine coordination on the in-plane asymmetry of the heme electronic structure of cytochrome c

The paramagnetic susceptibility ( chi) tensors of the oxidized forms of thermophile Hydrogenobacter thermophilus cytochrome c(552) (Ht cyt c(552)) and a quintuple mutant (F7A/V13 M/F34Y/E43Y/V78I; qm) of mesophile Pseudomonas aeruginosa cytochrome c(551) (Pa cyt c(551)) have been determined on the basis of the redox-dependent (1)H NMR shift changes of the main-chain NH and C(alpha)H proton resonances of non-coordinated amino acid residues and the NMR structures of the reduced forms of the corresponding proteins (J. Hasegawa, T. Yoshida, T. Yamazaki, Y. Sambongi, Y. Yu, Y. Igarashi, T. Kodama, K. Yamazaki, Y. Kyogoku, Y. Kobayashi (1998) Biochemistry 37:9641-9649; J. Hasegawa, S. Uchiyama, Y. Tanimoto, M. Mizutani, Y. Kobayashi, Y. Sambongi,Y. Igarashi (2000) J Biol Chem 275:37824-37828). From the chi tensors determined, we obtained the contact shifts for heme methyl proton resonances, which provided the heme electronic structures of the oxidized forms of Ht cyt c(552) and qm. We also characterized the heme electronic structure of the cyanide adducts of the proteins, where the axial Met was replaced by an exogenous cyanide ion, through the analysis of (1)H NMR spectra. The results indicated that the heme electronic structures of both the proteins in their oxidized forms with axial His and Met coordination are largely different to each other, while those in their cyanide adducts are similar to each other. These results demonstrated that the orientation of the axial Met sulfur lone pair, with respect to heme, predominantly contributes to the spin delocalization into the porphyrin-pi system of heme in the oxidized proteins with axial His and Met coordination.

Electronic Structures of Five-Coordinate Iron(III) Porphyrin Complexes with Highly Ruffled Porphyrin Ring

The spin states of the iron(III) complexes with a highly ruffled porphyrin ring, [Fe(TEtPrP)X] where X = F-, Cl-, Br-, I-, and ClO4(-), have been examined by 1H NMR, 13C NMR, EPR, and Mössbauer spectroscopy. While the F-, Cl-, and Br- complexes adopt a high-spin (S = 5/2) state, the I- complex exhibits an admixed intermediate-spin (S = 5/2, 3/2) state in CD2Cl2 solution. The I- complex shows, however, a quite pure high-spin state in toluene solution as well as in the solid. The results contrast those of highly saddled [Fe(OETPP)X] where the I- complex exhibits an essentially pure intermediate-spin state both in solution and in the solid. In contrast to the halide-ligated complexes, the ClO4(-) complex shows a quite pure intermediate-spin state. The 13C NMR spectra of [Fe(TEtPrP)ClO4] are characterized by the downfield and upfield shifts of the meso and pyrrole-alpha carbon signals, respectively: delta(meso) = +342 and delta(alpha-py) = -287 ppm at 298 K. The data indicate that the meso carbon atoms of [Fe(TEtPrP)ClO4] have considerable amounts of positive spin, which in turn indicate that the iron has an unpaired electron in the d(xy) orbital; the unpaired electron in the d(xy) orbital is delocalized to the meso positions due to the iron(d(xy))-porphyrin(a(2u)) interaction. Similar results have been obtained in analogous [Fe(TiPrP)X] though the intermediate-spin character of [Fe(TiPrP)X] is much larger than that of the corresponding [Fe(TEtPrP)X]. On the basis of these results, we have concluded that the highly ruffled intermediate-spin complexes such as [Fe(TEtPrP)ClO4] and [Fe(TiPrP)ClO4] adopt a novel (d(xz), d(yz))3(d(xy))1(d(z)(2)1 electron configuration; the electron configuration of the intermediate-spin complexes reported previously is believed to be (d(xy))2(d(xz)), d(yz))2(d(z)(2))1.

Analysis of heme structural heterogeneity in Mycobacterium tuberculosis catalase-peroxidase (KatG)

Mycobacterium tuberculosis catalase-peroxidase (KatG) is a heme enzyme considered important for virulence, which is also responsible for activation of the anti-tuberculosis pro-drug isoniazid. Here, we present an analysis of heterogeneity in KatG heme structure using optical, resonance Raman, and EPR spectroscopy. Examination of ferric KatG under a variety of conditions, including enzyme in the presence of fluoride, chloride, or isoniazid, and at different stages during purification in different buffers allowed for assignment of spectral features to both five- and six-coordinate heme. Five-coordinate heme is suggested to be representative of "native" enzyme, since this species was predominant in the enzyme examined immediately after one chromatographic protocol. Quantum mechanically mixed spin heme is the most abundant form in such partially purified enzyme. Reduction and reoxidation of six-coordinate KatG or the addition of glycerol or isoniazid restored five-coordinate heme iron, consistent with displacement of a weakly bound distal water molecule. The rate of formation of KatG Compound I is not retarded by the presence of six-coordinate heme either in wild-type KatG or in a mutant (KatG[Y155S]) associated with isoniazid resistance, which contains abundant six-coordinate heme. These results reveal a number of similarities and differences between KatG and other Class I peroxidases.

A simple protocol to study blue copper proteins by NMR

In the case of oxidized plastocyanin from Synechocystis sp. PCC6803, an NMR approach based on classical two and three dimensional experiments for sequential assignment leaves unobserved 14 out of 98 amino acids. A protocol which simply makes use of tailored versions of 2D HSQC and 3D CBCA(CO)NH and CBCANH leads to the identification of nine of the above 14 residues. The proposed protocol differs from previous approaches in that it does not involve the use of unconventional experiments designed specifically for paramagnetic systems, and does not exploit the occurrence of a corresponding diamagnetic species in chemical exchange with the blue copper form. This protocol is expected to extend the popularity of NMR in the structural studies of copper (II) proteins, allowing researchers to increase the amount of information available via NMR on the neighborhood of a paramagnetic center without requiring a specific expertise in the field. The resulting 3D spectra are standard spectra that can be handled by any standard software for protein NMR data analysis.

Models for cytochromes c': spin states of mono(imidazole)-ligated (meso-tetramesitylporphyrinato)iron(III) complexes as studied by UV-Vis, 13C NMR, 1H NMR, and EPR spectroscopy

A number of mono(imidazole)-ligated complexes of perchloro(meso-tetramesitylporphyrinato)iron(III), [Fe(TMP)L]ClO(4), have been prepared, and their spin states have been examined by (1)H NMR, (13)C NMR, and EPR spectroscopy as well as solution magnetic moments. All the complexes examined have shown a quantum mechanical spin admixed state of high and intermediate-spin (S = 5/2 and 3/2) states though the contribution of the S = 3/2 state varies depending on the nature of axial ligands. While the complex with extremely bulky 2-tert-butylimidazole (2-(t)()BuIm) has exhibited an essentially pure S = 5/2 state, the complex with electron-deficient 4,5-dichloroimidazole (4,5-Cl(2)Im) adopts an S = 3/2 state with 30% of the S = 5/2 spin admixture. On the basis of the (1)H and (13)C NMR results, we have concluded that the S = 3/2 contribution at ambient temperature increases according to the following order: 2-(t)BuIm < 2-(1-EtPr)Im < 2-MeIm <or= 2-EtIm <or= 2-(i)PrIm < 4,5-Cl(2)Im. The effective magnetic moments determined by the Evans method in CH(2)Cl(2) solution are 5.9 and 5.0 mu(B) at 25 degrees C for [Fe(TMP)(2-(t)BuIm)]ClO(4) and [Fe(TMP)(2-MeIm)]ClO(4), respectively, which further verify the order given above. Comparison of the NMR and EPR data has revealed that the S = 3/2 contribution changes sensitively by the temperature; the S = 3/2 contribution decreases as the temperature is lowered for all the mono(imidazole) complexes examined in this study. The solvent polarity also affects the spin state; polar solvents such as methanol and acetonitrile increase the S = 3/2 contribution while nonpolar solvents such as benzene decrease it. These results are explained in terms of the structurally flexible nature of the mono(imidazole) complexes; structural parameters such as the Fe(III)-N(axial) bond length, displacement of the iron from the N4 core, tilting of the Fe(III)-N(axial) bond to the heme normal, orientation of the coordinated imidazole ligand, etc., could be altered by the nature of the axial ligands as well as by the solvent polarity and temperature. Some mysteries on the spin states of cytochromes c' isolated from various bacterial sources are possibly explained in terms of the flexible nature of the mono(imidazole)-ligated structure.

Paramagnetic resonance of biological metal centers

The review deals with recent advances in magnetic resonance spectroscopy (hf EPR and NMR) of paramagnetic metal centers in biological macromolecules. In the first half of our chapter, we present an overview of recent technical developments in the NMR of paramagnetic bio-macromolecules. These are illustrated by a variety of examples deriving mainly from the spectroscopy of metalloproteins and their complexes. The second half focuses on recent developments in high-frequency EPR spectroscopy and the application of the technique to copper, iron, and manganese proteins. Special attention is given to the work on single crystals of copper proteins.