A combined NMR and EPR investigation on the effect of the disordered RGG regions in the structure and the activity of the RRM domain of FUS.

Structural disorder represents a key feature in the mechanism of action of RNA-binding proteins (RBPs). Recent insights revealed that intrinsically disordered regions (IDRs) linking globular domains modulate their capability to interact with various sequences of RNA, but also regulate aggregation processes, stress-granules formation, and binding to other proteins. The FET protein family, which includes FUS (Fused in Sarcoma), EWG (Ewing Sarcoma) and TAF15 (TATA binding association factor 15) proteins, is a group of RBPs containing three different long IDRs characterized by the presence of RGG motifs. In this study, we present the characterization of a fragment of FUS comprising two RGG regions flanking the RNA Recognition Motif (RRM) alone and in the presence of a stem-loop RNA. From a combination of EPR and NMR spectroscopies, we established that the two RGG regions transiently interact with the RRM itself. These interactions may play a role in the recognition of stem-loop RNA, without a disorder-to-order transition but retaining high dynamics.

NMR in the SPINE Structural Proteomics project.

This paper describes the developments, role and contributions of the NMR spectroscopy groups in the Structural Proteomics In Europe (SPINE) consortium. Focusing on the development of high-throughput (HTP) pipelines for NMR structure determinations of proteins, all aspects from sample preparation, data acquisition, data processing, data analysis to structure determination have been improved with respect to sensitivity, automation, speed, robustness and validation. Specific highlights are protonless (13)C-direct detection methods and inferential structure determinations (ISD). In addition to technological improvements, these methods have been applied to deliver over 60 NMR structures of proteins, among which are five that failed to crystallize. The inclusion of NMR spectroscopy in structural proteomics pipelines improves the success rate for protein structure determinations.

Synthesis, characterization, and cytotoxic activity of copper(II) and platinum(II) complexes of 2-benzoylpyrrole and X-ray structure of bis[2-benzoylpyrrolato(N,O)]copper(II).

Copper(II) and platinum(II) complexes of 2-benzoylpyrrole (2-BZPH) were synthesized and characterized with IR, 1H and 13C NMR spectroscopies and coordination geometry with ligands arranged in transoid fashion. The crystal structure of [Cu(II)(2-BZP)2] was determined by X-ray diffraction. Death of complex treated Jurkat cells was measured by flow cytometry. The bis-chelate complexes [Cu(II)(2-BZP)2] and [Pt(II)(2-BZP)2] adopt square-planar coordination geometry with ligands, arranged in transoid fashion. Concentrations of 1-10 microM Platinum(II) complexes reduced cell survival from 100% to 20%, in contrast to the copper(II) complex which caused no cell death at a concentration of 10 microM. While the Pt(II) complexes may have damaged DNA to induce cell death, treatment with the Cu(II) complex did not induce Jurkat cell death.

Development of NMR instrumentation to achieve excitation of large bandwidths in high-resolution spectra at high field.

A prototype 2.5-mm (1)H high-resolution probe for an 18.8-T (800 MHz) nuclear magnetic resonance spectrometer has been designed, together with a dedicated amplifier capable of delivering up to 1 kW of power. This probe permits a 90 degrees pulse length of 2 mus to be achieved at 300 W, corresponding to an excitation bandwidth of +/-125 kHz. Probe performances were tested on samples commonly used for this purpose as well as on protein and paramagnetic model compound samples. It is shown that this probe is useful for a wide range of applications at high magnetic field, especially in the study of systems characterized by very broad and far-shifted resonances and in experiments that require high-power radiofrequency irradiation.

Adduct of acetylene at sulfur in an oxygen- and sulfur-bridged open cubane cluster complex of tungsten.

Formation of a single carbon-sulfur bond is described. The reaction of incomplete cubane-type sulfur and oxygen-bridged isothiocyanato tungsten cluster [W3(mu3-S)(mu-O)(mu-S)2(NCS)9]5- (7) with acetylene affords [W3(mu3-S)(mu-O)(mu-S)(mu-SCH=CH2)(NCS)9]4- (8). The cluster 8 has been isolated as K0.5(Hpy)3.5[W3(mu3-S)(mu-O)(mu-S)(mu-SCH=CH2)(NCS)9] (8'), whose structure has been characterized by X-ray crystallography, electronic spectra, and 1H and 13C NMR spectroscopy. Crystal data of 8': triclinic system, space group P1, a = 14.465(5) A, b = 17.353(3) A, c = 10.202(2) A, alpha = 90.98(1) degrees, beta = 108.59(2) degrees, gamma = 98.13(2) degrees, V = 2397.6(10) A(3), Z = 2, D(c) = 2.096 g cm(-3), Dm = 2.08 g cm(-3), R (Rw) = 3.6 (5.5)% for 8786 reflections (I > 1.50 sigma(I)). The carbon-carbon distance is 1.27(1) A and is almost equidistant between ethylene (1.339 A) and acetylene (1.203 A). The electronic spectrum of 8' in 1.0 M HCl containing 1.5 M KSCN has a characteristic broad peak in the near-infrared region [lambda(max), nm (epsilon, M(-1) cm(-1)): 840 (650), 575 (1450)]. (1)H NMR and HH correlation spectroscopy (COSY) of 8' in CD3CN support the results of the X-ray structural analysis. The (1)H NMR spectrum shows three signals at 2.42 (1H, dd), 4.84 (1H, d, J = 8.8 Hz), and 4.89 (1H, d, J = 16.2 Hz) ppm due to the mu-SCH=CH2 moiety of 8'. The correlation spectrum shows spin couplings of the signal at 2.42 ppm with the signals at 4.84 and 4.89 ppm. The mechanism of the formation of 8 is suggested to proceed through an intermediate with acetylene bridging two of the sulfur atoms.

Isolation and physico-chemical characterization of a cytochrome c from the methylotrophic yeast Hansenula polymorpha.

Cytochrome c from the methylotrophic yeast Hansenula polymorpha was isolated and purified to homogeneity for the first time. The final yield of the highly purified protein from 1.4 kg (wet weight) cells was about 20 mg. The hemoprotein has an apparent molecular mass of 12 kDa and isoelectric point (pI) of 9.3. The purified protein was characterized by electronic, EPR and NMR spectroscopies. The redox potential of the cytochrome, E degrees, measured by cyclic voltammetry measurements at neutral pH, is 0.302 V. Both NMR spectroscopy and electrochemical measurements confirm the presence in the solution of several acid-base equilibria, the most pronounced being characterized by a pK(a) of 8.3. The latter pK(a) was attributed to the detachment of the iron(III) ion-coordinated methionine and its replacement by a lysine residue. The electrochemically derived thermodynamic parameters for neutral and alkaline protein species (DeltaS degrees (rc) and DeltaH degrees (rc)) were obtained from the temperature dependence of the redox potential.

Multinuclear (13C, 17O, 57Fe) NMR studies of carbonmonoxy heme proteins and synthetic model compounds.

13C, 17O and 57Fe NMR spectra of several carbonmonoxy hemoprotein models with varying polar and steric effects of the distal organic superstructure, constraints of the proximal side, and porphyrin ruffling are reported. Both heme models and heme proteins obey a similar excellent linear delta(13C) versus nu(C-O) relationship which is primarily due to modulation of pi-back-bonding from the Fe d(pi) to CO pi* orbital by the distal pocket polar interactions. The lack of correlation between delta(13C) and delta(17O) suggests that the two probes do not reflect a similar type of electronic and structural perturbation. delta(17O) is not primarily influenced by the local distal field interactions and does not correlate with any single structural property of the Fe-C-O unit; however, atropisomerism and deformation of the porphyrin geometry appear to play a significant role. 57Fe shieldings vary by nearly 900 ppm among various hemes and an excellent correlation was found between delta(57Fe) and the absolute crystallographic average displacement of the meso carbon atoms, /Cm/, relative to the porphyrin core mean plane. The excellent correlation between iron-57 shieldings and the average shieldings of the meso carbons of the porphyrin skeleton of TPP derivatives suggests that the two probes reflect a similar type of electronic and structural perturbation which is primarily porphyrin ruffling.

The interaction of the nitrate anion with cytochrome c peroxidase: a 15N-NMR study.

The interaction of the nitrate anion with cytochrome c peroxidase has been demonstrated by using 15N-NMR spectroscopy. The results indicate that the nitrate anion binds to the protein in a specific binding site and are consistent with the hypothesis of an interaction of this small anion in the active cavity of the enzyme, possibly in the proximity of the distal histidine and the distal arginine.

Analysis of the paramagnetic shifts of haem carbon resonances in bovine ferricytochrome b5.

Recently published chemical shifts for haem 13C nuclei in bovine ferricytochrome b5 (Lee KB, Kweon J, Park H (1995) Assignment of hyperfine-shifted heme carbon resonances in ferricytochrome b5. FEBS Lett. 367:77-80) are analysed in terms of haem molecular orbitals with perturbed D4h symmetry. Since a crystal structure of this protein is available, together with extensive 1H assignments both in the oxidised and reduced forms, the paramagnetic shifts can be separated into dipolar and Fermi contact contributions by using an empirical magnetic susceptibility tensor. The results are compared with the orientation of the tensor and the geometry of the haem ligands. This comparison casts doubt on one of the 13C assignments and demonstrates that the asymmetry of the haem electronic structure is dominated by the influence of both of the His ligands. The 13C chemical shifts of two haem methyl groups in the minor form of the protein, in which the haem is approximately rotated by 180 degrees about its 5CH-15CH axis, are also evaluated.

Determination of haem electronic structure in cytochrome b5 and metcyanomyoglobin.

The paramagnetic shifts of 13C nuclei positioned alpha to the haems in the A and B forms of rat cytochrome b5 and in metcyanomyoglobin have been analysed in terms of molecular orbitals based on D4h symmetry with a rhombic perturbation. The contribution to the 13C shifts from pseudocontact interactions is calculated from parameters obtained for a metal-centred dipolar shift tensor by fitting 1H shifts. The effect of electron delocalisation onto the vinyl groups of these haems b is separated with reference to the shifts of the vinyl beta carbons. In each case, it was found that the orientation of the magnetic axes in the plane of the haem is rotated away from the iron-nitrogen vectors in the opposite sense to the rotation of the rhombic perturbation and the molecular orbitals. The orientation of the orbitals is closely aligned with the normal to the single His ligand in metcyanomyoglobin, and with the average of the two normals in the bis-His cytochrome b5. It is concluded that the in-plane anisotropy of haems b is dominated by the orientation of the axial ligands in a similar manner to that in haems c and that the approximations used are weakened, but not invalidated, by the presence of partially conjugated vinyl groups.

The three-dimensional structure in solution of the paramagnetic high-potential iron-sulfur protein I from Ectothiorhodospira halophila through nuclear magnetic resonance.

The three-dimensional structure in solution of reduced recombinant high-potential iron-sulfur protein iso-I from Ectothiorhodospira halophila was determined using 948 relevant interproton NOEs out of the 1246 observed NOEs. The determination was accomplished using the XEASY program for spectral analysis and the distance geometry (DG) program DIANA for generation of the structure as described by Wüthrich [Wüthrich, K. (1989) Acc. Chem. Res. 22, 36-44]. The FeS cluster was simulated using an amino acid residue constructed for the present work from a cysteinyl residue with an iron and a sulfur atom attached to the terminal thiol. The family of structures obtained from distance geometry were subjected to energy minimization and molecular dynamics simulations using previously defined force field parameters. The quality of these structures at each stage of the refinement process is discussed with respect to the dihedral angle order parameter and the root-mean-square deviation of the atomic coordinates. The latter values for the backbone atoms vary from 67 pm for the distance-geometry structures to 60 pm for the energy-minimized structures to 51 pm for the structures subjected to restrained molecular dynamics. Finally, the structure in best agreement with the NOE constraints has been further treated with extensive restrained molecular dynamics in water. The solution structure is well defined and is very similar to the available X-ray structure. We do not know of any previous determination of the structure of a paramagnetic protein in solution by NMR. The effect of paramagnetism on the quality of the structure determination is discussed.

Strategies of signal assignments in paramagnetic metalloproteins. An NMR investigation of the thiocyanate adduct of the cobalt (II)-substituted human carbonic anhydrase II.

The title protein with MW 30,000 containing high-spin cobalt (II) has been thoroughly investigated through 1H NMR spectroscopy with the aid of selectively deuterated amino acids and 15N enrichment. The aim is that of showing the potentiality of the approach when local information by NMR is needed and the X-ray structure is available. The potential use of the pseudocontact shift is discussed; 90, 200, and 600 MHz spectrometers are used to investigate a spherical region at various distances from the metal ion. More than 35 signals of protons around cobalt (II) have been assigned.

Spectroscopic characterization of a newly isolated cytochrome P450 from Rhodococcus rhodochrous.

Cytochrome P450 (P450) from Rhodococcus rhodochrous have been characterized through circular dichroism and nuclear magnetic resonance (NMR) spectroscopy, both in the substrate-free and substrate-bound forms. The data are compared with those of P450cam and indicate a close similarity of the structure of the active site in the two proteins. The substrate-free species contains low-spin iron(III), while the 2-ethoxyphenol bound species contains high-spin iron(III). The substrate is in slow exchange on the NMR time scale. The binding of CN- has been investigated and the final adduct characterized through NMR spectra. Nuclear relaxation times of the isotropically shifted signals turn out to be shorter than in other heme proteins, both in the high- and in the low-spin species. This is the result of longer electron relaxation times in P450s than in peroxidases and metmyoglobin. This property, as well as the electron paramagnetic resonance (EPR) spectrum of the substrate-free form, are discussed in terms of the presence of the cysteine as the fifth ligand of the iron ion instead of a histidine as it occurs in peroxidases and myoglobin.

1H-NMR study of reduced heme proteins myoglobin and cytochrome P450.

The 1H-NMR spectra of deoxymyoglobin and reduced cytochrome P450 are analyzed by NOE spectroscopy. Progress has been made in the assignment of the hyperfine-shifted signals of deoxymyoglobin. The nuclear longitudinal-relaxation-time values indicate short electron-relaxation times whereas Curie relaxation contributes significantly to the signals linewidths. For reduced cytochrome P450 the linewidths are larger due to the Curie-relaxation contribution in a large protein. Therefore, the spectral information is poor. The electron-relaxation rates are discussed in terms of possible electronic structure.

The interaction of acetate and formate with cobalt carbonic anhydrase. An NMR study.

The interaction of formate and acetate ions with cobalt-substituted carbonic anhydrase (CA) has been investigated through 13C-NMR and one-dimensional and two-dimensional 1H-NMR spectroscopy. 13C data on formate are consistent with a regularly coordinated ligand, as previously proposed for the acetate anion [Bertini, I., Luchinat, C. & Scozzafava, A. (1977) J. Chem. Soc. Dalton Trans., 1962-1965]. 1H-NOE experiments on both anions give evidence of through-space interactions between ligand protons and protein protons. The latter are assigned to specific residues in the active cavity through nuclear Overhauser effect spectroscopy (NOESY) experiments. The 13C-derived and 1H-derived constrains allow reliable docking of these ligands in the active-site cavity. The resulting geometries are similar to one another and consistent with five-coordinated structures around the metal ion, as previously proposed from electronic spectroscopy [Bertini, I., Canti, G., Luchinat, C. & Scozzafava, A. (1978) J. Am. Chem. Soc. 100, 4873-4877]. The results are discussed in light of the current debate on anion binding to metal ions in carbonic anhydrase [Lindahl, M., Svensson, A. & Liljas, A. (1992) Proteins, in the press]; Bertini, I., Luchinat, C., Pierattelli, R. & Vila, A. J. (1992) Inorg. Chem., in the press; Banci, L. & Merz, K. (1992) unpublished results] and, in particular, of the proposed long Zn-O distance found in the recent X-ray results on the formate adduct [Hakanson, K., Carlsson, M., Svensson, A. & Liljas, A. (1992) J. Mol. Biol., in the press].

1H nuclear magnetic resonance investigation of cobalt(II) substituted carbonic anhydrase.

The structure of ClO4 and NO3 adducts of cobalt(II) substituted bovine carbonic anhydrase have been investigated through 1D NOE and 2D 1H nuclear magnetic resonance (NMR) spectroscopy. For the first time two-dimensional NMR techniques are applied to paramagnetic metalloproteins other than iron-containing proteins. Several active site signals have been assigned to specific protons on the grounds of their scalar and dipolar connectivities and T1 values. The experimental dipolar shifts for the protons belonging to noncoordinated residues have allowed the identification of a plausible orientation of the magnetic susceptibility tensor around the cobalt ion as well as of the magnitude and the anisotropy of the principal susceptibility values. In turn, a few more signals have been tentatively assigned on the grounds of their predicted dipolar shifts. The two inhibitor derivatives have a very similar orientation but a different magnitude of the chi tensor, and the protein structure around the active site is highly maintained. The results encourage a more extensive use of the two-dimensional techniques for obtaining selective structural information on the active site of metalloenzymes. With this information at hand, comparisons within homologous series of adducts with various inhibitors and/or mutants of the same enzyme of known structure should be possible using limited sets of NMR data.