Crystal‐Structure Determination of Powdered Paramagnetic Lanthanide Complexes by Proton NMR Spectroscopy

Shifts for crystals : Solid‐state NMR spectroscopy can be used for structure determination of microcrystalline paramagnetic solids at natural isotopic abundance. The protocol makes use of paramagnetic effects, measured on suitably recorded ¹H NMR spectra, to define the conformation of a molecule in the lattice and the intermolecular packing in the solid phase. The method is illustrated with a family of lanthanide compounds (see picture).

     

Bioconjugation of Proteins with a Paramagnetic NMR and Fluorescent Tag

Site‐specific labeling of proteins with lanthanide ions offers great opportunities for investigating the structure, function, and dynamics of proteins by virtue of the unique properties of lanthanides. Lanthanide‐tagged proteins can be studied by NMR, X‐ray, fluorescence, and EPR spectroscopy. However, the rigidity of a lanthanide tag in labeling of proteins plays a key role in the determination of protein structures and interactions. Pseudocontact shift (PCS) and paramagnetic relaxation enhancement (PRE) are valuable long‐range structure restraints in structural‐biology NMR spectroscopy. Generation of these paramagnetic restraints generally relies on site‐specific tagging of the target proteins with paramagnetic species. To avoid nonspecific interaction between the target protein and paramagnetic tag and achieve reliable paramagnetic effects, the rigidity, stability, and size of lanthanide tag is highly important in paramagnetic labeling of proteins. Here 4′‐mercapto‐2,2′: 6′,2′′‐terpyridine‐6,6′′‐dicarboxylic acid (4MTDA) is introduced as a a rigid paramagnetic and fluorescent tag which can be site‐specifically attached to a protein by formation of a disulfide bond. 4MTDA can be readily immobilized by coordination of the protein side chain to the lanthanide ion. Large PCSs and RDCs were observed for 4MTDA‐tagged proteins in complexes with paramagnetic lanthanide ions. At an excitation wavelength of 340 nm, the complex formed by protein–4MTDA and Tb³⁺ produces high fluorescence with the main emission at 545 nm. These interesting features of 4MTDA make it a very promising tag that can be exploited in NMR, fluorescence, and EPR spectroscopic studies on protein structure, interaction, and dynamics.     

Paramagnetic DOSY: An Accurate Tool for the Analysis of the Supramolecular Interactions between Lanthanide Complexes and Proteins

Diffusion ordered NMR is implemented to determine accurately the mobility of paramagnetic tris‐dipicolinate lanthanide complexes that are versatile probes of protein structure. It is shown that diffusion coefficient ratios can be measured with an accuracy of 1 % using a standard BPPLED pulse sequence, which allows for observing significant, though weak, variations when different species are interacting with the paramagnetic compound. We demonstrate that this approach is complementary to classical chemical shift titration experiments, and that it can be applied successfully to probe the supramolecular dynamic interactions between lanthanide complexes and small molecules on the one hand, or to determine rapidly their affinity for a targeted protein.     

Noncovalent Synthesis of Protein Dendrimers

The covalent synthesis of complex biomolecular systems such as multivalent protein dendrimers often proceeds with low efficiency, thereby making alternative strategies based on noncovalent chemistry of high interest. Here, the synthesis of protein dendrimers using a strong but noncovalent interaction between a peptide and complementary protein is proposed as an efficient strategy to arrive at dendrimers fully functionalized with protein domains. The association of S‐peptide to S‐protein results in the formation of an active enzyme (ribonuclease S) and therefore serves as an ideal system to explore this synthetic approach. Native chemical ligation was used to couple four S‐peptides by means of their C‐terminal thioester to a cysteine‐functionalized dendritic scaffold, thus yielding a tetravalent S‐peptide wedge. A fully functional ribonuclease S tetramer was prepared by addition of four equivalents of S‐protein. Biophysical techniques (isothermal titration calorimetry (ITC), surface plasmon resonance (SPR), and mass spectrometry) and an enzymatic activity assay were used to verify the formation of the multivalent complex. The noncovalent synthetic strategy presented here provides access to well‐defined, dynamic, semisynthetic protein assemblies in high yield and is therefore of interest to the field of nanomedicine as well as biomaterials.     

Design Principles and Theory of Paramagnetic Fluorine‐Labelled Lanthanide Complexes as Probes for 19F Magnetic Resonance: A Proof‐of‐Concept Study

The synthesis and spectroscopic properties of a series of CF₃‐labelled lanthanide(III) complexes (Ln=Gd, Tb, Dy, Ho, Er, Tm) with amide‐substituted ligands based on 1,4,7,10‐tetraazacyclododecane are described. The theoretical contributions of the ¹⁹F magnetic relaxation processes in these systems are critically assessed and selected volumetric plots are presented. These plots allow an accurate estimation of the increase in the rates of longitudinal and transverse relaxation as a function of the distance between the Ln^III ion and the fluorine nucleus, the applied magnetic field, and the re‐rotational correlation time of the complex, for a given Ln^III ion. Selected complexes exhibit pH‐dependent chemical shift behaviour, and a pK_a of 7.0 was determined in one example based on the holmium complex of an ortho‐cyano DO3A‐monoamide ligand, which allowed the pH to be assessed by measuring the difference in chemical shift (varying by over 14 ppm) between two ¹⁹F resonances. Relaxation analyses of variable‐temperature and variable‐field ¹⁹F, ¹⁷O and ¹H NMR spectroscopy experiments are reported, aided by identification of salient low‐energy conformers by using density functional theory. The study of fluorine relaxation rates, over a field range of 4.7 to 16.5 T allowed precise computation of the distance between the Ln^III ion and the CF₃ reporter group by using global fitting methods. The sensitivity benefits of using such paramagnetic fluorinated probes in ¹⁹F NMR spectroscopic studies are quantified in preliminary spectroscopic and imaging experiments with respect to a diamagnetic yttrium(III) analogue.     

Discriminating Halogen‐Bonding from Other Noncovalent Interactions by a Combined NOE NMR/DFT Approach

Herein a combined NOE NMR/DFT methodology to discriminate between adducts held together by halogen bonding (XB) and other noncovalent interactions (non‐XB, such as lone pair/π), based on the determination of the XB donors′ and acceptors′ relative orientation, is proposed. In particular, ¹⁹F,¹H HOESY NMR spectroscopy experiments and DFT calculations on different XB donors, such as perfluorohexyl iodide ( I1 ), iodopentafluorobenzene ( I2 ) and bromopentafluorobenzene ( Br ), combined with different Lewis bases, such as 1,4‐diazabicyclo[2.2.2]octane ( DABCO ) and 2,4,6‐trimethylpyridine ( Me₃Py ), were performed. The results clearly show that in the case DABCO / I1 the XB adduct is practically the only one present in solution, whereas for the other pairs a certain amount of non‐XB adduct is present. Combining DFT and HOESY results, the amount of non‐XB adducts can be roughly quantified under our experimental conditions as 4 % for DABCO / I2 , between 10 and 20 % for Me₃Py / I1 and Me₃Py / I2 , and 44 % for DABCO / Br.     

Lanthanide(III) Complexes with Two Hexapeptides Incorporating Unnatural Chelating Amino Acids: Secondary Structure and Stability

Unnatural metal‐chelating amino acids bearing aminodiacetate side‐chains have been introduced into two hexapeptides to obtain efficient lanthanide‐binding peptides. The synthesis of the enantiopure Fmoc‐Ada_n(tBu)₂‐OH synthons is described with overall yields of 32 and 50 % for n=2 and n=3 side‐chain carbon atoms, respectively. The two peptides AcWAda_nPGAda_nGNH₂ ( P ⁿ ) were synthesized from the protected synthons by standard solid‐phase peptide synthesis. Studies of the lanthanide complexes of the two peptides P ⁿ by luminescence titrations, mass spectrometry, circular dichroism, and solution NMR spectroscopy demonstrate that the Ada_n chain length has a dramatic effect on the complexation properties. Indeed, the flexible compound P³ forms a mononuclear complex of moderate stability (β₁₁=10^9.9), which tends to transform into a binuclear species in the presence of excess of the metal ion. Interestingly, the more compact peptide P² provides stable Ln³⁺ complexes with the exclusive formation of the mononuclear Ln P² adduct. The stability constant of Tb P² is two orders of magnitude higher (β₁₁=10^12.1) than that measured for P³ . The 800 MHz NMR spectrum of the La³⁺ complex of P² evidences a well‐defined type II β‐turn as well as a hydrophobic Trp(indole)–Pro interaction. These interactions exemplify the non‐innocent character of the peptide spacer in the complex La P² as well as the role of a peptide secondary structure in the stabilization of metal complexes.     

Site‐Specific Labeling of Proteins with a Chemically Stable,High‐Affinity Tag for Protein Study

Site‐specific labeling of proteins with paramagnetic lanthanides offers unique opportunities by virtue of NMR spectroscopy in structural biology. In particular, these paramagnetic data, generated by the anisotropic paramagnetism including pseudocontact shifts (PCS), residual dipolar couplings (RDC), and paramagnetic relaxation enhancement (PRE), are highly valuable in structure determination and mobility studies of proteins and protein–ligand complexes. Herein, we present a new way to label proteins in a site‐specific manner with a high‐affinity and chemically stable tag, 4‐vinyl(pyridine‐2,6‐diyl)bismethylenenitrilo tetrakis(acetic acid) (4VPyMTA), through thiol alkylation. Its performance has been demonstrated in G47C and E64C mutants of human ubiquitin both in vitro and in a crowded environment. In comparison with the published tags, 4VPyMTA has several interesting features: 1) it has a very high binding affinity for lanthanides (higher than EDTA), 2) there is no heterogeneity in complexes with lanthanides, 3) the derivatized protein is stable and potentially applicable to the in situ analysis of proteins.     

Magnetic Resonance of Paramagnetic Complexes

The line width of the ESR and NMR signals of paramagnetic transition metal complexes is determined mainly by the electron spin-lattice relaxation time τ_e. Values of τ_e greater than 10^?9 lead to ESR spectra that are readily resolved, while values smaller than 10^?11 give NMR spectra having small line widths. Since fast relaxation processes are effective in nearly all transition metal complexes with several unpaired electrons and in all complexes having an orbitally degenerate ground state, the NMR method has a wider scope. The sign and magnitude of the electron-nucleus coupling can be determined with great sensitivity from the NMR spectra, whereas only the magnitude of this interaction can be determined from the ESR spectra. Free spin densities can be found very accurately from the NMR shifts, and the method can therefore be advantageously applied to kinetic measurements, e.g. on short-lived contact complexes.     

NMR Spectroscopy of Paramagnetic Complexes

Serviceable NMR spectra can, with a few exceptions^[1,6], be recorded for paramagnetic complexes in solution. These spectra provide information about the structure of the complexes and the distribution of the unpaired electrons, and hence also about reactive centers in the molecule. The elucidation of intermolecular and intramolecular exchange phenomena, e.g. the determination of ligand exchange rate constants, the determination of rotation barriers, and the detection of contact complexes in solution, or even of occupation equilibria of the electrons, is possible in this way. It can be seen, therefore, that NMR studies on paramagnetic complexes can be a rich source of information.     

Exclusively Heteronuclear NMR Experiments to Obtain Structural and Dynamic Information on Proteins

Provided that ¹³C‐detected NMR experiments are either preferable or complementary to ¹H detection, we report here tools to determine C^α? C′, C′? N, and C^α? H^α residual dipolar couplings on the basis of the CON experiment. The coupling constants determined on ubiquitin are consistent with the subset measured with the ¹H‐detected HNCO sequences. Since the utilization of residual dipolar couplings may depend on the mobility of the involved nuclei, we also provide tools to measure longitudinal and transverse relaxation rates of N and C′. This new set of experiments is a further development of a whole strategy based on ¹³C direct‐detection NMR spectroscopy for the study of biological macromolecules.     

Fluoride Binding and Crystal‐Field Analysis of Lanthanide Complexes of Tetrapicolyl‐Appended Cyclen

Lanthanide complexes of tetrapicolyl cyclen displayed remarkably high affinities for fluoride (log K≈5) in water, and were shown to form 1:1 complexes. The behaviour of these systems can be rationalised by changes to the magnitude of the crystal‐field parameter, . However, such changes are not invariably accompanied by a change in sign of this parameter: for early lanthanides, the N8 donor set with a coordinated axial water molecule ensures that the magnetic anisotropy has the opposite sense to that observed in the analogous dehydrated lanthanide complexes.     

19F Paramagnetic Relaxation Enhancement: A Valuable Tool for Distance Measurements in Proteins

Fluorine NMR paramagnetic relaxation enhancement was evaluated as a versatile approach for extracting distance information in selectively F‐labeled proteins. Proof of concept and initial applications are presented for the HIV‐inactivating lectin cyanovirin‐N. Single F atoms were introduced at the 4‐, 5‐, 6‐ or 7 positions of Trp49 and the 4‐position of Phe4, Phe54, and Phe80. The paramagnetic nitroxide spin label was attached to Cys residues that were placed into the protein at positions 50 or 52. ¹⁹F‐T₂ NMR spectra with different relaxation delays were recorded and the transverse ¹⁹F‐PRE rate, ¹⁹F‐Γ₂, was used to determine the average distance between the F nucleus and the paramagnetic center. Our data show that experimental ¹⁹F PRE‐based distances correspond to 0.93 of the ¹H_N‐PRE distances, in perfect agreement with the gyromagnetic γ¹⁹F/γ¹H ratio, thereby demonstrating that ¹⁹F PREs are excellent alternative parameters for quantitative distance measurements in selectively F‐labeled proteins.     

NMR Studies of Mixed-Ligand Lanthanide (III) Complexes. Peculiarities of Molecular Structure, Dynamics and Paramagnetic Properties for Cerium Subgroup Chelates with Crown Ethers

The molecular structure, dynamics and paramagnetic properties of the complex cations [Ln(ptfa)₂ (18-crown-6)]⁺ in deuterated toluene were studied for Ln = La, Ce, Pr and Nd. The activation enthalpy values of 68 ± 5, 55 ± 15 and 60 ± 13 kJ mol^-1 for the 18-crown-6 conformationalinversion processes for the complexcations of Ce, Pr and Nd, respectively,were obtained. Quantitativeinvestigation of the lanthanide-induced chemical shifts shows a monotonic change of a spatial structure and magnetic susceptibility in comparison with the Bleaney predicted dependence. The free energy of molecular inversion activation for 18-crown-6 molecules in the complex cation [Ln(fod)₂(18-crown-6)]⁺ is 74 ± 9 kJ mol^-1 at 363 K, which is a little more than the value of the free energy of activation 64 ± 9 kJ mol^-1 at 363 K in the complex cation [Ln(ptfa)₂(18-crown-6)]⁺.     

Rare-earth tricyanomelaminates [NH(4)]Ln[HC(6)N(9)](2)[H(2)O](7)H(2)O (Ln=La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy): structural investigation, solid-state NMR spectroscopy, and photoluminescence

The rare-earth tricyanomelaminates, [NH(4)]Ln[HC(6)N(9)](2)[H(2)O](7)xH(2)O (LnTCM; Ln=La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy), have been synthesized through ion-exchange reactions. They have been characterized by powder as well as single-crystal X-ray diffraction analysis, vibrational spectroscopy, and solid-state (1)H, (13)C, and (15)N MAS NMR spectroscopy. The X-ray powder pattern common to all nine rare-earth tricyanomelaminates LnTCM (Ln=La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy) indicates that they are isostructural. The single-crystal X-ray diffraction pattern of LnTCM is indicative of non-merohedral twinning. The crystals are triclinic and separation of the twin domains as well as refinement of the structure were successfully carried out in the space group P1 for LaTCM (LaTCM; P1, Z=2, a=7.1014(14), b=13.194(3), c=13.803(3) A, alpha=90.11(3), beta=77.85(3), gamma=87.23(3) degrees , V=1262.8(4) A(3)). In the crystal structure, each Ln(3+) is surrounded by two nitrogen atoms from two crystallographically independent tricyanomelaminate moieties and seven oxygen atoms from crystal water molecules. The positions of all of the hydrogen atoms of the ammonium ions and water molecules could not be located from difference Fourier syntheses. The presence of [NH(4)](+) ions as well as two NH groups belonging to two crystallographically independent monoprotonated tricyanomelaminate moieties has only been confirmed by subjecting LaTCM to solid-state (1)H, (13)C, and (15)N{(1)H} cross-polarization (CP) MAS NMR and advanced CP experiments such as cross-polarization combined with polarization inversion (CPPI). The (1)H 2D double-quantum single-quantum homonuclear correlation (DQ SQ) spectrum and the (15)N{(1)H} 2D CP heteronuclear-correlation (HETCOR) spectrum have revealed the hydrogen-bonded (N--HN) dimer of monoprotonated tricyanomelaminate moieties as well as H-bonding through [NH(4)](+) ions and H(2)O molecules. The structures of the other eight rare-earth tricyanomelaminates (LnTCM; Ln=Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy) have been refined from X-ray powder diffraction data by the Rietveld method. Photoluminescence studies of [NH(4)]Eu[HC(6)N(9)](2)[H(2)O](7)xH(2)O have revealed orange-red (lambda(max)=615 nm) emission due to the (5)D(0)-(7)F(2) transition, whereas [NH(4)]Tb[HC(6)N(9)](2)[H(2)O](7)xH(2)O has been found to show green emission with a maximum at 545 nm arising from the (5)D(4)-(7)F(5) transition. DTA/TG studies of [NH(4)]Ln[HC(6)N(9)](2)[H(2)O](7)xH(2)O have indicated several phase transitions associated with dehydration of the compounds above 150 degrees C and decomposition above 200 degrees C.