Noncovalent Tagging Proteins with Paramagnetic Lanthanide Complexes for Protein Study

The site‐specific labeling of proteins with paramagnetic lanthanides offers unique opportunities for NMR spectroscopic analysis in structural biology. Herein, we report an interesting way of obtaining paramagnetic structural restraints by employing noncovalent interaction between a lanthanide metal complex, [Ln(L)₃]^n? (L=derivative of dipicolinic acid, DPA), and a protein. These complexes formed by lanthanides and DPA derivatives, which have different substitution patterns on the DPA derivatives, produce diverse thermodynamic and paramagnetic properties when interacting with proteins. The binding affinity of [Ln(L)₃]^n? with proteins, as well as the determined paramagnetic tensor, are tunable by changing the substituents on the ligands. These noncovalent interactions between [Ln(L)₃]^n? and proteins offer great opportunities in the tagging of proteins with paramagnetic lanthanides. We expect that this method will be useful for obtaining multiple angles and distance restraints of proteins in structural biology.     

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).

     

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.     

Insight of the Metal–Ligand Interaction in f-Element Complexes by Paramagnetic NMR Spectroscopy

The magnetic properties of Ln^III and An^III complexes formed with dipicolinate ligands have been studied by NMR spectroscopy. To know precisely the geometries of these complexes, a crystallographic study by single-crystal X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) in solution was performed. Several methods to separate the paramagnetic shifts observed in the NMR spectra were applied to these complexes. Methods using a number of nuclei of the dipicolinate ligands revealed an abrupt change in the geometries of the complexes and a metal–ligand interaction in the middle of the lanthanide series. A study of the variation of the paramagnetic shifts with temperature demonstrated that higher-order terms of the dipolar and contact contributions are required, especially for the lightest Ln^III and almost all the studied An^III. Bleaney's parameters <S_z>_a and relating to the contact and dipolar terms, respectively, were deduced from experimental data and compared with the results of ab initio calculations. Quite a good agreement was found for the temperature dependencies of <S_z>_a and . However, the values obtained from cation magnetic anisotropy calculations showed some discrepancies with the values derived from Bleaney's equation defined for Ln^III. Other parameters, such as the crystal field parameter and the hyperfine constants F_i obtained from the experimental data of the [An(ethyl-dpa)₃]³⁻ complexes (ethyl-dpa=4-ethyl-2,6-dipicolinic acid), are at odds with the assumptions underlying Bleaney's theory.     

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.     

A caged lanthanide complex as a paramagnetic shift agent for protein NMR

A lanthanide complex, named CLaNP (caged lanthanide NMR probe) has been developed for the characterisation of proteins by paramagnetic NMR spectroscopy. The probe consists of a lanthanide chelated by a derivative of DTPA (diethylenetriaminepentaacetic acid) with two thiol reactive functional groups. The CLaNP molecule is attached to a protein by two engineered, surface-exposed, Cys residues in a bidentate manner. This drastically limits the dynamics of the metal relative to the protein and enables measurements of pseudocontact shifts. NMR spectroscopy experiments on a diamagnetic control and the crystal structure of the probe-protein complex demonstrate that the protein structure is not affected by probe attachment. The probe is able to induce pseudocontact shifts to at least 40 A from the metal and causes residual dipolar couplings due to alignment at a high magnetic field. The molecule exists in several isomeric forms with different paramagnetic tensors; this provides a fast way to obtain long-range distance restraints.     

A Two‐Armed Lanthanoid‐Chelating Paramagnetic NMR Probe Linked to Proteins via Thioether Linkages

Paramagnetic NMR probes provide valuable long‐range structural information on proteins and protein complexes. A new, stable, two‐armed lanthanoid probe is reported that can be attached to a protein site‐specifically via chemically inert thioether linkages.     

Structure Determination of Binuclear Triple-Decker Phthalocyaninato Complexes by NMR via Paramagnetic Shifts Analysis Using Symmetry Peculiarities

The detailed knowledge about the structure of multinuclear paramagnetic lanthanide complexes for the targeted design of these compounds with special magnetic, sensory, optical and electronic properties is a very important task. At the same time, establishing the structure of such multinuclear paramagnetic lanthanide complexes in solution, using NMR is a difficult task, since several paramagnetic centers act simultaneously on the resulting chemical shift of a particular nucleus. In this paper, we have demonstrated the possibility of molecular structure determination in solution on the example of binuclear triple-decker lanthanide(III) complexes with tetra-15-crown-5-phthalocyanine Ln₂[(15C5)₄Pc]₃ {where Ln = Tb (1) and Dy (2)} by quantitative analysis of the pseudo-contact lanthanide-induced shifts (LIS). The symmetry of complexes was used for the simplification of the calculation of pseudo-contact shifts on the base of the expression for the magnetic susceptibility tensor in the arbitrary oriented magnetic axis system. Good agreement between the calculated and experimental shifts in the ¹H NMR spectra indicates the similarity of the structure for the complexes 1 and 2 in solution of CDCl₃ and the structure in the crystalline phase, found from the data of the X-ray structural study of the similar complex Lu₂[(15C5)₄Pc]₃. The described approach can be useful for LIS analysis of other polynuclear symmetric lanthanide complexes.     

N,N′-bis(substituted-phenyl)oxamides and their dinuclear pentacoordinate nickel(II) complexes

The preparation, spectroscopic characterization and magnetic study of N,N′-bis(substituted-phenyl)oxamidate-bridged nickel(II) dinuclear complexes of formula {[Ni(N₃-mc)]₂(μ-CONC₆H₄-X)}(PF₆)₂ (N₃-mc = 2,4,4-trimethyl-1,5,9-triazacyclo-dodec-1-ene (Me₃-N₃-mc) or 2,4,4,9-tetramethyl-1,5,9-triazacyclododec-1-ene (Me₄-N₃-mc), X = 2-Cl, 4-Cl, 2-OCH₃, 4-OCH₃) are reported. These paramagnetic nickel(II) complexes have been characterized by both one- and two-dimensional (COSY) ¹H NMR techniques. The COSY spectrum of 5 has allowed to achieve the assignment of the phenyl protons of the N,N′-diphenyloxamidate. The crystal structures of [Ni(Me₃-N₃-mc)(μ-CONC₆H₄-4-Cl)]₂(PF₆)₂ (6), [Ni(Me₃-N₃-mc)(μ-CONC₆H₄-4-OMe)]₂(PF₆)₂ (8) and [Ni(Me₄-N₃-mc)(μ-CONC₆H₄-2-Cl)]₂(PF₆)₂ (9) have been determined and their magnetic properties have been studied. The value of magnetic coupling between the two nickel(II) ions across the oxamidate bridge [J = − 37.6 (6), −39.9 (8) and −39.7 cm⁻¹ (9)] is sensitive to the distortion of the coordination sphere of the metal ions and the topology of the molecular bridge.     

Aluminum alkyls with intramolecularly coordinated oxygen

Organoaluminum alkyls L¹AlMe₂ ( 1 ), L²AlMe₂ ( 2 ) and L²AlⁱBu₂ ( 3 ) with O,C,O‐chelating ligands L¹ and L² [L¹ = 2, 6‐(MeOCH₂)₂C₆H₃ and L² = 2, 6‐(^tBuOCH₂)₂C₆H₃] were prepared. The compounds have been characterized by elemental analysis, ¹H, ¹³C, ²⁷Al NMR spectroscopy and X‐ray diffraction analysis ( 3 ). Solution NMR studies indicated the four coordinated aluminum atom and dissociation/association dynamic process in solution of 1 – 3 . The X‐ray diffraction analysis of 3 showed that the aluminum atom is [4 + 1] coordinated with the trans‐trigonal bipyramidal geometry. The reactivity of 2 was investigated. Reactions of 2 with MeOH and I₂ resulted in aluminum alkoxide [L²Al(OMe)₂ ( 4 )] and iodides [L²AlI₂· THF ( 5 ) and L²AlI₂ ( 6 )], respectively, characterized by elemental analysis, IR and ¹H, ¹³C and ²⁷Al NMR spectroscopy. Copyright © 2005 John Wiley & Sons, Ltd.     

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.     

Protein Unfolding: 1H‐NMR Studies of Paramagnetic Ferricytochrome c‐550 from Horse Heart

Electronic transfer protein cytochrome c‐550 from horse heart is studied in the unfolded state by means of paramagnetic ¹H NMR. The protein contains 104 aminoacid residues and a heme group with low spin Fe^III ion in the oxidized form of protein. The global secondary structure is of the α‐helix type as occurs in the case of very other cytochromes c investigated such as cyt c‐550 from Thiobacillus versutus or cyt c‐551 from Pseudomonas aeruginosa. We have studied the coordination characteristic and electronic properties of heme iron horse heart ferricytochrome c‐550 at increasing denaturing conditions (up to 3.1 M GuHCl and 288‐323 K). The ¹H T₁ values of the signals were measured and some resonance assignments made based on EXSY experiments. The electronic structure of the iron(III) is discussed on the basis of the temperature dependence of the isotropic shifts and relaxation times. These results show that it is produced a change of spin, from low‐spin iron(III) (²T₂, S=1/2) in the folded state to high‐spin iron(III) (⁶A₁, S=5/2) in the unfolded state. It seems to be possible that in the opened structure the ferricyt c‐550 loses one axial ligand (His/‐) appearing the spin transition.     

Highly Fluorescent and Water‐Soluble Diketopyrrolopyrrole Dyes for Bioconjugation

The preparation of highly water‐soluble and strongly fluorescent diketopyrrolopyrrole (DPP) dyes using an unusual taurine‐like sulfonated linker has been achieved. Exchanging a phenyl for a thienyl substituent shifts the emission wavelength to near λ=600 nm. The free carboxylic acid group present in these new derivatives was readily activated and the dyes were subsequently covalently linked to a model protein (bovine serum albumin; BSA). The bioconjugates were characterized by electronic absorption, fluorescence spectroscopy and MALDI‐TOF mass spectrometry, thus enabling precise determination of the labeling density (ratio DPP/BSA about 3 to 8). Outstanding values of fluorescence quantum yield (30 % to 59 %) for these bioconjugates are obtained. The photostability of these DPP dyes is considerably greater than that of fluorescein under the same irradiation conditions. Remarkably low detection limits between 80 and 300 molecules/μm² were found for the BSA bioconjugates by fluorescence imaging with a epifluorescence microscope.     

Paramagnetic Solid-State NMR to Localize the Metal-Ion Cofactor in an Oligomeric DnaB Helicase

Paramagnetic metal ions can be inserted into ATP-fueled motor proteins by exchanging the diamagnetic Mg²⁺ cofactor with Mn²⁺ or Co²⁺. Then, paramagnetic relaxation enhancement (PRE) or pseudo-contact shifts (PCSs) can be measured to report on the localization of the metal ion within the protein. We determine the metal position in the oligomeric bacterial DnaB helicase from Helicobacter pylori complexed with the transition-state ATP-analogue ADP:AlF₄⁻ and single-stranded DNA using solid-state NMR and a structure-calculation protocol employing CYANA. We discuss and compare the use of Mn²⁺ and Co²⁺ in localizing the ATP cofactor in large oligomeric protein assemblies. ³¹P PCSs induced in the Co²⁺-containing sample are then used to localize the DNA phosphate groups on the Co²⁺ PCS tensor surface enabling structural insights into DNA binding to the DnaB helicase.     

Novel macrocyclic EuII complexes: fast water exchange related to an extreme M-O water distance

Eu(II) complexes are potential candidates for pO(2)-responsive contrast agents in magnetic resonance imaging. In this regard, we have characterized two novel macrocyclic Eu(II) chelates, [Eu(II)(DOTA)(H(2)O)](2-) and [Eu(II)(TETA)](2-) (H(4)DOTA=1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid, H(4)TETA=1,4,8,11-tetraazacyclotetradecane-1,4,8,11-tetraacetic acid) in terms of redox and thermodynamic complex stability, proton relaxivity, water exchange, rotation and electron spin relaxation. Additionally, solid-state structures were determined for the Sr(II) analogues. They revealed no inner-sphere water in the TETA and one inner-sphere water molecule in the DOTA complex. This hydration pattern is retained in solution, as the (17)O chemical shifts and (1)H relaxation rates proved for the corresponding Eu(II) compounds. The thermodynamic complex stability, determined from the formal redox potential and by pH potentiometry, of [Eu(II)(DOTA)(H(2)O)](2-) (lg K(Eu(II))=16.75) is the highest among all known Eu(II) complexes, whereas the redox stabilities of both [Eu(II)(DOTA)(H(2)O)](2-) and [Eu(II)(TETA)](2-) are inferior to that of 18-membered macrocyclic Eu(II) chelates. Variable-temperature (17)O NMR, NMRD and EPR studies yielded the rates of water exchange, rotation and electron spin relaxation. Water exchange on [Eu(II)(DOTA)(H(2)O)](2-) is remarkably fast (k298(ex)=2.5 x 10(9) s(-1)). The near zero activation volume (DeltaV++ =+0.1+/-1.0 cm(3) mol(-1)), determined by variable-pressure (17)O NMR spectroscopy, points to an interchange mechanism. The fast water exchange can be related to the low charge density on Eu(II), to an unexpectedly long M-O(water) distance (2.85 A) and to the consequent interchange mechanism. Electron spin relaxation is considerably slower on [Eu(II)(DOTA)(H(2)O)](2-) than on the linear [Eu(II)(DTPA)(H(2)O)](3-) (H(5)DTPA=diethylenetriaminepentaacetic acid), and this difference is responsible for its 25 percent higher proton relaxivity (r(1)=4.32 mM(-1) s(-1) for [Eu(II)(DOTA)(H(2)O)](2-) versus 3.49 mM(-1) s(-1) for [Eu(II)(DTPA)(H(2)O)](3-); 20 MHz, 298 K).     

Long-range-distance NMR effects in a protein labeled with a lanthanide-DOTA chelate

A two-thiol reactive lanthanide-DOTA (1,4,7,10-tetraazacyclododecane-N,N',N',N'-tetraacetic acid) chelate, CLaNP-3 (CLaNP=caged lanthanide NMR probe), was synthesized for the rigid attachment to cysteine groups on a protein surface, and used to obtain long-range-distance information from the {15N,1H} HSQC spectra of the protein-lanthanide complex. The DOTA ring exhibits several isomers that are in exchange; however, single resonances were observed for most amide groups in the protein, allowing determination of a single, apparent magnetic-susceptibility tensor. Pseudocontact shifts caused by Yb-containing CLaNP-3 were observed for atoms at 15-35 A from the metal. By using Gd-containing CLaNP-3, relaxation effects were observed, allowing distances up to 30 A from the paramagnetic center to be determined accurately. Similar results were obtained with a Gd-DTPA (diethylene-triaminepentaacetic acid) chelate, CLaNP-1, bound in the same bidentate manner to the protein. This study demonstrates that bidentate attachment of a paramagnetic probe enables determination of long-range distances.