Design, synthesis, and evaluation of a lanthanide chelating protein probe: CLaNP-5 yields predictable paramagnetic effects independent of environment

Immobilized lanthanide ions offer the opportunity to refine structures of proteins and the complexes they form by using restraints obtained from paramagnetic NMR experiments. We report the design, synthesis, and spectroscopic evaluation of the lanthanide chelator, Caged Lanthanide NMR Probe 5 (CLaNP-5) readily attachable to a protein surface via two cysteine residues. The probe causes tunable pseudocontact shifts, alignment, paramagnetic relaxation enhancement, and luminescence, by chelating it to the appropriate lanthanide ion. The observation of single shifts and the finding that the magnetic susceptibility tensors obtained from shifts and alignment analyses are highly similar strongly indicate that the probe is rigid with respect to the protein backbone. By placing the probe at various positions on a model protein it is demonstrated that the size and orientation of the magnetic susceptibility tensor of the probe are independent of the local protein environment. Consequently, the effects of the probe are readily predictable using a protein structure only. These findings designate CLaNP-5 as a protein probe to deliver unambiguous high quality structural restraints in studies on protein-protein and protein-ligand interactions.     

Lanthanide-binding peptides for NMR measurements of residual dipolar couplings and paramagnetic effects from multiple angles

Lanthanide-binding peptide tags (LBTs) containing a single cysteine residue can be attached to proteins via a disulfide bond, presenting a flexible means of tagging proteins site-specifically with a lanthanide ion. Here we show that cysteine residues placed in different positions of the LBT can be used to expose the protein to different orientations of the magnetic susceptibility anisotropy (delta chi) tensor and to generate different molecular alignments in a magnetic field. Delta chi tensors determined by nuclear magnetic resonance (NMR) spectroscopy for LBT complexes with Yb3+, Tm3+, and Er3+ suggest a rational way of producing alignment tensors with different orientations. In addition, knowledge of the delta chi tensor of LBT allows modeling of the protein-LBT structures. Despite evidence for residual mobility of the LBTs with respect to the protein, the pseudocontact shifts and residual dipolar couplings displayed by proteins disulfide-bonded to LBTs are greater than those achievable with most other lanthanide binding tags.     

A New Class of Lanthanide Complexes with Three Ligand Centered Radicals: NMR Evaluation of Ligand Field Energy Splitting and Magnetic Coupling

Combination of three radical anionic Ph-BIAN ligands (Ph-BIAN=bis-(phenylimino)-acenaphthenequinone) with lanthanoid ions leads to a series of homoleptic, six-coordinate complexes of the type Ln(Ph-BIAN)₃. Magnetic coupling data were measured by paramagnetic solution NMR spectroscopy. Combining ¹H NMR with ²H NMR of partially deuterated compounds allowed a detailed study of the magnetic susceptibility anisotropies over a large temperature range. The observed chemical shifts were separated into ligand- and metal-centered contributions by comparison with the Y analogue (diamagnetic at the metal). The metal-centered contributions of the complexes with the paramagnetic ions could then be separated into pseudocontact and Fermi contact shifts. The latter is large within the Ph-BIAN scaffold, which shows that magnetic coupling is significant between the lanthanide ion and the radical ligand. Pseudocontact shifts were further correlated to structural data obtained from X-ray diffraction experiments. Ligand-field parameters were determined by fitting the temperature dependence of the observed magnetic susceptibility anisotropies. The electronic structure determined by this approach shows, that the Er and Tm analogues are candidates for single molecule magnets (SMM). These results demonstrate the possibilities for the application of NMR spectroscopy in investigations of paramagnetic systems in general and single molecule magnets in particular.     

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.     

Strategies for measurements of pseudocontact shifts in protein NMR spectroscopy.

Paramagnetic metal ions bound to proteins generate a dipolar field that can be accurately probed by pseudocontact shifts (PCS) displayed by the protein's nuclear spins. PCS are highly useful for determining the coordinates of individual spins in the molecule and for rapid structure determinations of entire protein-protein and protein-ligand complexes. However, PCS measurements require reliable resonance assignments for the molecule in its paramagnetic state and in a diamagnetic reference state. This article discusses different approaches for pairwise resonance assignments, with emphasis on a strategy which exploits chemical exchange between the two states.     

Magnetic susceptibility tensor anisotropies for a lanthanide ion series in a fixed protein matrix.

The full series of lanthanide ions (except the radioactive promethium and the S-state gadolinium) has been incorporated into the C-terminal calcium binding site of the dicalcium protein calbindin D(9k). A fairly constant coordination environment is maintained throughout the series. At variance with several lanthanide complexes with small chelating ligands investigated in the past, the large protein moiety provides a large number of NMR signals whose hyperfine shifts can be exclusively ascribed to pseudocontact shifts (PCS). The chemical shifts of 1H and 15N backbone and side chain amide NH groups were accurately measured through HSQC experiments. 1097 PCS were estimated from these by subtracting the diamagnetic contributions measured on HSQC spectra of either the 4f(0) lanthanum(III) or the 4f(14) lutetium(III) derivatives and used to define a quality factor for the structure. The differences in diamagnetic chemical shifts between the two diamagnetic blanks were relatively small, although some were not negligible especially for the nuclei closest to the metal center. These differences were used as a tolerance for the PCS. The magnetic susceptibility tensor anisotropies for each paramagnetic lanthanide ion were obtained as the result of the solution structure determination performed by using the NOEs of the cerium(III) derivative and the PCS of all lanthanides simultaneously. This set of reliable magnetic data permits an experimental assessment of Bleaney's theory relative to the magnetic properties for an extended series of lanthanide complexes in solution. All of the obtained tensors show some rhombicity, as could be expected from the lack of symmetry of the protein environment. The directions of the largest magnetic susceptibility component for Ce, Pr, Nd, Sm, Tb, Dy, and Ho and of the smallest magnetic susceptibility component for Eu, Er, Tm, and Yb were found to be all within 15 degrees from their average (within 20 degrees for Sm), confirming the essential similarity of the coordination environment for all lanthanides. Bleaney's theory is in excellent qualitative agreement with the observed pattern of axial anisotropies. Its quantitative agreement is substantially better than that suggested by previous analyses performed on more limited sets of PCS data for small lanthanide complexes, the so-called crystal field parameter varying only within +/-30% from one lanthanide to another. These variations are even smaller (+/-15%) if a reasonable T(-3) correction is taken into consideration. A knowledge of magnetic susceptibility anisotropy properties of lanthanides is essential in determining the self-orienting properties of lanthanide complexes in solution when immersed in magnetic fields.     

Paramagnetically induced residual dipolar couplings for solution structure determination of lanthanide binding proteins

Lanthanides may substitute calcium in calcium-binding proteins, such as, for instance, EF-hand proteins. Paramagnetic lanthanides are capable of orienting the protein in high magnetic fields to an extent similar to that obtained by using orienting devices, and each lanthanide orients according to its magnetic susceptibility tensor. Here, Ce(3+), Tb(3+), Dy(3+), Ho(3+), Er(3+), Tm(3+), Yb(3+) in the C-terminal site of calbindin D(9k) have been investigated. Such systems provide (1)H-(15)N residual dipolar couplings (rdc) which can be used for solution structure determinations. Within the frame of optimizing the use of residual dipolar couplings for efficient solution structure determination, it is proposed here to use a number of lanthanides (e.g., >2) to obtain the orientations of the internuclear vectors with respect to an arbitrary reference system. This is facilitated by the independent knowledge of the magnetic susceptibility anisotropy tensor of each metal, obtained from the analysis of the pseudocontact shifts. A further module of the program PARAMAGNETIC-DYANA, called RDCDYANA-ANGLES, is developed to efficiently incorporate such rdc-derived orientations, instead of the rdc themselves, as constraints in the solution structure calculation. This strategy is absolutely general and can be extended to any other pair of dipole-dipole coupled nuclei. The effect of mobility is also assessed. In principle, information on the mobility can be obtained with a number of lanthanide ions >5, or by combining a smaller number of lanthanide ions with a few orienting devices.     

On the possibility of aligning paramagnetic molecules or ions in a magnetic field

Strong magnetic fields can hybridize low rotational states of paramagnetic molecules or molecular ions whose electronic angular momentum is coupled to the molecular axis. The hybridization creates pendular states in which the molecular axis is confined to librate over a limited angular range about the field direction. In this way substantial spatial alignment associated with large Zeeman shifts can be attained for many ground-state radicals or ions and electronically excited states of diatomic or linear molecules. The magnetic hybridization is analogous to that recently demonstrated for polar molecules in electric fields. The magnetic version can only provide ensemble alignment rather than orientation, but offers complementary chemical scope by virtue of its applicability to nonpolar molecules and ions.     

Backbone-only protein solution structures with a combination of classical and paramagnetism-based constraints: a method that can be scaled to large molecules.

Herein, it is shown that a medium-resolution solution structure of a protein can be obtained with the sole assignment of the protein backbone and backbone-related constriants if a derivative with a firmly bound paramagnetic metal is available. The proof-of-concept is provided on calbindin D9k, a calcium binding protein in which one of the two calcium ions can be selectively substituted by a paramagnetic lanthanide ion. The constraints used are HN (and Ha) nuclear Overhauser effects (NOEs), hydrogen bonds, dihedral angle constriants from chemical shifts, and the following paramagnetism-based constraints: 1) pseudocontact shifts, acquired by substituting one (or more) lanthanide(s) in the C-terminal calcium binding site; 2) N-HN residual dipolar couplings due to self-orientation induced by the paramagnetic lanthanide(s); 3) cross-correlations between the Curie and internuclear dipole-dipole interactions; and 4) paramagnetism-induced relaxation rate enhancements. An upper distance limit for internuclear distances between any two backbone atoms was also given according to the molecular weight of the protein. For this purpose, the paramagnetism-based constraints were collectively implemented in the program CYANA for solution structure determinations, similarly to what was previously done for the program DYANA. The method is intrinsically suitable for large molecular weight proteins.     

3‐Mercapto‐2,6‐Pyridinedicarboxylic Acid: A Small Lanthanide‐Binding Tag for Protein Studies by NMR Spectroscopy

Paramagnetic effects from lanthanide ions present powerful tools for protein studies by nuclear magnetic resonance (NMR) spectroscopy provided that the lanthanide can be site‐specifically and rigidly attached to the protein. A new, particularly small and rigid lanthanide‐binding tag, 3‐mercapto‐2,6‐pyridinedicarboxylic acid (3MDPA), was synthesized and attached to two different proteins via a disulfide bond. The complexes of the N‐terminal domain of the E. coli arginine repressor (ArgN) with seven different paramagnetic lanthanide ions and Co²⁺ were analyzed in detail by NMR spectroscopy. The magnetic susceptibility anisotropy (Δχ) tensors and metal position were determined from pseudocontact shifts. The 3MDPA tag generated very different Δχ tensor orientations compared to the previously studied 4‐mercaptomethyl‐DPA tag, making it a highly complementary and useful tool for protein NMR studies.     

Engineering of a bis-chelator motif into a protein α-helix for rigid lanthanide binding and paramagnetic NMR spectroscopy

Attachment of two nitrilotriacetic acid-based ligands to a protein α-helix in an i, i + 4 configuration produces an octadentate chelating motif that is able to bind paramagnetic lanthanide ions rigidly and with high affinity, leading to large pseudocontact shifts and residual dipolar couplings in the NMR spectrum.     

Structure elucidation with lanthanide induced shifts. 7—development of a reliable method for structure evaluation and the application to organic nitriles

A useful and reliable procedure has been developed for the evaluation of the structures of organic nitriles using lanthanide shift reagents. The procedure is based on a statistical comparison of the experimental lanthanide induced shifts (LIS) with values which are predicted with the pseudocontact equation for a proposed structure. The experimental LIS are obtained by nonlinear regression analysis of the chemical shifts observed in the presence of varying amounts of the shift reagent, Eu(fod)₃. The precise geometry for a proposed structure is obtained from molecular mechanics calculations. The LIS are then predicted with the pseudocontact equation using k=976.6 and a europium-nitrogen bond length of 2.50 Å. (Detailed arguments are presented in support of these values.) The carbon-nitrogen-europium array is approximately linear, although small distortions from linearity are both expected and observed.     

Lanthanide labeling offers fast NMR approach to 3D structure determinations of protein-protein complexes

A novel nuclear magnetic resonance (NMR) strategy based on labeling with lanthanides achieves rapid determinations of accurate three-dimensional (3D) structures of protein-protein complexes. The method employs pseudocontact shifts (PCS) induced by a site-specifically bound lanthanide ion to anchor the coordinate system of the magnetic susceptibility tensor in the molecular frames of the two molecules. Simple superposition of the tensors detected in the two protein molecules brings them together in a 3D model of the protein-protein complex. The method is demonstrated with the 30 kDa complex between two subunits of Escherichia coli polymerase III, comprising the N-terminal domain of the exonuclease subunit epsilon and the subunit theta. The 3D structures of the individual molecules were docked based on a limited number of PCS observed in 2D 15N-heteronuclear single quantum coherence spectra. Degeneracies in the mutual orientation of the protein structures were resolved by the use of two different lanthanide ions, Dy3+ and Er3+.     

Dynamics of the glycosidic bond: conformational space of lactose

The dynamics of the glycosidic bond of lactose was studied by a paramagnetic tagging‐based NMR technique, which allowed the collection of an unusually large series of NMR data for a single compound. By the use of distance‐ and orientation‐dependent residual dipolar couplings and pseudocontact shifts, the simultaneous fitting of the probabilities of computed conformations and the orientation of the magnetic susceptibility tensor of a series of lanthanide complexes of lactose show that its glycosidic bond samples syn/syn, anti/syn and syn/anti ?/ψ regions of the conformational space in water. The analysis indicates a higher reliability of pseudocontact shift data as compared to residual dipolar couplings with the presently available weakly orienting paramagnetic tagging technique. The method presented herein allows for an improved understanding of the dynamic behaviour of oligosaccharides.     

Ion solvation by channel carbonyls characterized by 17O solid-state NMR at 21 T

Recently available ultrahigh magnetic fields offer new opportunities for studies of quadrupole nuclei in biological solids because of the dramatic enhancement in sensitivity and resolution associated with the reduction of second-order quadrupole interactions. Here, we present a new approach for understanding the function and energetics of ion solvation in channels using solid-state 17O NMR spectroscopy of single-site 17O-labeled gramicidin A. The chemical shift and quadrupole coupling parameters obtained in powder samples of lyophilized material are similar to those shown in the literature for carbonyl oxygens. In lipid bilayers, it is found that the carbonyl 17O anisotropic chemical shift of Leu10, one of the three carbonyl oxygens contributing to the ion binding site in gramicidin A, is altered by 40 ppm when K+ ion binds to the channel, demonstrating a high sensitivity to such interactions. Moreover, considering the large breadth of the carbonyl 17O chemical shift (>500 ppm), the recording of anisotropic 17O chemical shifts in bilayers aligned with respect to magnetic field B0 offers high-quality structural restraints similar to 15N and 13C anisotropic chemical shifts.     

Beyond Bleaney's Theory: Experimental and Theoretical Analysis of Periodic Trends in Lanthanide‐Induced Chemical Shift

A detailed analysis of paramagnetic NMR shifts in a series of isostructural lanthanide complexes relavant to PARASHIFT contrast agents reveals unexpected trends in the magnetic susceptibility anisotropy that cannot be explained by the commonly used Bleaney's theory. Ab initio calculations reveal that the primary assumption of Bleaney's theory—that thermal energy is larger than the ligand field splitting—does not hold for the lanthanide complexes in question, and likely for a large fraction of lanthanide complexes in general. This makes the orientation of the magnetic susceptibility tensor differ significantly between complexes of different lanthanides with the same ligand: one of the most popular assumptions about isostructural lanthanide series is wrong.     

Homonuclear decoupling for liquid-state NMR

We present a solution to the problem of decoupling of a homonuclear two-spin system having weak isotropic scalar coupling. We describe non-selective pulse sequences that create an effective field perpendicular to the coupling interaction over a broad range of chemical shifts, with a magnitude proportional to the chemical shifts. Effective decoupling is achieved when the difference in chemical shifts imprinted on the perpendicular field is sufficiently larger than the coupling between the spins. The proposed methods scale down the chemical shifts. The pulse sequences may be useful in various applications in nuclear magnetic resonance spectroscopy.     

Structure elucidation with lanthanide-induced shifts. 4—Bound shifts vs relative shifts

The use of lanthanide shift reagents (LSR's) to obtain additional structural information from nuclear magnetic resonance studies has gained widespread acceptance. However, there has not been general agreement with regard to the most appropriate methodology for analysis of the shifted NMR spectra. We present arguments that only the bound shifts (Δ₁) corresponding to the LS complex should be used for correlation of lanthanide-induced shifts with molecular structure by means of the pseudocontact equation. Several examples are discussed of compounds for which the relative induced shifts are dependent on the concentration of LSR. For such cases it is not possible for both Δ₁ and Δ₂ (the bound shift corresponding to the LS₂ complex) to correlate successfully with the correct structure. Alternative methods of obtaining bound shifts are critically evaluated.     

Solution Structure of a Lanthanide-binding DNA Aptamer Determined Using High Quality pseudocontact shift restraints

In this contribution we report the high-resolution NMR structure of a recently identified lanthanide-binding aptamer (LnA). We demonstrate that the rigid lanthanide binding by LnA allows for the measurement of anisotropic paramagnetic NMR restraints which to date remain largely inaccessible for nucleic acids. One type of such restraints - pseudocontact shifts (PCS) induced by four different paramagnetic lanthanides - was extensively used throughout the current structure determination study and the measured PCS turned out to be exceptionally well reproduced by the final aptamer structure. This finding opens the perspective for a broader application of paramagnetic effects in NMR studies of nucleic acids through the transplantation of the binding site found in LnA into other DNA/RNA systems.     

Structure determination by restrained molecular dynamics using NMR pseudocontact shifts as experimentally determined constraints

The structure of a DNA octamer d(TTGGCCAA)(2) complexed to chromomycin-A(3) and a single divalent cobalt ion has been solved by using the pseudocontact shifts due to the unpaired electrons on the cobalt. A protocol was developed and critically evaluated for using the pseudocontact shifts in structure determination. The pseudocontact shifts were input as experimental restraints in molecular dynamics simulations with or without NOE constraints. Both the magnitude and orientation of the susceptibility anisotropy tensor required for the shift calculations were determined during the simulations by iterative refinement. The pseudocontact shifts could be used to define the structure to a very high precision and accuracy compared with a corresponding NOE-determined structure. Convergence was obtained from different starting structures and tensors. A structure determination using both NOE's and pseudocontact shifts revealed a general agreement between the two data sets. However, some evidence for a discrepancy between NOE's and pseudocontact shifts was observed in the backbone and terminal base pairs of the DNA. Violations in shift or NOE restraints remaining in the final structures were examined and may be a reflection of motional averaging of the constraints and evidence for flexibility. This work demonstrates that pseudocontact shifts are a powerful tool for NMR structure determination.