Advances in the NMR investigation of paramagnetic molecules in solution (original) (raw)
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Perspectives in paramagnetic NMR of metalloproteins
Dalton Trans., 2008
NMR experiments and tools for the characterization of the structure and dynamics of paramagnetic proteins are presented here. The focus is on the importance of 13 C direct-detection NMR for the assignment of paramagnetic systems in solution, on the information contained in paramagnetic effects observed both in solution and in the solid state, and on novel paramagnetism-based tools for the investigation of conformational heterogeneity in protein-protein complexes or in multi-domain proteins.
A double armed, hydrophilic, transition metal complex as paramagnetic NMR probe
Angewandte Chemie, 2019
Synthetic metal complexes can be used as paramagnetic probes for the study of proteins and protein complexes.H erein, two transition metal NMR probes (TraNPs) are reported. TraNPs are attached through two arms to ap rotein to generate ap seudocontact shift (PCS) using cobalt(II), or paramagnetic relaxation enhancement (PRE) with manganese(II). The PCS analysis of TraNPs attached to three different proteins shows that the size of the anisotropic component of the magnetic susceptibility depends on the probe surroundings at the surface of the protein, contrary to what is observed for lanthanoid-based probes.T he observed PCS are relatively small, making cobalt-based probes suitable for localized studies,such as of an active site.The obtained PREs are stronger than those obtained with nitroxide spin labels and the possibility to generate both PCS and PRE offers advantages.T he properties of TraNPs in comparison with other cobalt-based probes are discussed.
Journal of the American Chemical Society, 2012
A natural bond orbital (NBO) analysis of unpaired electron spin density in metalloproteins is presented, which allows a fast and robust calculation of paramagnetic NMR parameters. Approximately 90% of the unpaired electron spin density occupies metal−ligand NBOs, allowing the majority of the density to be modeled by only a few NBOs that reflect the chemical bonding environment. We show that the paramagnetic relaxation rate of protons can be calculated accurately using only the metal−ligand NBOs and that these rates are in good agreement with corresponding rates measured experimentally. This holds, in particular, for protons of ligand residues where the point-dipole approximation breaks down. To describe the paramagnetic relaxation of heavy nuclei, also the electron spin density in the local orbitals must be taken into account. Geometric distance restraints for 15 N can be derived from the paramagnetic relaxation enhancement and the Fermi contact shift when local NBOs are included in the analysis. Thus, the NBO approach allows us to include experimental paramagnetic NMR parameters of 15 N nuclei as restraints in a structure optimization protocol. We performed a molecular dynamics simulation and structure determination of oxidized rubredoxin using the experimentally obtained paramagnetic NMR parameters of 15 N. The corresponding structures obtained are in good agreement with the crystal structure of rubredoxin. Thus, the NBO approach allows an accurate description of the geometric structure and the dynamics of metalloproteins, when NMR parameters are available of nuclei in the immediate vicinity of the metal-site.
Long-range paramagnetic NMR data can provide a closer look on metal coordination in metalloproteins
Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry, 2018
Paramagnetic NMR data can be profitably incorporated in structural refinement protocols of metalloproteins or metal-substituted proteins, mostly as distance or angle restraints. However, they could in principle provide much more information, because the magnetic susceptibility of a paramagnetic metal ion is largely determined by its coordination sphere. This information can in turn be used to evaluate changes occurring in the coordination sphere of the metal when ligands (e.g.: inhibitors) are bound to the protein. This gives an experimental handle on the molecular structure in the vicinity of the metal which falls in the so-called blind sphere. The magnetic susceptibility anisotropy tensors of cobalt(II) and nickel(II) ions bound to human carbonic anhydrase II in free and inhibited forms have been determined. The change of the magnetic susceptibility anisotropy is directly linked to the binding mode of different ligands in the active site of the enzyme. Indication about the metal c...
ACS Symposium Series, 2003
Although it is well established that paramagnetic NMR spectroscopy is a powerful tool to derive structural information, the methodology is still not yet universally applied to paramagnetic small molecule complexes. In this paper paramagnetic 1 H NMR spectroscopy is investigated as a convenient method for the experimental inorganic chemist to elucidate solution structures and speciation of small molecule metal complexes derived from 2,6-pyridinedicarboxylic acid as ligand. Spectra of complexes with O h geometry, in which the spin states of the metal ion range from d 3 (Cr 3+), d 5 (Fe 3+), d 6 (Fe 2+), d 7 (Co 2+) to d 8 (Ni 2+), were recorded and analyzed. For all complexes the 1 H NMR spectra give well-resolved, easy detectable lines, which depending on the spin state and electron relaxation time of the metal ion and the pH of the solution can be fairly broad. Regardless, the spectra allow complexes of 1:1 and 1:2 stoichiometries to be distinguished in spite of the metal nucleus short nuclear correlation and relaxation times, and the magnitude of the hyperfine shift spread. The pH stability profile and the ability of the complexes to undergo ligand exchange reactions were also investigated for each of the complexes. This work demonstrates that paramagnetic 1 H NMR spectroscopy is very useful for characterizing small molecule complexes and their solution chemistry without requiring a detailed analysis of the hyperfine shifts and relaxivities.
Perspectives on paramagnetic NMR from a life sciences infrastructure
Journal of Magnetic Resonance, 2017
The effects arising in NMR spectroscopy because of the presence of unpaired electrons, collectively referred to as ''paramagnetic NMR" have attracted increasing attention over the last decades. From the standpoint of the structural and mechanistic biology, paramagnetic NMR provides long range restraints that can be used to assess the accuracy of crystal structures in solution and to improve them by simultaneous refinements through NMR and X-ray data. These restraints also provide information on structure rearrangements and conformational variability in biomolecular systems. Theoretical improvements in quantum chemistry calculations can nowadays allow for accurate calculations of the paramagnetic data from a molecular structural model, thus providing a tool to refine the metal coordination environment by matching the paramagnetic effects observed far away from the metal. Furthermore, the availability of an improved technology (higher fields and faster magic angle spinning) has promoted paramagnetic NMR applications in the fast-growing area of biomolecular solid-state NMR. Major improvements in dynamic nuclear polarization have been recently achieved, especially through the exploitation of the Overhauser effect occurring through the contact-driven relaxation mechanism: the very large enhancement of the 13 C signal observed in a variety of liquid organic compounds at high fields is expected to open up new perspectives for applications of solution NMR.
The solution structure of paramagnetic metalloproteins
Progress in Biophysics and Molecular Biology, 1996
Paramagnetism causes broadening of the NMR lines and therefore makes dif®cult the detection of the constraints (NOEs and 3 J) which are necessary for the determination of solution structures. The broadening is due to the fast nuclear relaxation rates, which are induced by the coupling of the nucleus with the unpaired electrons. Nevertheless, an NMR methodology has been developed, allowing the detection of classical constraints. This has allowed us to solve the ®rst solution structure of a paramagnetic metalloprotein in 1994. Since then, several solution structures of paramagnetic proteins have appeared. In addition, paramagnetism has been exploited in order to obtain new, nonclassical constraints. First, the nuclear relaxation has been exploited to obtain metal±proton distances. The position of nuclei with respect to the magnetic susceptibility tensor axes has been determined by the use of pseudocontact shifts. The contact shifts have been used as constraints after discovering or con®rming the shift dependence on dihedral angles. Paramagnetic molecules can be strongly magnetically anisotropic and therefore display partial orientation in strong external magnetic ®elds. These orientational effects result in dipolar contributions to the 15 N-1 H 1 J coupling. Such contributions can yield powerful structural constraints. In summary, the solution structure of many paramagnetic metalloproteins has been solved and described, and several new strategies have been developed for such solution structure determinations.