Nuclear Magnetic Resonance Paramagnetic Relaxation Research Articles

Field- and Temperature-Dependent Paramagnetic Relaxation Enhancements in Co(II) Trispyrazolylmethanes.

A comprehensive field- and temperature-dependent examination of nuclear magnetic resonance paramagnetic relaxation enhancements (PREs) for the constitutive protons of [Co(Tpm)2][BF4]2 is presented. Data for an apically substituted derivative clearly establish that bis-Tpm complexes of Co(II) undergo Jahn-Teller dynamics about the molecular threefold axis. PREs from the parent Tpm complex were used to numerically extract the electron relaxation times (T1e). The Tpm complex showed field-dependent behavior, with an approximately 40% higher activation barrier than the related trispyrazolylborate (Tp) complex, based on fits to the T1e vs T, B0 data. Analysis of the field-dependent line widths revealed a surprisingly large contribution from susceptibility (Curie) relaxation (20-35% at the highest field), and a molecular radius (9.5 Å) that is consistent with a tightly associated counterion slowing rotation in solution. Density functional theory showed a shared vibration that is consistent with the Jahn-Teller and appears proportionately higher in energy in [Co(Tpm)2]2+. Complete active-space self-consistent field calculations support ascribing electron relaxation to enhanced mixing of the two Eg orbital sets that accompanies the tetragonal distortion and the differences in electron correlation times to the higher Jahn-Teller activation barrier in [Co(Tpm)2]2+.

Insights into the Gelation Mechanism of Metal-Coordinated Hydrogels by Paramagnetic NMR Spectroscopy and Molecular Dynamics

Metal-coordination complexes are attracting increasing attention as supramolecular cross-linkers to develop polymeric hydrogel networks with tunable and dynamic mechanical properties. Nonetheless, the rational design of these materials is still hindered by the limited mechanistic understanding of how metal–ligand interactions influence the structure and properties of the hydrogel. Here, we report a detailed mechanistic investigation using nuclear magnetic resonance (NMR) spectroscopy combined with molecular dynamics (MD) simulations to explore the formation of cellulose-based hydrogels induced by coordination with paramagnetic Fe3+ ions. We demonstrate how NMR paramagnetic relaxation enhancement can be used to probe the distances between the metal center and NMR active nuclei on the polymer chain, informing on the metal–ligand coordination network. Experimental results, together with supporting MD simulations, allow us to uncover a structuration of water around the cross-linked metals within the hydrogel, in addition to the establishment of different orientations of the chains governed by hydrogen bonds networks. Progress in understanding the gelation mechanism of metal-coordinated hydrogels will fuel their exploitation for a wide variety of biomedical applications.

Conformational Heterogeneity in the Activation Mechanism of Bax

Bax is known for its pro-apoptotic role within the mitochondrial pathway of apoptosis. However, the mechanism for transitioning Bax from cytosolic to membrane-bound oligomer remains elusive. Previous nuclear magnetic resonance (NMR) and electronparamagnetic resonance (EPR) studies defined monomeric Bax as conformationally homogeneous. Yet it has recently been proposed that monomeric Bax exists in equilibrium with a minor state that is distinctly different from its NMR structure. Here, we revisited the structural analysis of Bax using methods uniquely suited for unveiling "invisible" states of proteins, namely, NMR paramagnetic relaxation enhancements and EPR double electron-electron resonance (DEER). Additionally we examined the effect of glycerol, the co-solvent of choice in DEER studies, on the structure of Bax using NMR chemical-shift perturbations and residual dipolar couplings. Based on our combined NMR and EPR results, Bax is a conformationally homogeneous protein prior to its activation.

Solution Conformations and Dynamics of Substrate-Bound Cytochrome P450 MycG

MycG is a P450 monooxygenase that catalyzes the sequential hydroxylation and epoxidation of mycinamicin IV (M-IV), the last two steps in the biosynthesis of mycinamicin II, a macrolide antibiotic isolated from Micromonospora griseorubida. The crystal structure of MycG with M-IV bound was previously determined but showed the bound substrate in an orientation that did not rationalize the observed regiochemistry of M-IV hydroxylation. Nuclear magnetic resonance paramagnetic relaxation enhancements provided evidence of an orientation of M-IV in the MycG active site more compatible with the observed chemistry, but substrate-induced changes in the enzyme structure were not characterized. We now describe the use of amide 1H-15N residual dipolar couplings as experimental restraints in solvated "soft annealing" molecular dynamics simulations to generate solution structural ensembles of M-IV-bound MycG. Chemical shift perturbations, hydrogen-deuterium exchange, and 15N relaxation behavior provide insight into the dynamic and electronic perturbations in the MycG structure in response to M-IV binding. The solution and crystallographic structures are compared, and the possibility that the crystallographic orientation of bound M-IV represents an inhibitory mode is discussed.

Structural Analysis of Protein-RNA Complexes in Solution Using NMR Paramagnetic Relaxation Enhancements.

Biological activity in the cell is predominantly mediated by large multiprotein and protein-nucleic acid complexes that act together to ensure functional fidelity. Nuclear magnetic resonance (NMR) spectroscopy is the only method that can provide information for high-resolution three-dimensional structures and the conformational dynamics of these complexes in solution. Mapping of binding interfaces and molecular interactions along with the characterization of conformational dynamics is possible for very large protein complexes. In contrast, de novo structure determination by NMR becomes very time consuming and difficult for protein complexes larger than 30 kDa as data are noisy and sparse. Fortunately, high-resolution structures are often available for individual domains or subunits of a protein complex and thus sparse data can be used to define their arrangement and dynamics within the assembled complex. In these cases, NMR can therefore be efficiently combined with complementary solution techniques, such as small-angle X-ray or neutron scattering, to provide a comprehensive description of the structure and dynamics of protein complexes in solution. Particularly useful are NMR-derived paramagnetic relaxation enhancements (PREs), which provide long-range distance restraints (ca. 20Å) for structural analysis of large complexes and also report on conformational dynamics in solution. Here, we describe the use of PREs from sample production to structure calculation, focusing on protein-RNA complexes. On the basis of recent examples from our own research, we demonstrate the utility, present protocols, and discuss potential pitfalls when using PREs for studying the structure and dynamic features of protein-RNA complexes.

Exploring the Minimally Frustrated Energy Landscape of Unfolded ACBP

The unfolded state of globular proteins is not well described by a simple statistical coil due to residual structural features, such as secondary structure or transiently formed long-range contacts. The principle of minimal frustration predicts that the unfolded ensemble is biased toward productive regions in the conformational space determined by the native structure. Transient long-range contacts, both native-like and non-native-like, have previously been shown to be present in the unfolded state of the four-helix-bundle protein acyl co-enzyme binding protein (ACBP) as seen from both perturbations in nuclear magnetic resonance (NMR) chemical shifts and structural ensembles generated from NMR paramagnetic relaxation data. To study the nature of the contacts in detail, we used paramagnetic NMR relaxation enhancements, in combination with single-point mutations, to obtain distance constraints for the acid-unfolded ensemble of ACBP. We show that, even in the acid-unfolded state, long-range contacts are specific in nature and single-point mutations affect the free-energy landscape of the unfolded protein. Using this approach, we were able to map out concerted, interconnected, and productive long-range contacts. The correlation between the native-state stability and compactness of the denatured state provides further evidence for native-like contact formation in the denatured state. Overall, these results imply that, even in the earliest stages of folding, ACBP dynamics are governed by native-like contacts on a minimally frustrated energy landscape.

Paramagnetic Relaxation Enhancement Experiments: A Valuable Tool for the Characterization of Micellar Nanodevices

Micellar incorporation of hydrophobic molecular receptors is a promising strategy to obtain efficient nanodevices that work in water. In order to fully evaluate the potential of this approach, information on the localization and orientation of the receptor inside the micelle are necessary. Systematic studies undertaken on a uranyl-salophen receptor incorporated into CTABr and CTACl micelles show that nuclear magnetic resonance paramagnetic relaxation enhancement (NMR-PRE) experiments are particularly suitable to provide this type of information. The effect on the measurements of surfactant concentration, nature of the surfactant polar head, and ionic strength is also reported. Notably the normalization procedure applied to the obtained data can be considered of general application, thus enabling the comparison of information collected for different types of supramolecular micelle/receptor systems.

Structural insights into the targeting of mRNA GU-rich elements by the three RRMs of CELF1

The CUG-BP, Elav-like family (CELF) of RNA-binding proteins control gene expression at a number of different levels by regulating pre-mRNA splicing, deadenylation and mRNA stability. We present structural insights into the binding selectivity of CELF member 1 (CELF1) for GU-rich mRNA target sequences of the general form 5′-UGUNxUGUNyUGU and identify a high affinity interaction (Kd ∼ 100 nM for x = 2 and y = 4) with simultaneous binding of all three RNA recognition motifs within a single 15-nt binding element. RNA substrates spin-labelled at either the 3′ or 5′ terminus result in differential nuclear magnetic resonance paramagnetic relaxation enhancement effects, which are consistent with a non-sequential 2-1-3 arrangement of the three RNA recognition motifs on UGU sites in a 5′ to 3′ orientation along the RNA target. We further demonstrate that CELF1 binds to dispersed single-stranded UGU sites at the base of an RNA hairpin providing a structural rationale for recognition of CUG expansion repeats and splice site junctions in the regulation of alternative splicing.

Optimal Mutation Sites for PRE Data Collection and Membrane Protein Structure Prediction

Nuclear magnetic resonance paramagnetic relaxation enhancement (PRE) measures long-range distances to isotopically labeled residues, providing useful constraints for protein structure prediction. The method usually requires labor-intensive conjugation of nitroxide labels to multiple locations on the protein, one at a time. Here a computational procedure, based on protein sequence and simple secondary structure models, is presented to facilitate optimal placement of a minimum number of labels needed to determine the correct topology ofa helical transmembrane protein. Tests on DsbB (four helices) using just one label lead to correct topology predictions in four of five cases, with the predicted structures <6 Å to the native structure. Benchmark results using simulated PRE data show that we can generally predict the correct topology for five and six to seven helices using two and three labels, respectively, with an average success rate of 76% and structures of similar precision. The results show promise in facilitating experimentally constrained structure prediction of membrane proteins.

SAXS Ensemble Refinement of ESCRT-III CHMP3 Conformational Transitions

We developed and implemented an ensemble-refinement method to study dynamic biomolecular assemblies with intrinsically disordered segments. Data from small angle X-ray scattering (SAXS) experiments and from coarse-grained molecular simulations were combined by using a maximum-entropy approach. The method was applied to CHMP3 of ESCRT-III, a protein with multiple helical domains separated by flexible linkers. Based on recent SAXS data by Lata etal. (J. Mol. Biol. 378, 818, 2008), we constructed ensembles of CHMP3 at low-and high-salt concentration to characterize its closed autoinhibited state and open active state. At low salt, helix α(5) is bound to the tip of helices α(1) and α(2), in excellent agreement with a recent crystal structure. Helix α(6) remains free in solution and does not appear to be part of the autoinhibitory complex. The simulation-based ensemble refinement is general and effectively increases the resolution of SAXS beyond shape information to atomically detailed structures.

Probing the Folding Intermediate of Bacillus subtilis RNase P Protein by Nuclear Magnetic Resonance

Protein folding intermediates are often imperative for overall folding processes and consequent biological functions. However, the low population and transient nature of the intermediate states often hinder their biochemical and biophysical characterization. Previous studies have demonstrated that Bacillus subtilis ribonuclease P protein (P protein) is conformationally heterogeneous and folds with multiphasic kinetics, indicating the presence of an equilibrium and kinetic intermediate in its folding mechanism. In this study, nuclear magnetic resonance (NMR) spectroscopy was used to study the ensemble corresponding to this intermediate (I). The results indicate that the N-terminal and C-terminal helical regions are mostly unfolded in I. 1H−15N heteronuclear single-quantum coherence NMR spectra collected as a function of pH suggest that the protonation of His 22 may play a major role in the energetics of the equilibria among the unfolded, intermediate, and folded state ensembles of P protein. NMR paramagnetic relaxation enhancement experiments were also used to locate the small anion binding sites in both the intermediate and folded ensembles. The results for the folded protein are consistent with the previously modeled binding regions. These structural insights suggest a possible role for I in the RNase P holoenzyme assembly process.

Nuclear spin relaxation due to paramagnetic species in solution: Effect of anisotropy in the zero field splitting tensor

The NMR (nuclear magnetic resonance) paramagnetic relaxation enhancement (NMR-PRE) that is produced by paramagnetic solutes in solution has been investigated theoretically with respect to the influence of zero field splitting (zfs) interactions in the electron spin Hamiltonian, in particular with respect to the effects of anisotropy in the zfs tensor. These effects are a physical consequence of the influence of the zfs on the motion of the electron spin vector S̄. When the zfs energy is large compared to the Zeeman energy (the zfs limit), the precessional motion of S̄ is quantized in the molecule-fixed coordinate system that diagonalizes the zfs tensor. The uniaxial portion of the zfs tensor influences the NMR-PRE primarily through its influence on the quantization axes of S̄; the characteristic behavior of the NMR-PRE under the influence of a uniaxial zfs has been described in detail previously. Anisotropy in the zfs tensor induces oscillatory motion in Sz. This motion has a profound influence on the NMR-PRE, the major part of which normally arises from low frequency components of the local magnetic field that are associated with Sz, rather than from the rapidly precessing local fields that are associated with the transverse components S±. For this reason, the NMR-PRE is a sensitive function of zfs anisotropy, which acts to lower the NMR-PRE below the value that occurs in the uniaxial situation. The magnitude of this effect depends on the ratio (E/D) of the anisotropic and uniaxial zfs parameters, on the reduced dipolar correlation time, and on the location of the nuclear spin in the molecular coordinate frame. A second physical effect of zfs anisotropy on the NMR-PRE arises from a resonance between the electron spin precessional motion in the transverse plane with the precessional motion that is perpendicular to the transverse plane (the latter due to zfs anisotropy). Resonance of these motions, which occurs spin energy levels crossings, gives rise to low frequency transverse components of S̄ which result in a resonant increase in the NMR-PRE within a restricted range of E/D ratios.

Characteristic properties of the nuclear magnetic resonance–paramagnetic relaxation enhancement arising from integer and half-integer electron spins

The influence of zero field splitting (zfs) interactions on the magnetic field dispersion profile of the nuclear magnetic resonance–paramagnetic relaxation (NMR–PRE) (i.e., the enhancement of nuclear magnetic relaxation rates that is produced by paramagnetic solute species in solution) has been explored systematically for S=1, 3/2, 2, and 5/2 spin systems using recently developed theory. To facilitate comparison of results for different spin values, the theory was expressed in a reduced form with Larmor frequencies in units of ωD (the uniaxial zfs parameter D in rad s−1), and correlation times and spin relaxation times in units of ωD−1. For S=1, the functional form of the profile can be described in terms of five types of qualitative features. Two of these are characteristic of Zeeman-limit [Solomon, Bloembergen, and Morgan (SBM)] theory and result from the magnetic field dependence of the spin energy level splittings. The remaining three have no analog in Zeeman-limit theory and arise from a change in the quantization axis of the electron spin precessional motion which, in the zfs limit, lies along molecule-fixed coordinate axes, and, in the Zeeman limit, lies along the external field direction. The reduced field dispersion profiles for the integer spin systems S=1 and S=2 were found to be very similar to each other, the principal difference being that the midfield positions of the requantization features (types 2, 3, and 4) are shifted for S=2 relative to S=1, the magnitude and sign of the shift depending on the position of the nuclear spin in the molecular coordinate frame. For half-integer spins, the dispersion profiles exhibit, in addition to the five features characteristic of integer spins, a sixth type of feature, which is centered somewhat to low field of ωSτc=1, where τc is the dipolar correlation time. The type-6 feature results from field-dependent level splitting of the mS=±1/2 Kramers doublet. It is present when ωDτc≥1. These theoretical predictions have been examined by means of reinterpretations of the NMR–PRE data for tris-(acetylacetonato)–metal complexes of V(III) (S=1), Cr(III) (S=3/2), Mo(III) (S=3/2), Mn(III) (S=2), and Fe(III) (S=5/2). As predicted, type-6 features are absent for the integer spin complexes, for which the T1 field dispersion profiles are nearly field independent. The experimental profiles were successfully simulated quantitatively by the generalized theory, but not by Zeeman-limit theory. For the half-integer spin systems, the predicted zfs-related type-6 features appear to be present in the profiles, particularly for Mo(acac)3, for which the data deviate significantly from the Zeeman-limit profile in a manner that is explained by the generalized theory.

Nuclear magnetic resonance paramagnetic relaxation method for the determination of micellar solubilization equilibria applied to anionic micelles

The NMR paramagnetic relaxation method has been developed (Z. Gao, R. E. Wasylishen and J. C. T. Kwak, J. Phys. Chem., 1989, 93, 2190) as an alternative procedure for the determination of micellar distribution equilibria. The 3-carboxyproxyl anion has been suggested as a suitable relaxation agent for the case of anionic micelles. In a recent paper (P. J. Bratt, H. Choudhury, P. B. Chowdhury, D. G. Gillies, A. M. L. Krebber and L. H. Sutcliffe, J. Chem. Soc. Faraday Trans., 1990, 86, 3313) it was noted that the acid form 3-carboxyproxyl is partially located in the micellar phase, and therefore cannot be used as a relaxation agent in this method. In this paper, the difference between 3-carboxyproxyl (acid form) and sodium-3-carboxyproxyl (salt form) is demonstrated by measuring 1H T1 values of sodiumdodecylsulphate alkyl protons and of completely solubilized tert-butylcyclohexane in the presence of these two relaxation agents. The paramagnetic 3-carboxyproxyl anion does not influence the T1 values of surfactant or solubilizate protons in the micellar phase. It is concluded that the anionic form of 3-carboxyproxyl can be used to determine distribution coefficients of neutral solubilizates in anionic micelles.