An NMR study of the origin of dioxygen-induced spin-lattice relaxation enhancement and chemical shift perturbation

Solvent paramagnetic relaxation enhancement as a versatile method for studying structure and dynamics of biomolecular systems

Solvent paramagnetic relaxation enhancement (sPRE) is a versatile nuclear magnetic resonance (NMR)-based method that allows characterization of the structure and dynamics of biomolecular systems through providing quantitative experimental information on solvent accessibility of NMR-active nuclei. Addition of soluble paramagnetic probes to the solution of a biomolecule leads to paramagnetic relaxation enhancement in a concentration-dependent manner. Here we review recent progress in the sPRE-based characterization of structural and dynamic properties of biomolecules and their complexes, and aim to deliver a comprehensive illustration of a growing number of applications of the method to various biological systems. We discuss the physical principles of sPRE measurements and provide an overview of available co-solute paramagnetic probes. We then explore how sPRE, in combination with complementary biophysical techniques, can further advance biomolecular structure determination, identification of interaction surfaces within protein complexes, and probing of conformational changes and low-population transient states, as well as deliver insights into weak, nonspecific, and transient interactions between proteins and co-solutes. In addition, we present examples of how the incorporation of solvent paramagnetic probes can improve the sensitivity of NMR experiments and discuss the prospects of applying sPRE to NMR metabolomics, drug discovery, and the study of intrinsically disordered proteins.

Sensitivity enhancement for membrane proteins reconstituted in parallel and perpendicular oriented bicelles obtained by using repetitive cross-polarization and membrane-incorporated free radicals

Multidimensional separated local-field and spin-exchange experiments employed by oriented-sample solid-state NMR are essential for structure determination and spectroscopic assignment of membrane proteins reconstituted in macroscopically aligned lipid bilayers. However, these experiments typically require a large number of scans in order to establish interspin correlations. Here we have shown that a combination of optimized repetitive cross polarization (REP-CP) and membrane-embedded free radicals allows one to enhance the signal-to-noise ratio by factors 2.4-3.0 in the case of Pf1 coat protein reconstituted in magnetically aligned bicelles with their normals being either parallel or perpendicular to the main magnetic field. Notably, spectral resolution is not affected at the 2:1 radical-to-protein ratio. Spectroscopic assignment of Pf1 coat protein in the parallel bicelles has been established as an illustration of the method. The proposed methodology will advance applications of oriented-sample NMR technique when applied to samples containing smaller quantities of proteins and three-dimensional experiments.

Sensitivity enhancement and contrasting information provided by free radicals in oriented-sample NMR of bicelle-reconstituted membrane proteins

Elucidating structure and topology of membrane proteins (MPs) is essential for unveiling functionality of these important biological constituents. Oriented-sample solid-state NMR (OS-NMR) is capable of providing such information on MPs under nearly physiological conditions. However, two dimensional OS-NMR experiments can take several days to complete due to long longitudinal relaxation times combined with the large number of scans to achieve sufficient signal sensitivity in biological samples. Here, free radicals 5-DOXYL stearic acid, TEMPOL, and CAT-1 were added to uniformly (15)N-labeled Pf1 coat protein reconstituted in DMPC/DHPC bicelles, and their effect on the longitudinal relaxation times (T1Z) was investigated. The dramatically shortened T1Z's allowed for the signal gain per unit time to be used for either: (i) up to a threefold reduction of the total experimental time at 99% magnetization recovery or (ii) obtaining up to 74% signal enhancement between the control and radical samples during constant experimental time at "optimal" relaxation delays. In addition, through OS-NMR and high-field EPR studies, free radicals were able to provide positional constraints in the bicelle system, which provide a description of the location of each residue in Pf1 coat protein within the bicellar membranes. This information can be useful in the determination of oligomerization states and immersion depths of larger membrane proteins.

Solution NMR studies on the orientation of membrane-bound peptides and proteins by paramagnetic probes

Many peptides and proteins are attached to or immersed in a biological membrane. In order to understand their function not only the structure but also their topology in the membrane is important. Solution NMR spectroscopy is one of the most often used approaches to determine the orientation and localization of membrane-bound peptides and proteins. Here we give an application-oriented overview on the use of paramagnetic probes for the investigation of membrane-bound peptides and proteins. The examples discussed range from the large pool of antimicrobial peptides, bacterial toxins, cell penetrating peptides to domains of larger proteins or the calcium regulating protein phospholamban. Topological information is obtained in all these examples by the use of either attached or freely mobile paramagnetic tags. For some examples information obtained from the paramagnetic probes was included in the structure determination.

Jahn-Teller dynamics in a series of high-symmetry Co(II) chelates determine paramagnetic relaxation enhancements

NMR paramagnetic relaxation enhancements (PREs) of a series of structurally characterized, trigonal bis-trispyrazolylborate (Tp) chelates of high-spin Co(II), spanning 100-850 MHz in field, are reported. Prior knowledge of the metal-nucleus distances allows numerical extraction of position-dependent electron spin relaxation rates (τ(c)(-1)) from direct measurement of the individual PREs of the four symmetry distinct protons in Co(Tp)(2), using available closed-form expressions. The data for this electronically complex system where spin-orbit coupling defines the ground state electronic structure are analyzed in terms of the Solomon-Bloembergen-Morgan (SBM) relations, as well as available zero-field splitting limit theories. A simple angular correction is shown to be sufficient to reconcile the individual τ(c)(T) data for the four classes of protons. The data identify a previously unrecognized dynamic Jahn-Teller effect in these historically important complexes, with a barrier of ~230 cm(-1), pointing to a level of dynamics in trispyrazolylborate chemistry that has not been described before, and further show that it is the Jahn-Teller that is responsible for the PREs in fluid solution. A field-dependent component is also identified for the two protons nearest g(//), which is suggested to arise due to Zeeman mixing of excited state character into the ground level.

MR oximetry

MR oximetry includes methods for assessing tissue oxygenation. This chapter focuses on direct measurements of oxygenation. These can be divided into three methods. The first and most common has been termed BOLD MRI and relates to the quantification of deoxyhemoglobin. The second method uses an injected fluorinated agent which has a T (1) that is sensitive to tissue oxygen levels. The third is a direct measurement of T (1) under conditions where the variation in T (1) can be limited to that caused by changes in pO(2). These conditions can be met in the vitreous of the eye or the cerebrospinal fluids. Such changes in the eye have been called the retinal oxygenation response.

Unexpected proton spin-lattice relaxation in the solutions of polyolefin and tetrachloroethane

'Unexpected' proton spin-lattice relaxation (T(1)) times are reported for the solutions of poly(ethylene-co-1-octene) and tetrachloroethane-d(2). For the residual protons of the deuterated solvent and the methyl and vinyl protons at the polymer chain ends, their T(1) relaxation times vary significantly with both the polymer concentration and molecular weight over a wide range. The T(1)s also decrease with increasing temperature at relative high temperatures. Such behaviors are in contrast to most reported polymer solutions in which the T(1) has nearly no concentration or molecular weight dependence in the dilute and semi-dilute regime, and normal dependence on temperature. Further investigation revealed that the paramagnetic oxygen effect did shorten the measured proton T(1)s, but cannot account for the unexpected T(1) dependences. Spin rotation is proposed to provide a reasonable explanation.

A solution NMR approach to the measurement of amphiphile immersion depth and orientation in membrane model systems

Oxygen and Ni(II) are ideal paramagnetic species for NMR studies of immersion depth since they establish prominent concentration gradients across the membrane-water interface of either bilayers or micelles. Corresponding gradients of paramagnetic shifts and relaxation rates are observed by NMR for membrane embedded amphiphiles. Specifically, upon dissolution of oxygen at a partial pressure of 20 bar or more, (13)C NMR spectra of membrane embedded amphiphiles reveal chemical shift perturbations which depend sensitively on average immersion depth in the membrane. Similarly, depth-dependent enhancements of spin-lattice relaxation rates can be detected by (1)H NMR. Generally, such paramagnetic effects depend both on steric or accessibility factors and on the local concentration of the paramagnet. The steric terms can be factored out by combining paramagnetic rates arising from O(2) and Ni, in the form of a ratio, R(1P)(O(2))/R(1P)(Ni). The natural logarithm of this ratio is shown to depend linearly on immersion depth in a micelle. The analysis is verified using molecular dynamics simulations of dodecylphosphocholine in a detergent micelle, while thorough consideration of the paramagnetic rate data also allows for the determination of the orientation of imipramine in the micelle. Thus, a complete picture of topology arises from this approach which is readily applicable to studies of drugs and amphiphiles in fast-tumbling bicelles, small unilamellar vesicles, and micelles.

An NMR method for the determination of protein binding interfaces using TEMPOL-induced chemical shift perturbations

BACKGROUND

The determination of protein-protein interfaces is of crucial importance to understand protein function and to guide the design of compounds. To identify protein-protein interface by NMR spectroscopy, 13C NMR paramagnetic shifts induced by freely diffusing 4-hydroxy-2, 2, 6, 6-tetramethyl-piperidine-1-oxyl (TEMPOL) are promising, because TEMPOL affects distinct 13C NMR chemical shifts of the solvent accessible nuclei belonging to proteins of interest, while 13C nuclei within the interior of the proteins may be distinguished by a lack of such shifts.

METHOD

We measured the 13C NMR paramagnetic shifts induced by TEMPOL by recording 13C-(13)C TOCSY spectra for ubiquitin in the free state and the complex state with yeast ubiquitin hydrolase1 (YUH1).

RESULTS

Upon complexation of ubiquitin with YUH1, 13C NMR paramagnetic shifts associated with the protein binding interface were reduced by 0.05 ppm or more. The identified interfacial atoms agreed with the prior X-ray crystallographic data.

CONCLUSIONS

The TEMPOL-induced 13C chemical shift perturbation is useful to determine precise protein-protein interfaces.

GENERAL SIGNIFICANCE

The present method is a useful method to determine protein-protein interface by NMR, because it has advantages in easy sample preparations, simple data analyses, and wide applicabilities.

Model of drug-loaded fluorocarbon-based micelles studied by electron-spin induced (19)f relaxation NMR and molecular dynamics simulation

Rf-IPDU-PEGs belong to a class of fluoroalkyl-ended poly(ethylene glycol) polymers (Rf-PEGs), where the IPDU (isophorone diurethane) functions as a linker to connect each end of the PEG chain to a fluoroalkyl group. The Rf-IPDU-PEGs form hydrogels in water with favorable sol-gel coexistence properties. Thus, they are promising for use as drug delivery agents. In this study, we introduce an electron-spin induced 19F relaxation NMR technique to probe the location and drug-loading capacity for an electron-spin labeled hydrophobic drug, CT (chlorambucil-tempol adduct), enclosed in the Rf-IPDU-PEG micelle. With the assistance of molecular dynamics simulations, a clear idea regarding the structures of the Rf-IPDU-PEG micelle and its CT-loaded micelle was revealed. The significance of this research lies in the finding that the hydrophobic drug molecules were loaded within the intermediate IPDU shells of the Rf-IPDU-PEG micelles. The molecular structures of IPDU and that of CT are favorably comparable. Consequently, it appears that this study opens a window to modify the linker between the Rf group and the PEG chain for achieving customized structure-based drug-loading capabilities for these hydrogels, while the advantage of the strong affinity among the Rf groups to hold individual micelles together and to interconnect the micellar network is still retained in hopes of maintaining the sol-gel coexistence of the Rf-PEGs.

Mapping the orientation of helices in micelle-bound peptides by paramagnetic relaxation waves

Many antimicrobial peptides form alpha-helices when bound to a membrane. In addition, around 80% of residues in membrane-bound proteins are found in alpha-helical regions. The orientation and location of such helical peptides and proteins in the membrane are key factors determining their function and activity. Here we present a new solution state NMR method for obtaining the orientation of helical peptides in a membrane-mimetic environment (micelle-bound) without any chemical perturbation of the peptide-micelle system. By monitoring proton longitudinal relaxation rates upon addition of the freely water-soluble and inert paramagnetic probe Gd(DTPA-BMA) to an alpha-helical peptide, a wavelike pattern with a periodicity of 3.6 residues per turn is observed. The tilt and azimuth (rotation) angle of the helix determine the shape of this paramagnetic relaxation wave and can be obtained by least-square fitting of measured relaxation enhancements. Results are presented for the 15-residue antimicrobial peptide CM15 which forms an amphipathic helix almost parallel to the surface of the micelle. Thus, a few fast experiments enable the identification of helical regions and determination of the helix orientation within the micelle without the need for covalent modification, isotopic labeling, or sophisticated equipment. This approach opens a path toward the topology determination of alpha-helical membrane-proteins without the need for a complete NOE-based structure determination.

Oxygen as a Paramagnetic Probe of Clustering and Solvent Exposure in Folded and Unfolded States of an SH3 Domain

The N-terminal SH3 domain of the Drosophila modular protein Drk undergoes slow exchange between a folded (Fexch) and highly populated unfolded (Uexch) state under nondenaturing buffer conditions, enabling both Fexch and Uexch states to be simultaneously monitored. The addition of dissolved oxygen, equilibrated to a partial pressure of either 30 atm or 60 atm, provides the means to study solvent exposure with atomic resolution via 13C NMR paramagnetic shifts in 1H,13C HSQC (heteronuclear single quantum coherence) spectra. Absolute differences in these paramagnetic shifts between the Fexch and Uexch states allow the discrimination of regions of the protein which undergo change in solvent exposure upon unfolding. Contact with dissolved oxygen for both the Fexch and Uexch states could also be assessed through 13C paramagnetic shifts which were normalized based on the corresponding paramagnetic shifts seen in the free amino acids. In the Fexch state, the 13C nuclei belonging to the hydrophobic core of the protein exhibited very weak normalized paramagnetic shifts while those with greater solvent accessible surface area exhibited significantly larger normalized shifts. The Uexch state displayed less varied 13C paramagnetic shifts although distinct regions of protection from solvent exposure could be identified by a lack of such shifts. These regions, which included Phe9, Thr12, Ala13, Lys21, Thr22, Ile24, Ile27, and Arg38, overlapped with those found to have residual nativelike and non-native structures in previous studies and in some cases provided novel information. Thus, the paramagnetic shifts from dissolved oxygen are highly useful in the study of a transient structure or clustering in disordered systems, where conventional NMR measurements (couplings, chemical shift deviations from random coil values, and NOEs) may give little information.