Dynamic of binary molecular systems-Advantages and limitations of NMR relaxometry

1H spin-lattice relaxation studies have been performed for binary systems, including glycerol as the first component and alanine, glycine, and aspartic acid (with different levels of deuteration) as the second one. The relaxation studies have been performed in the frequency range from 10 kHz to 10 MHz vs temperature. A theoretical framework, including all relevant 1H-1H and 1H-2H relaxation pathways, has been formulated. The theory has been exploited for a thorough interpretation of a large set of the experimental data. The importance of the 1H-2H relaxation contributions has been discussed, and the possibility of revealing dynamical properties of individual liquid components in binary liquids has been carefully investigated. As far as the dynamical properties of the specific binary liquids, chosen as an example, are considered, it has been shown that in the presence of the second component (alanine, glycine, and aspartic acid), both molecular fractions undergo dynamics similar to that of glycerol in bulk.

Water Dynamics in Highly Concentrated Protein Systems-Insight from Nuclear Magnetic Resonance Relaxometry

¹H spin-lattice relaxation experiments have been performed for water-Bovine Serum Albumin (BSA) mixtures, including 20%wt and 40%wt of BSA. The experiments have been carried out in a frequency range encompassing three orders of magnitude, from 10 kHz to 10 MHz, versus temperature. The relaxation data have been thoroughly analyzed in terms of several relaxation models with the purpose of revealing the mechanisms of water motion. For this purpose, four relaxation models have been used: the data have been decomposed into relaxation contributions expressed in terms of Lorentzian spectral densities, then three-dimensional translation diffusion has been assumed, next two-dimensional surface diffusion has been considered, and eventually, a model of surface diffusion mediated by acts of adsorption to the surface has been employed. In this way, it has been demonstrated that the last concept is the most plausible. Parameters describing the dynamics in a quantitative manner have been determined and discussed.

Solid-state NMR methods for the characterization of bioconjugations and protein-material interactions

Protein solid-state NMR has evolved dramatically over the last two decades, with the development of new hardware and sample preparation methodologies. This technique is now ripe for complex applications, among which one can count bioconjugation, protein chemistry and functional biomaterials. In this review, we provide our account on this aspect of protein solid-state NMR.

Multiscale Water Dynamics on Protein Surfaces: Protein-Specific Response to Surface Ions

Proteins function in crowded aqueous environments, interacting with a diverse range of compounds, and among them, dissolved ions. These interactions are water-mediated. In the present study, we combine field-dependent NMR relaxation (NMRD) and theory to probe water dynamics on the surface of proteins in concentrated aqueous solutions of hen egg-white lysozyme (LZM) and bovine serum albumin (BSA). The experiments reveal that the presence of salts (NaCl or NaI) leads to an opposite ion-specific response for the two proteins: an addition of salt to LZM solutions increases water relaxation rates with respect to the salt-free case, while for BSA solutions, a decrease is observed. The magnitude of the change depends on the ion identity. The developed model accounts for the non-Lorentzian shape of the NMRD profiles and reproduces the experimental data over four decades in Larmor frequency (10 kHz to 110 MHz). It is applicable up to high protein concentrations. The model incorporates the observed ion-specific effects via changes in the protein surface roughness, represented by the surface fractal dimension, and the accompanying changes in the surface water residence times. The response is protein-specific, linked to geometrical aspects of the individual protein surfaces, and goes beyond protein-independent Hofmeister-style ordering of ions.

Unveiling protein dynamics in solution with field-cycling NMR relaxometry

Field-cycling NMR relaxometry is a well-established technique that can give information on molecular structure and dynamics of biological systems. It provides the nuclear relaxation rates as a function of the applied magnetic field, starting from fields as low as ~ 10^-4 T up to about 1-3 T. The profiles so collected, called nuclear magnetic relaxation dispersion (NMRD) profiles, can be extended to include the relaxation rates at the largest fields achievable with high resolution NMR spectrometers. By exploiting this wide range of frequencies, the NMRD profiles can provide information on motions occurring on time scales from 10^-6 to 10^-9 s. ¹H NMRD measurements have proved very useful also for the characterization of paramagnetic proteins, because they can help characterise a number of parameters including the number, distance and residence time of water molecules coordinated to the paramagnetic center, the reorientation correlation times and the electron spin relaxation time, and the electronic structure at the metal site.

Water dynamics in eggs by means of Nuclear Magnetic Resonance relaxometry

¹H Nuclear Magnetic Resonance relaxometry has been applied to reveal dynamical properties of water molecules embedded into egg yolk and white of three species: turkey, chicken and quail. Two fractions of water molecules, referred to as confined-water and free-water fractions, have been revealed. It has been demonstrated that translation diffusion of the confined-water fraction is three-dimensional. The dynamics of the confined-water has been quantitatively described in terms of diffusion coefficients and rotational correlation times. The parameters have been compared for egg yolk and white for all the species. In addition to these quantities, the number of the confined-water molecules per unit volume has been provided for all cases. The obtained parameters provide insight into the dynamics of water in eggs of different origin and allow to identify similarities and differences between them in connection to the structure of the network formed by the macromolecular fraction of egg yolk and white.

1H spin-lattice NMR relaxation in the presence of residual dipolar interactions - Dipolar relaxation enhancement

A model of spin-lattice relaxation for spin-1/2 nuclei in the presence of a residual dipole-dipole coupling has been presented. For slow dynamics the model predicts a bi-exponential relaxation at low frequencies, when the residual dipole-dipole interaction dominates the Zeeman coupling. Moreover, according to the model a frequency-specific relaxation enhancement, referred to as Dipolar Relaxation Enhancement (DRE) in analogy to the Quadrupole Relaxation Enhancement (QRE) is expected. The frequency position of the relaxation maximum is determined by the amplitude of the residual dipole-dipole interaction. Experimental examples of relaxation properties that might be attributed to the DRE are presented. The DRE effect has the potential to be exploited, in analogy to QRE, as a unique source of information about molecular dynamics and structure.

Slow dynamics of solid proteins - Nuclear magnetic resonance relaxometry versus dielectric spectroscopy

¹H Nuclear Magnetic Resonance (NMR) relaxometry and Dielectric Spectroscopy (DS) have been exploited to investigate the dynamics of solid proteins. The experiments have been carried out in the frequency range of about 10 kHz-40 MHz for NMR relaxometry and 10^-2Hz-20 MHz for DS. The data sets have been analyzed in terms of theoretical models allowing for a comparison of the correlation times revealed by NMR relaxometry and DS. The ¹H spin-lattice relaxation profiles have been decomposed into relaxation contributions associated with ¹H-¹H and ¹H-¹⁴N dipole - dipole interactions. The ¹H-¹H relaxation contribution has been interpreted in terms of three dynamical processes of time scales of 10^-6s, 10^-7s and 10^-8s. It has turned out that the correlation times do not differ much among proteins and they are only weakly dependent on temperature. The analysis of DS relaxation spectra has also revealed three motional processes characterized by correlation times that considerably depend on temperature in contrast to those obtained from the ¹H relaxation. This finding suggest that for solid proteins there is a contribution to the ¹H spin-lattice relaxation associated with a kind of motion that is not probed in DS as it does not lead to a reorientation of the electric dipole moment.

Dynamics of Solid Proteins by Means of Nuclear Magnetic Resonance Relaxometry

¹H Nuclear magnetic resonance (NMR) relaxometry was exploited to investigate the dynamics of solid proteins. The relaxation experiments were performed at 37 °C over a broad frequency range, from approximately 10 kHz to 40 MHz. Two relaxation contributions to the overall ¹H spin-lattice relaxation were revealed; they were associated with ¹H-¹H and ¹H-¹⁴N magnetic dipole-dipole interactions, respectively. The ¹H-¹H relaxation contribution was interpreted in terms of three dynamical processes occurring on timescales of 10^-6 s, 10^-7 s, and 10^-8 s, respectively. The ¹H-¹⁴N relaxation contribution shows quadrupole relaxation enhancement effects. A thorough analysis of the data was performed revealing similarities in the protein dynamics, despite their different structures. Among several parameters characterizing the protein dynamics and structure (e.g., electric field gradient tensor at the position of ¹⁴N nuclei), the orientation of the ¹H-¹⁴N dipole-dipole axis, with respect to the principal axis system of the electric field gradient, was determined, showing that, for lysozyme, it was considerably different than for the other proteins. Moreover, the validity range of a closed form expression describing the ¹H-¹⁴N relaxation contribution was determined by a comparison with a general approach based on the stochastic Liouville equation.

Dynamics of solid alanine by means of nuclear magnetic resonance relaxometry

¹H nuclear magnetic resonance relaxometry was applied to investigate the dynamics of l-alanine in the solid phase (powder). The experimental studies were carried out in a very broad frequency range, covering four orders of magnitude-from 4 kHz to 40 MHz (referring to the ¹H resonance frequency) in order to probe motional processes of much different time scales by a single experiment. To get access to the dynamics of different proton groups of alanine, the ¹H spin-lattice relaxation measurements were performed for non-deuterated and partially deuterated alanine. The experiments were carried out in the temperature range of 293 K-370 K (non-deuterated alanine) and 318 K-370 K (partially deuterated alanine). As a result of a thorough theoretical analysis of the extensive set of experimental results, three motional processes occurring on different time scales are identified and quantitatively described. The slowest process occurs on a time scale of μs and it is attributed to the collective dynamics of a 3D hydrogen bond network of alanine, while the intermediate, attributed to the dynamics of the NH₃ group, corresponds to the range of tenths of ns. The fast process describes the rotation of the CH₃ group.

On the use of ultracentrifugal devices for routine sample preparation in biomolecular magic-angle-spinning NMR

A number of recent advances in the field of magic-angle-spinning (MAS) solid-state NMR have enabled its application to a range of biological systems of ever increasing complexity. To retain biological relevance, these samples are increasingly studied in a hydrated state. At the same time, experimental feasibility requires the sample preparation process to attain a high sample concentration within the final MAS rotor. We discuss these considerations, and how they have led to a number of different approaches to MAS NMR sample preparation. We describe our experience of how custom-made (or commercially available) ultracentrifugal devices can facilitate a simple, fast and reliable sample preparation process. A number of groups have since adopted such tools, in some cases to prepare samples for sedimentation-style MAS NMR experiments. Here we argue for a more widespread adoption of their use for routine MAS NMR sample preparation.

Differences in Dynamics between Crosslinked and Non-Crosslinked Hyaluronates Measured by using Fast Field-Cycling Relaxometry

The dynamic properties of water molecules in gels containing linear and crosslinked hyaluronic acid polymers are investigated by using an integrated approach that includes relaxometry, solid-state NMR spectroscopy, and scanning electron microscopy. A model-free analysis of field-dependent nuclear relaxation is applied to obtain information on mobility and the population of different pools of water molecules in the gels. Differences between linear and crosslinked hyaluronic acid polymers are observed, indicating that crosslinking increases both the fraction and the correlation time of water molecules with slow dynamics.

Coupling between overall rotational diffusion and domain motions in proteins and its effect on dielectric spectra

In this work, we formulate a closed-form solution of the model of a semirigid molecule for the case of fluctuating and reorienting molecular electric dipole moment. We illustrate with numeric calculations the impact of protein domain motions on dielectric spectra using the example of the 128 kDa protein dimer of Enzyme I. We demonstrate that the most drastic effect occurs for situations when the characteristic time of protein domain dynamics is comparable to the time of overall molecular rotational diffusion. We suggest that protein domain motions could be a possible explanation for the high-frequency contribution that accompanies the major relaxation dispersion peak in the dielectric spectra of protein aqueous solutions. We propose that the presented computational methodology could be used for the simultaneous analysis of dielectric spectroscopy and nuclear magnetic resonance data. Proteins 2015; 83:1571-1581. © 2015 Wiley Periodicals, Inc.

NMR of sedimented, fibrillized, silica-entrapped and microcrystalline (metallo)proteins

Resolution and sensitivity in solid state NMR (SSNMR) can rival the results achieved by solution NMR, and even outperform them in the case of large systems. However, several factors affect the spectral quality in SSNMR samples, and not all systems turn out to be equally amenable for this methodology. In this review we attempt at analyzing the causes of this variable behavior and at providing hints to increase the chances of experimental success.

Can metal ion complexes be used as polarizing agents for solution DNP? A theoretical discussion

Dynamic nuclear polarization (DNP) can be used to dramatically increase the NMR signal intensities in solutions and solids. DNP is usually performed using nitroxide radicals as polarizing agents, characterized by sharp EPR lines, fast rotation, fast diffusion, and favorable distribution of the unpaired electron. These features make the nitroxide radicals ideally suited for solution DNP. Here, we report some theoretical considerations on the different behavior of some inorganic compounds with respect to nitroxide radicals. The relaxation profiles of slow relaxing paramagnetic metal aqua ions [copper(II), manganese(II), gadolinium(III) and oxovanadium(IV)] and complexes have been re-analyzed according to the standard theory for dipolar and contact relaxation, in order to estimate the coupling factor responsible for the maximum DNP enhancement that can be achieved in solution and its dependence on field, temperature and relative importance of outer-sphere versus inner-sphere relaxation.

Topical Developments in High-Field Dynamic Nuclear Polarization

We report our recent efforts directed at improving high-field DNP experiments. We investigated a series of thiourea nitroxide radicals and the associated DNP enhancements ranging from ε = 25 to 82 that demonstrate the impact of molecular structure on performance. We directly polarized low-gamma nuclei including ¹³C, ²H, and ¹⁷O using trityl via the cross effect. We discuss a variety of sample preparation techniques for DNP with emphasis on the benefit of methods that do not use a glass-forming cryoprotecting matrix. Lastly, we describe a corrugated waveguide for use in a 700 MHz / 460 GHz DNP system that improves microwave delivery and increases enhancements up to 50%.

DNP-enhanced MAS NMR of bovine serum albumin sediments and solutions

Protein sedimentation sans cryoprotection is a new approach to magic angle spinning (MAS) and dynamic nuclear polarization (DNP) nuclear magnetic resonance (NMR) spectroscopy of proteins. It increases the sensitivity of the experiments by a factor of ∼4.5 in comparison to the conventional DNP sample preparation and circumvents intense background signals from the cryoprotectant. In this paper, we investigate sedimented samples and concentrated frozen solutions of natural abundance bovine serum albumin (BSA) in the absence of a glycerol-based cryoprotectant. We observe DNP signal enhancements of ε ∼ 66 at 140 GHz in a BSA pellet sedimented from an aqueous solution containing the biradical polarizing agent TOTAPOL and compare this with samples prepared using the conventional protocol (i.e., dissolution of BSA in a glycerol/water cryoprotecting mixture). The dependence of DNP parameters on the radical concentration points to the presence of an interaction between TOTAPOL and BSA, so much so that a frozen solution sans cryoprotectant still gives ε ∼ 50. We have studied the interaction of BSA with another biradical, SPIROPOL, that is more rigid than TOTAPOL and has been reported to give higher enhancements. SPIROPOL was also found to interact with BSA, and to give ε ∼ 26 close to its maximum achievable concentration. Under the same conditions, TOTAPOL gives ε ∼ 31, suggesting a lesser affinity of BSA for SPIROPOL with respect to TOTAPOL. Altogether, these results demonstrate that DNP is feasible in self-cryoprotecting samples.

SedNMR: a web tool for optimizing sedimentation of macromolecular solutes for SSNMR

We have proposed solid state NMR (SSNMR) of sedimented solutes as a novel approach to sample preparation for biomolecular SSNMR without crystallization or other sample manipulations. The biomolecules are confined by high gravity--obtained by centrifugal forces either directly in a SSNMR rotor or in a ultracentrifugal device--into a hydrated non-crystalline solid suitable for SSNMR investigations. When gravity is removed, the sample reverts to solution and can be treated as any solution NMR sample. We here describe a simple web tool to calculate the relevant parameters for the success of the experiment.

Practical considerations over spectral quality in solid state NMR spectroscopy of soluble proteins

Great theoretical and methodological advances are pushing the limits of resolution and sensitivity in solid state NMR (SSNMR). However, sample preparation remains a critical issue for the success of an experiment. The factors affecting spectral quality in SSNMR samples are discussed, examining cases encountered in the literature and presenting new experimental data. A discussion on resolution and sensitivity in sedimented solutes is framed in this context.