Elucidation of the Mechanisms of Inter-domain Coupling in the Monomeric State of Enzyme I by High-pressure NMR

The catalytic cycle of Enzyme I (EI), a phosphotransferase enzyme responsible for converting phosphoenolpyruvate (PEP) into pyruvate, is characterized by a series of local and global conformational rearrangements. This multistep process includes a monomer-to-dimer transition, followed by an open-to-closed rearrangement of the dimeric complex upon PEP binding. In the present study, we investigate the thermodynamics of EI dimerization using a range of high-pressure solution NMR techniques complemented by SAXS experiments. 1H-15N TROSY and 1H-13C methyl TROSY NMR spectra combined with 15N relaxation measurements revealed that a native-like engineered variant of full-length EI fully dissociates into stable monomeric state above 1.5 kbar. Conformational ensembles of EI monomeric state were generated via a recently developed protocol combining coarse-grained molecular simulations with experimental backbone residual dipolar coupling measurements. Analysis of the structural ensembles provided detailed insights into the molecular mechanisms driving formation of the catalytically competent dimeric state, and reveals that each step of EI catalytical cycle is associated with a significant reduction in either inter- or intra-domain conformational entropy. Altogether, this study completes a large body work conducted by our group on EI and establishes a comprehensive structural and dynamical description of the catalytic cycle of this prototypical multidomain, oligomeric enzyme.

MD Simulations to Calculate NMR Relaxation Parameters of Vanadium(IV) Complexes: A Promising Diagnostic Tool for Cancer and Alzheimer's Disease

Early phase diagnosis of human diseases has still been a challenge in the medicinal field, and one of the efficient non-invasive techniques that is vastly used for this purpose is magnetic resonance imaging (MRI). MRI is able to detect a wide range of diseases and conditions, including nervous system disorders and cancer, and uses the principles of NMR relaxation to generate detailed internal images of the body. For such investigation, different metal complexes have been studied as potential MRI contrast agents. With this in mind, this work aims to investigate two systems containing the vanadium complexes [VO(metf)2]·H2O (VC1) and [VO(bpy)2Cl]+ (VC2), being metformin and bipyridine ligands of the respective complexes, with the biological targets AMPK and ULK1. These biomolecules are involved in the progression of Alzheimer's disease and triple-negative breast cancer, respectively, and may act as promising spectroscopic probes for detection of these diseases. To initially evaluate the behavior of the studied ligands within the aforementioned protein active sites and aqueous environment, four classical molecular dynamics (MD) simulations including VC1 + H2O (1), VC2 + H2O (2), VC1 + AMPK + H2O (3), and VC2 + ULK1 + H2O (4) were performed. From this, it was obtained that for both systems containing VCs and water only, the theoretical calculations implied a higher efficiency when compared with DOTAREM, a famous commercially available contrast agent for MRI. This result is maintained when evaluating the system containing VC1 + AMPK + H2O. Nevertheless, for the system VC2 + ULK1 + H2O, there was observed a decrease in the vanadium complex efficiency due to the presence of a relevant steric hindrance. Despite that, due to the nature of the interaction between VC2 and ULK1, and the nature of its ligands, the study gives an insight that some modifications on VC2 structure might improve its efficiency as an MRI probe.

Water Molecules' and Lithium Cations' Mobility in Sulfonated Polystyrene Studied by Nuclear Magnetic Resonance

The hydration of ions and charge groups controls electro mass transfer through ion exchange systems. The self-diffusion and local mobility of water molecules as well as lithium cations in poly (4-styrenesulfonic acid) and its lithium, sodium and cesium salts were investigated for the first time using pulsed-field gradient NMR (PFG NMR) and NMR relaxation techniques. The temperature dependences of the water molecule and Li+ cation self-diffusion coefficients exhibited increasing self-diffusion activation energy in temperature regions below 0 °C, which is not due to the freezing of parts of the water. The self-diffusion coefficients of water molecules and lithium cations, as measured using PFG NMR, are in good agreement with the self-diffusion coefficients calculated based on Einstein's equation using correlation times obtained from spin-lattice relaxation data. It was shown that macroscopic water molecules' and lithium cations' transfer is controlled by local particles jumping between neighboring sulfonated groups. These results are similar to the behavior of water and cations in sulfonic cation exchanger membranes and resins. It was concluded that polystyrenesulfonic acid is appropriate model of the ionogenic part of membranes based on this polymer.

Comparing CT and MR Properties of Artificial Thrombi According to Their Composition

This study aims to determine whether and to what extent the structure and composition of thrombi can be assessed using NMR and CT measurements. Seven different thrombus models, namely, six RBC thrombi with hematocrit levels (HTs) of 0%, 20%, 40%, 60%, 80% and 100% and one platelet thrombus model, were analyzed using proton NMR at 100 MHz and 400 MHz, with measurements of T₁ and T₂ NMR relaxation times and measurements of the apparent diffusion coefficient (ADC). In addition, the thrombus models were CT-scanned in a dual-energy mode (80 kV and 140 kV) and in a single-energy mode (80 kV) to measure their CT numbers. The results confirmed that RBC thrombi can be distinguished from platelet thrombi by using ADC and CT number measurements in all three settings, while they cannot be distinguished by using T₁ and T₂ measurements. All measured parameters allowed for the differentiation of RBC thrombi according to their HT values, but the best sensitivity to HT was obtained with ADC and single-energy CT measurements. The importance of this study also lies in the potential application of its results for the characterization of actual thrombi in vivo.

Hydration and Mobility of Alkaline Metal Cations in Sulfonic Cation Exchange Membranes

The interconnection of ionogenic channel structure, cation hydration, water and ionic translational mobility was revealed in Nafion and MSC membranes based on polyethylene and grafted sulfonated polystyrene. A local mobility of Li⁺, Na⁺ and Cs⁺ cations and water molecules was estimated via the ¹H, ⁷Li, ²³Na and ¹³³Cs spin relaxation technique. The calculated cation and water molecule self-diffusion coefficients were compared with experimental values measured using pulsed field gradient NMR. It was shown that macroscopic mass transfer is controlled by molecule and ion motion near sulfonate groups. Lithium and sodium cations whose hydrated energy is higher than water hydrogen bond energy move together with water molecules. Cesium cations in possession of low hydrated energy are directly jumping between neighboring sulfonate groups. Cation Li⁺, Na⁺ and Cs⁺ hydration numbers (h) in membranes were calculated from ¹H chemical shift water molecule temperature dependences. The values calculated from the Nernst-Einstein equation and the experimental conductivity values were close to each other in Nafion membranes. In MSC membranes, calculated conductivities were one order of magnitude more compared to the experimental ones, which is explained by the heterogeneity of the membrane pore and channel system.

Humin Formation on SBA-15-pr-SO3H Catalysts during the Alcoholysis of Furfuryl Alcohol to Ethyl Levulinate: Effect of Pore Size on Catalyst Stability, Transport, and Adsorption

Herein, the alcoholysis of furfuryl alcohol in a series of SBA-15-pr-SO₃H catalysts with different pore sizes is reported. Elemental analysis and NMR relaxation/diffusion methods show that changes in pore size have a significant effect on catalyst activity and durability. In particular, the decrease in catalyst activity after catalyst reuse is mainly due to carbonaceous deposition, whereas leaching of sulfonic acid groups is not significant. This effect is more pronounced in the largest-pore-size catalyst C3, which rapidly deactivates after one reaction cycle, whereas catalysts with a relatively medium and small average pore size (named, respectively, C2 and C1) deactivate after two reaction cycles and to a lesser extent. CHNS elemental analysis showed that C1 and C3 experience a similar amount of carbonaceous deposition, suggesting that the increased reusability of the small-pore-size catalyst can be attributed to the presence of SO₃H groups mostly present on the external surface, as corroborated by results on pore clogging obtained by NMR relaxation measurements. The increased reusability of the C2 catalyst is attributed to a lower amount of humin being formed and, at the same time, reduced pore clogging, which helps to maintain accessible the internal pore space.

New experimental evidence for pervasive dynamics in proteins

There is ample computational, but only sparse experimental data suggesting that pico-ns motions with 1 Å amplitude are pervasive in proteins in solution. Such motions, if present in reality, must deeply affect protein function and protein entropy. Several NMR relaxation experiments have provided insights into motions of proteins in solution, but they primarily report on azimuthal angle variations of vectors of covalently-linked atoms. As such, these measurements are not sensitive to distance fluctuations, and cannot but under-represent the dynamical properties of proteins. Here we analyze a novel NMR relaxation experiment to measure amide proton transverse relaxation rates in uniformly 15 N labeled proteins, and present results for protein domain GB1 at 283 and 303 K. These relaxation rates depend on fluctuations of dipolar interactions between 1 HN and many nearby protons on both the backbone and sidechains. Importantly, they also report on fluctuations in the distances between these protons. We obtained a large mismatch between rates computed from the crystal structure of GB1 and the experimental rates. But when the relaxation rates were calculated from a 200 ns molecular dynamics trajectory using a novel program suite, we obtained a substantial improvement in the correspondence of experimental and theoretical rates. As such, this work provides novel experimental evidence of widespread motions in proteins. Since the improvements are substantial, but not sufficient, this approach may also present a new benchmark to help improve the theoretical forcefields underlying the molecular dynamics calculations.

Fast Motions Dominate Dynamics of Intrinsically Disordered Tau Protein at High Temperatures

Reorientational dynamics of intrinsically disordered proteins (IDPs) contain multiple motions often clustered around three motional modes: ultrafast librational motions of amide groups, fast local backbone conformational fluctuations and slow chain segmental motions. This dynamic picture is mainly based on ¹⁵ N NMR relaxation studies of IDPs at relatively low temperatures where the amide-water proton exchange rates are sufficiently small. Less is known, however, about the dynamics of IDPs at more physiological temperatures. Here, we investigate protein dynamics in a 441-residue long IDP, tau protein, in the temperature range from 0-25 °C, using ¹⁵ N NMR relaxation rates and spectral density analysis. While at these temperatures relaxation rates are still better described in terms of amide group librational motions, local backbone dynamics and chain segmental motions, the temperature-dependent trend of spectral densities suggests that the timescales of fast backbone conformational fluctuations and slower chain segmental motions might become inseparable at higher temperatures. Our data demonstrate the remarkable dynamic plasticity of this prototypical IDP and highlight the need for dynamic studies of IDPs at multiple temperatures.

Conformational exchange divergence along the evolutionary pathway of eosinophil-associated ribonucleases

The evolutionary role of conformational exchange in the emergence and preservation of function within structural homologs remains elusive. While protein engineering has revealed the importance of flexibility in function, productive modulation of atomic-scale dynamics has only been achieved on a finite number of distinct folds. Allosteric control of unique members within dynamically diverse structural families requires a better appreciation of exchange phenomena. Here, we examined the functional and structural role of conformational exchange within eosinophil-associated ribonucleases. Biological and catalytic activity of various EARs was performed in parallel to mapping their conformational behavior on multiple timescales using NMR and computational analyses. Despite functional conservation and conformational seclusion to a specific domain, we show that EARs can display similar or distinct motional profiles, implying divergence rather than conservation of flexibility. Comparing progressively more distant enzymes should unravel how this subfamily has evolved new functions and/or altered their behavior at the molecular level.

Conformational Dynamics of Phytoglobin BvPgb1.2 from Beta vulgaris ssp. vulgaris

Plant hemoglobins, often referred to as phytoglobins, play important roles in abiotic stress tolerance. Several essential small physiological metabolites can be bound to these heme proteins. In addition, phytoglobins can catalyze a range of different oxidative reactions in vivo. These proteins are often oligomeric, but the degree and relevance of subunit interactions are largely unknown. In this study, we delineate which residues are involved in dimer formation of a sugar beet phytoglobin type 1.2 (BvPgb1.2) using NMR relaxation experiments. E. coli cells harboring a phytoglobin expression vector were cultivated in isotope-labeled (²H, ¹³C and ¹⁵N) M9 medium. The triple-labeled protein was purified to homogeneity using two chromatographic steps. Two forms of BvPgb1.2 were examined, the oxy-form and the more stable cyanide-form. Using three-dimensional triple-resonance NMR experiments, sequence-specific assignments for CN-bound BvPgb1.2 were achieved for 137 backbone amide cross-peaks in the ¹H-¹⁵N TROSY spectrum, which amounts to 83% of the total number of 165 expected cross-peaks. A large proportion of the non-assigned residues are located in α-helixes G and H, which are proposed to be involved in protein dimerization. Such knowledge around dimer formation will be instrumental for developing a better understanding of phytoglobins' roles in planta.

DNA base order parameter determination without influence of chemical exchange

Nuclear magnetic resonance (NMR) spectroscopy is a versatile tool used to investigate the dynamic properties of biological macromolecules and their complexes. NMR relaxation data can provide order parameters S2, which represent the mobility of bond vectors reorienting within a molecular frame. Determination of S2 parameters typically involves the use of transverse NMR relaxation rates. However, the accuracy in S2 determination can be diminished by elevation of the transverse relaxation rates through conformational or chemical exchange involving protonation/deprotonation or non-Watson-Crick base-pair states of nucleic acids. Here, we propose an approach for determination of S2 parameters without the influence of exchange processes. This approach utilizes transverse and longitudinal 13C chemical shift anisotropy (CSA) - dipole-dipole (DD) cross-correlation rates instead of 13C transverse relaxation rates. Anisotropy in rotational diffusion is taken into consideration. An application of this approach to nucleotide base CH groups of a uniformly 13C/15N-labeled DNA duplex is demonstrated.

NMR Studies of Two Lysine Based Dendrimers with Insertion of Similar Histidine-Arginine and Arginine-Histidine Spacers Having Different Properties for Application in Drug Delivery

In this paper we study two lysine-based peptide dendrimers with Lys-His-Arg and Lys-Arg-His repeating units and terminal lysine groups. Combination of His and Arg properties in a dendrimer could be important for biomedical applications, especially for prevention of dendrimer aggregation and for penetration of dendrimers through various cell membranes. We describe the synthesis of these dendrimers and the confirmation of their structure using 1D and 2D Nuclear Magnetic Resonance (NMR) spectroscopy. NMR spectroscopy and relaxation are used to study the structural and dynamic properties of these macromolecules and to compare them with properties of previously studied dendrimers with Lys-2Arg and Lys-2His repeating units. Our results demonstrate that both Lys-His-Arg and Lys-Arg-His dendrimers have pH sensitive conformation and dynamics. However, properties of Lys-His-Arg at normal pH are more similar to those of the more hydrophobic Lys-2His dendrimer, which has tendency towards aggregation, while the Lys-Arg-His dendrimer is more hydrophilic. Thus, the conformation with the same amino acid composition of Lys-His-Arg is more pH sensitive than Lys-Arg-His, while the presence of Arg groups undoubtedly increases its hydrophilicity compared to Lys-2His. Hence, the Lys-His-Arg dendrimer could be a more suitable (in comparison with Lys-2His and Lys-Arg-His) candidate as a pH sensitive nanocontainer for drug delivery.

Slow methyl axes motions in perdeuterated villin headpiece subdomain probed by cross-correlated NMR relaxation measurements

Protein methyl groups can participate in multiple motional modes on different time scales. Sub-nanosecond to nano-second time scale motions of methyl axes are particularly challenging to detect for small proteins in solutions. In this work we employ NMR relaxation interference between the methyl H-H/H-C dipole-dipole interactions [Sun&Tugarinov, J. Magn. Reason. 2012] to characterize methyl axes motions as a function of temperature in a small model protein villin headpiece subdomain (HP36), in which all non-exchangeable protons are deuterated with the exception of methyl groups of leucine and valine residues. The data points to the existence of slow motional modes of methyl axes on sub-nanosecond to nanosecond time scales. Further, at high temperatures for which the overall tumbling of the protein is on the order of 2 ns, we observe a coupling between the slow internal motion and the overall molecular tumbling, based on the anomalous order parameters and their temperature-dependent trends. The addition of 28%(w/w) glycerol-d8 increases the viscosity of the solvent and separates the timescales of internal and overall tumbling, thus permitting for another view of the necessity of the coupling assumption for these sites at high temperatures.

Continuous Monitoring of the Agglomeration and Sedimentation of Indomethacin Nanosuspensions Using T2 Relaxation Time with Time-Domain NMR

The time-domain NMR technique was utilized to monitor precisely the physicochemical stability of indomethacin (IMC) nanosuspensions using T2 relaxation time (T2). We investigated whether T2 values can distinguish between agglomeration and sedimentation. Nanosuspensions of IMC were prepared using aqueous wet bead milling with polyvinylpyrrolidone as a stabilizer. Prepared nanosuspensions were divided into two fractions: one was stored in the NMR equipment for continuous T2 measurements and the other was stored in the dispersion analyzer. Measurements of both nanosuspensions were carried out, without dilution, over a period of 24 h at 10-min intervals. Transmission profiles based on multilight scattering technology showed that agglomeration predominantly occurred at 25 and 35 °C immediately after wet bead milling up to 4 h, followed by sedimentation from 4 to 24 h. Upon measuring the T2 relaxation, T2 values at both 25 and 35 °C showed a two-step change-there was a significant prolongation in T2 values immediately after preparation of nanosuspensions up to approx. 4 h and a gradual prolongation in T2 values from approx. 4 to 24 h. Considering the results of transmission profiles, these two-step T2 changes correspond to agglomeration and sedimentation. In other words, this study established that monitoring the T2 values of nanosuspensions could be used to evaluate the agglomeration and sedimentation of contained drug particles. This technique does not directly observe the nanoparticles themselves, but the water molecules. Thus, measurement of T2 relaxation is considered to be a general-purpose technique, independent of the type of drug or polymer.

How does it really move? Recent progress in the investigation of protein nanosecond dynamics by NMR and simulation

Nuclear magnetic resonance (NMR) spin relaxation experiments currently probe molecular motions on timescales from picoseconds to nanoseconds. The detailed interpretation of these motions in atomic detail benefits from complementarity with the results from molecular dynamics (MD) simulations. In this mini-review, we describe the recent developments in experimental techniques to study the backbone dynamics from ¹⁵N relaxation and side-chain dynamics from ¹³C relaxation, discuss the different analysis approaches from model-free to dynamics detectors, and highlight the many ways that NMR relaxation experiments and MD simulations can be used together to improve the interpretation and gain insights into protein dynamics.

Natural and engineered inflammasome adapter proteins reveal optimum linker length for self-assembly

The inflammasome is a multiprotein complex that triggers the activation of proinflammatory cytokines. The adapter ASC and its isoform ASCb mediate inflammasome assembly via self-association and oligomerization with other inflammasome proteins by homotypic interactions of their two identical Death Domains, PYD and CARD, connected by a linker of different length: 23 (ASC) and 4 (ASCb) amino acids long. However, ASC is a more potent inflammasome activator compared to ASCb. Thus, adapter isoforms might be involved in the regulation of the inflammatory response. As previously reported, ASC's faster and less polydisperse self-association compared to ASCb points to interdomain flexibility resulting from the linker length as a key factor in inflammasome regulation. To test the influence of linker length in self-association, we have engineered the isoform ASC3X with identical PYD and CARD connected by a 69 amino acid-long linker (i.e., three-times longer than ASC's linker). Real-time NMR and dynamic light scattering data indicate that ASC3X polymerization is less effective and more polydisperse compared to ASC or ASCb. However, transmission electron micrographs show that ASC3X can polymerize into filaments. Comparative interdomain dynamics of the three isoforms obtained from NMR relaxation data reveal that ASCb tumbles as a rod, whereas the PYD and CARD of ASC and ASC3X tumble independently with marginally higher interdomain flexibility in ASC3X. Altogether, our data suggest that ASC's linker length is optimized for self-association by allowing enough flexibility to favor intermolecular homotypic interactions but simultaneously keeping both domains sufficiently close for essential participation in filament formation.

Evaluation of alumina slurry dispersion by nuclear magnetic resonance relaxation as a comparison to conventional dispersion evaluation methods

In this paper, we evaluated the particle dispersion degree of alumina slurry containing a dispersant by solvent nuclear magnetic resonance (NMR) relaxation and compared it with conventional dispersion evaluation methods such as viscosity, particle size, and sedimentation height measurements. The dispersion of slurry was evaluated via numerical analysis of the transverse relaxation time (T₂ ). The effect of the changes in different parameters of the experiment in terms of milling time, solid loading, and dispersant amount was investigated by NMR relaxation as well as conventional methods. The results of NMR relaxation measurements revealed that T₂ correlates well with other dispersion evaluation methods; thus, it is an efficient technique to evaluate the dispersion of alumina slurry, specifically, when studying the effect of the change in milling time and dispersion amount.

Deuteron rotating frame relaxation for the detection of slow motions in rotating solids

We demonstrate experimental and computational approaches for measuring ²H rotating frame NMR relaxation for solid samples under magic angle spinning (MAS) conditions. The relaxation properties of the deuterium spin-1 system are dominated by the reorientation of the anisotropic quadrupolar tensors, with the effective quadrupolar coupling constant around 55 kHz for methyl groups. The technique is demonstrated using the model compound dimethyl-sulfone at MAS rates of 10 and 60 kHz as well as for an amyloid fibril sample comprising an amyloid-β (1-40) protein with a selective methyl group labeled in the disordered domain of the fibrils, at an MAS rate of 8 kHz. For both systems, the motional parameters fall well within the ranges determined by other techniques, thus validating its feasibility. Experimental and computational factors such as i) the probe's radio frequency inhomogeneity profiles, ii) rotary resonances at conditions for which the spin-lock field strength matches the half- or full-integer of the MAS rate, iii) the choice of MAS rates and spin-lock field strengths, and iv) simulations that account for the interconversion of multiple coherences for the spin-1 system under MAS and deviations from the analytical Redfield treatment are thoroughly considered.

Optimized radio frequency coil for noninvasive magnetic resonance relaxation detection of human finger

Noninvasive NMR measurement of human tissues, such as fingers, to achieve early detection for metabolic diseases is of important significance. The NMR relaxation measurements have a wide application prospect due to simplicity, portability, and low cost, as the static magnetic field is not required to be highly homogeneous. However, the inhomogeneous radiofrequency (RF) magnetic field (B₁) results in errors in the magnetic resonance relaxation times. This is inevitable in in-vivo localized human tissue measurements with a portable MR scanner, as signals from tissues close to the edge of RF coil are excited with a different B₁ field amplitude. A novel RF coil termed T coil with high B₁ field homogeneity is presented. Numerical simulation and phantom measurements were implemented. The novel RF coil was compared with a regular solenoid coil and a variable width coil. In-vivo experiments were performed. The T coil has a better B₁ field homogeneity than the regular solenoid coil and the variable width coil, producing more accurate magnetic resonance relaxation times. Improved detection accuracy has been achieved with the T coil. This work may promote the development of noninvasive human tissue diagnosis based on NMR relaxation methods.

Structural and dynamic studies of the human RNA binding protein RBM3 reveals the molecular basis of its oligomerization and RNA recognition

Human RNA-binding motif 3 protein (RBM3) is a cold-shock protein which functions in various aspects of global protein synthesis, cell proliferation and apoptosis by interacting with the components of basal translational machinery. RBM3 plays important roles in tumour progression and cancer metastasis, and also has been shown to be involved in neuroprotection and endoplasmic reticulum stress response. Here, we have solved the solution NMR structure of the N-terminal 84 residue RNA recognition motif (RRM) of RBM3. The remaining residues are rich in RGG and YGG motifs and are disordered. The RRM domain adopts a βαββαβ topology, which is found in many RNA-binding proteins. NMR-monitored titration experiments and molecular dynamic simulations show that the beta-sheet and two loops form the RNA-binding interface. Hydrogen bond, pi-pi and pi-cation are the key interactions between the RNA and the RRM domain. NMR, size exclusion chromatography and chemical cross-linking experiments show that RBM3 forms oligomers in solution, which is favoured by decrease in temperature, thus, potentially linking it to its function as a cold-shock protein. Temperature-dependent NMR studies revealed that oligomerization of the RRM domain occurs via nonspecific interactions. Overall, this study provides the detailed structural analysis of RRM domain of RBM3, its interaction with RNA and the molecular basis of its temperature-dependent oligomerization.

Low-Field Functional Group Resolved Nuclear Spin Relaxation in Mesoporous Silica

Solid-fluid interactions underpin the efficacy of functional porous materials across a diverse array of chemical reaction and separation processes. However, detailed characterization of interfacial phenomena within such systems is hampered by their optically opaque nature. Motivated by the need to bridge this capability gap, we report low-magnetic-field two-dimensional (2D) ¹H nuclear spin relaxation measurements as a noninvasive probe of adsorbate identity and interfacial dynamics, exploring the relaxation characteristics exhibited by liquid hydrocarbon adsorbates confined to a model mesoporous silica. For the first time, we demonstrate the capacity of this approach in distinguishing functional group-specific relaxation phenomena across a diverse range of alcohols and carboxylic acids employed as solvents, reagents, and liquid hydrogen carriers, with distinct relaxation responses assigned to the alkyl and hydroxyl moieties of each confined liquid. Uniquely, this relaxation behavior is shown to correlate with adsorbate acidity, with the observed relationship rationalized on the basis of surface-adsorbate proton-exchange dynamics. Our results demonstrate that nuclear spin relaxation provides a molecular-level perspective on sorbent/sorbate interactions, motivating the exploration of such measurements as a unique probe of adsorbate identity within optically opaque porous media.

Model-Free or Not?

Relaxation in nuclear magnetic resonance is a powerful method for obtaining spatially resolved, timescale-specific dynamics information about molecular systems. However, dynamics in biomolecular systems are generally too complex to be fully characterized based on NMR data alone. This is a familiar problem, addressed by the Lipari-Szabo model-free analysis, a method that captures the full information content of NMR relaxation data in case all internal motion of a molecule in solution is sufficiently fast. We investigate model-free analysis, as well as several other approaches, and find that model-free, spectral density mapping, LeMaster's approach, and our detector analysis form a class of analysis methods, for which behavior of the fitted parameters has a well-defined relationship to the distribution of correlation times of motion, independent of the specific form of that distribution. In a sense, they are all "model-free." Of these methods, only detectors are generally applicable to solid-state NMR relaxation data. We further discuss how detectors may be used for comparison of experimental data to data extracted from molecular dynamics simulation, and how simulation may be used to extract details of the dynamics that are not accessible via NMR, where detector analysis can be used to connect those details to experiments. We expect that combined methodology can eventually provide enough insight into complex dynamics to provide highly accurate models of motion, thus lending deeper insight into the nature of biomolecular dynamics.

Accelerating 15N and 13C R1 and R1ρ relaxation measurements by multiple pathway solid-state NMR experiments

Magic angle spinning (MAS) Solid-state NMR is a powerful technique to probe dynamics of biological systems at atomic resolution. R₁ and R_1ρ relaxation measurements can provide detailed insight on amplitudes and time scales of motions, especially when information from several different site-specific types of probes is combined. However, such experiments are time-consuming to perform. Shortening the time necessary to record relaxation data for different nuclei will greatly enhance practicality of such approaches. Here, we present staggered acquisition experiments to acquire multiple relaxation experiments from a single excitation to reduce the overall experimental time. Our strategy enables one to collect ¹⁵N and ¹³C relaxation data in a single experiment in a fraction of the time necessary for two separate experiments, with the same signal to noise ratio.

Anhydrous fat crystallization of ultrasonic treated goat milk: DSC and NMR relaxation studies

Methods of NMR relaxation and differential scanning calorimetry (DSC) were used to study the crystallization of anhydrous milk fat (AMF) obtained from milk and subjected to ultrasonic (US) processing. Amongst the changes in the crystallization nature under the influence of ultrasound are the decrease in the crystallization temperature and the increase in the melting enthalpy of the anhydrous milk fat samples. The increase is ∼30% at 20 min of isothermal crystallization and is presumably explained by the additional formation of β'-form crystals from the melt. The parameters of the Avrami equation applied to the description of experimental data show an increase in the crystallization rate in samples with ultrasonic treatment and a change in the dimension of crystallization with a change in melting temperature.

EPR and NMR study of molecular components mobility and organization in goat milk under ultrasound treatment

The effect of ultrasound treatment on molecular mobility and organization of the main components in raw goat milk was studied by EPR and NMR spectroscopies. NMR relaxation studies showed an increase in the spin-lattice T₁ and spin-spin T₂ relaxation times in goat milk products (cream, anhydrous fat) and change in the diffusion of proton-containing molecules during ultrasound treatment. The diffusion became more uniform and could be rather accurately approximated by one effective diffusion coefficient D_eff, which indicates homogenization of goat milk components, dispersion of globular and supermicellar formations under sonication. EPR studies have shown that molecular mobility and organization of hydrophobic regions in goat milk are similar to those observed in micellar formations of surfactants with a hydrocarbon chain length C12-C16. Ultrasound treatment did not affect submicellar and protein globule organization. Free radicals arising under ultrasound impact of milk reacted quickly with components of goat milk (triglycerides, proteins, fatty acids) and were not observed by spin trapping method.

Atomic view of cosolute-induced protein denaturation probed by NMR solvent paramagnetic relaxation enhancement

The cosolvent effect arises from the interaction of cosolute molecules with a protein and alters the equilibrium between native and unfolded states. Denaturants shift the equilibrium toward the latter, while osmolytes stabilize the former. The molecular mechanism whereby cosolutes perturb protein stability is still the subject of considerable debate. Probing the molecular details of the cosolvent effect is experimentally challenging as the interactions are very weak and transient, rendering them invisible to most conventional biophysical techniques. Here, we probe cosolute-protein interactions by means of NMR solvent paramagnetic relaxation enhancement together with a formalism we recently developed to quantitatively describe, at atomic resolution, the energetics and dynamics of cosolute-protein interactions in terms of a concentration normalized equilibrium average of the interspin distance, [Formula: see text], and an effective correlation time, τ_c The system studied is the metastable drkN SH3 domain, which exists in dynamic equilibrium between native and unfolded states, thereby permitting us to probe the interactions of cosolutes with both states simultaneously under the same conditions. Two paramagnetic cosolute denaturants were investigated, one neutral and the other negatively charged, differing in the presence of a carboxyamide group versus a carboxylate. Our results demonstrate that attractive cosolute-protein backbone interactions occur largely in the unfolded state and some loop regions in the native state, electrostatic interactions reduce the [Formula: see text] values, and temperature predominantly impacts interactions with the unfolded state. Thus, destabilization of the native state in this instance arises predominantly as a consequence of interactions of the cosolutes with the unfolded state.

Investigation of Adsorption Behavior of Anticancer Drug on Zinc Oxide Nanoparticles: A Solid State NMR and Cyclic Voltammetry (CV) Analysis

The present study aims to comprehend the adsorption behavior of a set of anticancer drugs namely 5-fluorouracil (5-FU), doxorubicin and daunorubicin on ZnO nanoparticles (ZnO NPs) proposed as drug delivery systems employing solid state (ss) NMR, FTIR and Cyclic Voltammetry (CV) analysis. FTIR and ¹H MAS ssNMR data recorded for bare ZnO nanoparticle confirmed the presence of adsorbed -OH groups on the surface. ¹³C CP-MAS NMR spectra recorded for free and ZnO surface adsorbed drug samples exhibited considerable line broadening and chemical shift changes that complemented our earlier report on UV-DRS and XRD data of surface adsorption in case of 5-FU. Moreover, a remarkable enhancement of ¹³C signal intensity in case of loaded 5-FU was observed. This clearly indicated rigid nature of the drug on the surface allowing efficient transfer of ¹H polarization from the hetero nitrogen of 5-FU to ZnO to form surface hydroxyl (-OH) groups and the same has been observed in the quantum chemical calculations. To further analyze the motional dynamics of the surface adsorbed 5-FU, longitudinal relaxation times (T₁) were quantified employing Torchia method that revealed significant enhancement of ¹³C relaxation rate of adsorbed 5-FU. The enhanced rate suggested an effective role of quadrupolar contribution from ⁶⁷Zn to the ¹³C relaxation mechanism of ZnO_5-FU. The heterogeneous rate constant (k_het), average free energy of activation (∆G^≠) and point of zero charge (PZC) measured for free and drug loaded ZnO NPs samples using CV further support the SS-NMR results.

Glass Transition in Rice Pasta as Observed by Combined Neutron Scattering and Time-Domain NMR

Experimental protocols aiming at the characterisation of glass transition often suffer from ambiguity. The ambition of the present study is to describe the glass transition in a complex, micro heterogeneous system, the dry rice pasta, in a most unambiguous manner, minimising the influence of technique-specific bias. To this end, we apply an unprecedented combination of experimental techniques. Apart from the usually used NMR and DSC, we employ, in a concurrent manner, neutron transmission, diffraction, and Compton scattering. This enables us to investigate the glass transition over a range of spatio-temporal scales that stretches over seven orders of magnitude. The results obtained by neutron diffraction and DSC reveal that dry rice pasta is almost entirely amorphous. Moreover, the glass transition is evidenced by neutron transmission and diffraction data and manifested as a significant decrease of the average sample number density in the temperature range between 40 and 60 °C. At the microscopic level, our NMR, neutron transmission and Compton scattering results provide evidence of changes in the secondary structure of the starch within the dry rice pasta accompanying the glass transition, whereby the long-range order provided by the polymer structure within the starch present in the dry rice pasta is partially lost.

Probing hydrocarbon dynamics at asphaltene/maltene interfaces for the global characterization of bitumen

HYPOTHESIS

The objective is to noninvasively probe the local hydrocarbon dynamics at asphaltene/maltene interfaces to reveal the global characteristics of bitumen at increasing temperatures and under various mechanical constraints.

EXPERIMENTS

We propose multidimensional (1D and 2D) nuclear magnetic relaxation (NMR) experiments to characterize the dynamic properties of hydrocarbons for a set of bitumen from 40 to 180 °C. The convergence towards universal theoretical modelling of NMR relaxation experiments gives a comprehensive understanding of hydrocarbon transport in these very weakly permeable samples. Moreover, a multivariate statistical analysis allows for correlating these NMR relaxation data for all bitumen samples to the main empirical parameters by qualifying the bitumen grading, such as the penetrability, softening and fragility points over a large range of temperatures.

FINDINGS

These new experimental and theoretical multiscale approaches link hydrocarbon interfacial dynamics to the global characteristics of various bitumen types. This is critical for grading these universally encountered materials.

RING NMR dynamics: software for analysis of multiple NMR relaxation experiments

Molecular motions are fundamental to the existence of life, and NMR spectroscopy remains one of the most useful and powerful methods to measure their rates and molecular characteristics. Multiple experimental methods are available for measuring the NMR relaxation properties and these can require different methods for extracting model parameters. We present here a new software application, RING NMR Dynamics, that is designed to support analysis of multiple relaxation types. The initial release of RING NMR Dynamics supports the analysis of exponential decay experiments such as T₁ and T₂, as well as CEST and R₂ and R_1ρ relaxation dispersion. The software runs on multiple operating systems in both a command line mode and a user-friendly GUI that allows visualizing and simulating relaxation data. Interaction with another program, NMRFx Analyst, allows drilling down from the derived relaxation parameters to the raw spectral data.

Carbonyl 13C-detect solution-state protein NMR experiments to circumvent amide-solvent exchange broadening: Application to β2-microglobulin

The ¹⁵N-¹H heteronuclear single-quantum correlation (HSQC) technique in protein NMR spectroscopy suffers from line-broadening effects, such as chemical exchange of labile protons with solvent, and exchange broadening for residues undergoing conformational dynamics. The amide resonance of β₂-microglobulin residue S88 is not observed in the HSQC spectrum but can be obtained through ¹³C-detect experiments that circumvent the problem of amide-solvent exchange broadening. Line broadening of S88 resonance beyond detection in the HSQC spectrum is not attributed to conformational exchange but rather to solvent exchange occurring on the order of ~10³ s^-1.

The influence of extruded flour on water content and retrogradation process in muffins during storage: NMR relaxation study

A comparative study of the moisture content, mobility of water protons and retrogradation process in muffin samples with the addition of extruded (ME) flour (10%) during storage (14 days) was carried out and compared to control samples without the addition (MO). A significant increase in water content during swelling of the extruded flour was found. The proton magnetic relaxation signal for both ME and MO showed a two-component character for the fast-decay region (free induction decay, FID experiment) and a three-component character for the slow-decay (CPMG experiment) one. The relaxation times T₂ characterizing the protons of both water and non-aqueous fraction decreased during the experiment except for the protons of the fat fraction. The values of relaxation times T₂ for ME exceeded the values for MO, which reflects the increased water content in ME. The amplitude of the signal of water protons (two components of CPMG) decreased for ME more slowly (by about 3-5 days), which can serve as a characterization the shelf life of the muffins. Estimation of the retrogradation rate according to the Avrami model showed a lower value of the rate for ME compared to MO, which may reflect the increased moisture content in ME.

C60 in a peptidic cage: a case of symmetry mismatch studied by crystallography and solid-state NMR

A supramolecular complex, formed by encapsulation of C60 fullerene in a molecular container built from two resorcin[4]arene rims zipped together by peptidic arms hydrogen bonded into a cylindrical β-sheet, was studied by X-ray crystallography, solid-state and solution NMR, EPR spectroscopy and differential scanning calorimetry (DSC). The crystal structure, determined at 100 K, reveals that the complex occupies 422 site symmetry, which is compatible with the molecular symmetry of the container but not of the fullerene molecule, which has only 222 symmetry. The additional crystallographic symmetry leads to a complicated but discrete disorder, which could be resolved and modelled using advanced features of the existing refinement software. Solid-state NMR measurements at 184-333 K indicate that the thermal motion of C60 in this temperature range is fast but has different activation energies at different temperatures, which was attributed to a phase transition, which was confirmed by DSC. Intriguingly, the activation energy for reorientations of C60 in the solid state is very similar for the free and encaged molecules. Also, the rotational diffusion coefficients seem to be very similar or even slightly higher for the encaged fullerene compared to the free molecule. We also found that chemical shift anisotropy (CSA) is not the main relaxation mechanism for the 13C spins of C60 in the studied complex.

Pro4 prolyl peptide bond isomerization in human galectin-7 modulates the monomer-dimer equilibrum to affect function

Human galectin-7 (Gal-7; also termed p53-induced gene 1 product) is a multifunctional effector by productive pairing with distinct glycoconjugates and protein counter-receptors in the cytoplasm and nucleus, as well as on the cell surface. Its structural analysis by NMR spectroscopy detected doubling of a set of particular resonances, an indicator of Gal-7 existing in two conformational states in slow exchange on the chemical shift time scale. Structural positioning of this set of amino acids around the P4 residue and loss of this phenomenon in the bioactive P4L mutant indicated cis-trans isomerization at this site. Respective resonance assignments confirmed our proposal of two Gal-7 conformers. Mapping hydrogen bonds and considering van der Waals interactions in molecular dynamics simulations revealed a structural difference for the N-terminal peptide, with the trans-state being more exposed to solvent and more mobile than the cis-state. Affinity for lactose or glycan-inhibitable neuroblastoma cell surface contact formation was not affected, because both conformers associated with an overall increase in order parameters (S2). At low µM concentrations, homodimer dissociation is more favored for the cis-state of the protein than its trans-state. These findings give direction to mapping binding sites for protein counter-receptors of Gal-7, such as Bcl-2, JNK1, p53 or Smad3, and to run functional assays at low concentration to test the hypothesis that this isomerization process provides a (patho)physiologically important molecular switch for Gal-7.

Revealing the Influence of Microparticles on Geopolymers' Synthesis and Porosity

Geopolymers are zeolites like structures based on hydrated aluminosilicates units of SiO₄ and AlO₄. These units, known as poly(sialate), poly(sialate)-siloxo or poly(sialate)-disiloxo are chemically balanced by the group I cations of K⁺, Li⁺, or Na⁺. Simultaneously, the chemical reaction of formation, known as geopolymerization, governs the orientation of the unit, generating mesoporous structures. Multiple methods can be used for pore structure and porosity characterization. Among them, nuclear magnetic resonance (NMR) relaxometry allows the detection of the porous structure in a completely nonperturbative manner. NMR relaxometry may be used to monitor the relaxation of protons belonging to the liquid molecules confined inside the porous structure and, thus, to get access to the pore size distribution. This monitoring can take place even during the polymerization process. The present study implements transverse relaxation measurements to monitor the influence introduced by the curing time on the residual liquid phase of geopolymers prepared with two different types of reinforcing particles. According to our results, the obtained geopolymers contain three types of pores formed by the arrangement of the OH⁻ and Si groups (Si-OH), Si-O-Si groups, Si-O-Al groups, and Si-O rings. After 48 days, the samples cured for 8 h show a high percentage of all three types of pores, however, by increasing the curing time and the percentage of reinforcing particle, the percent of pores decrease, especially, the gel pores.

Hybrid Thermophilic/Mesophilic Enzymes Reveal a Role for Conformational Disorder in Regulation of Bacterial Enzyme I

Conformational disorder is emerging as an important feature of biopolymers, regulating a vast array of cellular functions, including signaling, phase separation, and enzyme catalysis. Here we combine NMR, crystallography, computer simulations, protein engineering, and functional assays to investigate the role played by conformational heterogeneity in determining the activity of the C-terminal domain of bacterial Enzyme I (EIC). In particular, we design chimeric proteins by hybridizing EIC from thermophilic and mesophilic organisms, and we characterize the resulting constructs for structure, dynamics, and biological function. We show that EIC exists as a mixture of active and inactive conformations and that functional regulation is achieved by tuning the thermodynamic balance between active and inactive states. Interestingly, we also present a hybrid thermophilic/mesophilic enzyme that is thermostable and more active than the wild-type thermophilic enzyme, suggesting that hybridizing thermophilic and mesophilic proteins is a valid strategy to engineer thermostable enzymes with significant low-temperature activity.

The effect of ultrasound treatment on the interaction of brine with pork meat proteins

The objective of the study is to elucidate the effect of ultrasound treated salt solution on curing of pork meat. The interactions of salt (NaCl) solutions of 3 and 25% with the proteins of pork meat are studied. High intensity ultrasound operating at 20 kHz was used. The differential scanning calorimetry (DSC), NMR spin-spin relaxation time, unfrozen water and water diffusion coefficient measurements were carried out in meat cured with ultrasound treated and untreated salt solutions. The effect of ultrasonication was most evident from measured spin-spin relaxation times T₂₁, the rate of chemical exchange of water protons k and the amount of unfrozen water W_unf in the meat. The measured diffusion coefficient of water D_w in meat cured with ultrasound treated and control salt solution did not show significant difference. The nuclear magnetic resonance (NMR) relaxation data, differential scanning calorimetry (DSC) and the diffusion coefficient data reliably show that the possible action of ultrasound to salt solution was manifested on the first 2 days of the experiment with a 3% salt solution.

Location of paramagnetic defects in detonation nanodiamond from proton spin-lattice relaxation data

We developed an approach for determining location of intrinsic paramagnetic defects in nanodiamonds from the data of proton spin-lattice relaxation of the surface hydrogen atoms. The approach was applied to the detonation nanodiamond (DND) of the diameter of 5 nm. We found that dangling bonds with unpaired electron spins are located within the near-surface belt at the distance of 0.3-0.9 nm from the DND surface. The NMR data are compared with the results of EPR measurements.

Impact of enrichment with egg constituents on water status in gluten-free rice pasta - nuclear magnetic resonance and thermogravimetric approach

Effects of freeze-dried egg white, yolk and whole egg enrichment on water behaviour in fresh pasta dough, dried and cooked rice pasta with respect to control samples were studied by ¹H nuclear magnetic resonance (NMR) relaxometry and thermogravimetric analysis. Enrichments caused lower mobility of water (T₂) localised within the starch-protein matrix in fresh dough as well as dried pasta. Water compartmentalization was also downgraded in cooked products. Water fractions with different T₂ values were linked to temperature peaks at the first derivative of the thermogravimetric (DTG) curve. From the DTG curve strong interaction of water molecules with proteins of egg white was revealed. Egg proteins also influenced viscoelastic properties of dough, and enhanced the firmness and chewiness of cooked pasta. Structural changes induced by various types of enrichment were reflected in the different molecular mobility at the water-matrix interface (T₁). The enrichments also altered the colour and cooking properties.

Protein Interactions with Nanoparticle Surfaces: Highlighting Solution NMR Techniques

In the last decade, nanoparticles (NPs) have become a key tool in medicine and biotechnology as drug delivery systems, biosensors and diagnostic devices. The composition and surface chemistry of NPs vary based on the materials used: typically organic polymers, inorganic materials, or lipids. Nanoparticle classes can be further divided into sub-categories depending on the surface modification and functionalization. These surface properties matter when NPs are introduced into a physiological environment, as they will influence how nucleic acids, lipids, and proteins will interact with the NP surface. While small-molecule interactions are easily probed using NMR spectroscopy, studying protein-NP interactions using NMR introduces several challenges. For example, globular proteins may have a perturbed conformation when attached to a foreign surface, and the size of NP-protein conjugates can lead to excessive line broadening. Many of these challenges have been addressed, and NMR spectroscopy is becoming a mature technique for in situ analysis of NP binding behavior. It is therefore not surprising that NMR has been applied to NP systems and has been used to study biomolecules on NP surfaces. Important considerations include corona composition, protein behavior, and ligand architecture. These features are difficult to resolve using classical surface and material characterization strategies, and NMR provides a complementary avenue of characterization. In this review, we examine how solution NMR can be combined with other analytical techniques to investigate protein behavior on NP surfaces.

Unraveling the structure and dynamics of the human DNAJB6b chaperone by NMR reveals insights into Hsp40-mediated proteostasis

J-domain chaperones are involved in the efficient handover of misfolded/partially folded proteins to Hsp70 but also function independently to protect against cell death. Due to their high flexibility, the mechanism by which they regulate the Hsp70 cycle and how specific substrate recognition is performed remains unknown. Here we focus on DNAJB6b, which has been implicated in various human diseases and represents a key player in protection against neurodegeneration and protein aggregation. Using a variant that exists mainly in a monomeric form, we report the solution structure of an Hsp40 containing not only the J and C-terminal substrate binding (CTD) domains but also the functionally important linkers. The structure reveals a highly dynamic protein in which part of the linker region masks the Hsp70 binding site. Transient interdomain interactions via regions crucial for Hsp70 binding create a closed, autoinhibited state and help retain the monomeric form of the protein. Detailed NMR analysis shows that the CTD (but not the J domain) self-associates to form an oligomer comprising ∼35 monomeric units, revealing an intricate balance between intramolecular and intermolecular interactions. The results shed light on the mechanism of autoregulation of the Hsp70 cycle via conserved parts of the linker region and reveal the mechanism of DNAJB6b oligomerization and potentially antiaggregation.

Nonlinear sampling in ultrafast Laplace NMR

Ultrafast Laplace NMR (UF-LNMR) reduces the experiment time of multidimensional relaxation and diffusion measurements to a fraction. Here, we demonstrate a method for nonlinear (in this case logarithmic) sampling of the indirect dimension in UF-LNMR measurements. The method is based on the use of frequency-swept pulses with the frequency nonlinearly increasing with time. This leads to an optimized detection of exponential experimental data and significantly improved resolution of LNMR parameters.

Accounting for the temperature dependence of 13C spin-lattice relaxation of methyl groups in the glycyl-alanyl-leucine model system under MAS with spin diffusion

The difficulties in quantitatively modeling the temperature dependence of spin-lattice relaxation in a model isotope-enriched peptide are explored as a prelude to obtaining dynamics parameters for motions in proteins from such measurements. The degree to which this can be handled by adding spin diffusion to a bath in standard rate matrix relaxation theory is studied using a small tri-peptide model system, glycyl-alanyl-leucine (GAL). We observe in this molecule that the relaxation of backbone carbons CO and Cα is not dominated by local fluctuations of the ¹³C-¹H dipolar couplings, but rather by ¹³C-¹³C spin diffusion to nearby methyl relaxation sinks. A treatment of the methyl relaxation itself, which ignores ¹³C-¹³C spin diffusion effects back to the otherwise slowly relaxing bath, provides poor agreement between theory and experimental data obtained for the temperature dependence of the methyl relaxation rates. Closed form approximate spectral densities and relaxation rates for a methyl group during magic angle spinning are obtained to compute the needed transition rates. These average computed rates, in conjunction with an extended form of the Solomon equations, are found to adequately model the temperature dependence of the methyl relaxation rates when spin diffusion is included. The barrier to rotation for the alanine methyl in GAL is determined to be 3.5 kcal mol^-1.

Nuclear magnetic relaxation and diffusion study of the ionic liquids 1-ethyl- and 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide confined in porous glass

The molecular dynamics of the room-temperature ionic liquid 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (Bmim Tf2N) confined in porous glass is studied by nuclear magnetic resonance (NMR) relaxometry and diffusometry and is compared with the bulk dynamics over a wide temperature range. The molecular reorientation processes for anions and cations alike are found to be significantly affected by the presence of the glass interface at high temperatures. In this respect, the ionic liquid behaves similarly to polar liquids where proton NMR relaxation is governed by reorientations mediated by translational displacements (RMTDs). This process becomes less significant towards lower temperatures when the characteristic translational correlation times of the ions approach a timescale comparable with those of the RMTD process, and the relaxation dispersions in bulk and in confinement become similar below a temperature corresponding to about 1.2T_g , a value where the onset of dynamic heterogeneity has been observed before. The self-diffusion coefficient, on the other hand, is found to be strongly reduced than the bulk within the accessible temperature range of 248 K and above and is significantly slower than expected from the tortuosity effect, suggesting that ion-surface interactions affect the macroscopic properties.

Surface influence on the rotational and translational dynamics of molecules confined inside a mesoporous carbon xerogel

Low-field nuclear magnetic resonance techniques are employed to extract information about the effects introduced by the interaction with the surface on the rotational and translational dynamics of molecules confined inside a mesoporous carbon xerogel. The molecules under study were water, cyclohexane, and hexane. They were chosen due to their different interaction strength with the carbonaceous matrix. Frequency dependent longitudinal relaxation measurements, using the fast field cycling technique, allowed extraction of the fractal dimension of the carbon xerogel surface. It was observed that the measured value is influenced by the molecule affinity to the surface. Diffusion measurements, using the pulse field gradient technique, have revealed that the stronger interaction with the surface of cyclohexane and hexane molecules leads to an increased diffusive tortuosity, as compared with water.

Regularized inversion of the Laplace transform for series of experiments

Not only in low-field nuclear magnetic resonance, Laplace inversion is a relevant and challenging topic. Considerable conceptual and technical progress has been made, especially for the inversion of data encoding two decay dimensions. Distortion of spectra by overfitting of even moderate noise is counteracted requiring a priori smooth spectra. In this contribution, we treat the case of simple and fast one-dimensional decay experiments that are repeated many times in a series in order to study the evolution of a sample or process. Incorporating the a priori knowledge that also in the series dimension evolution should be smooth, peak position can be stabilized and resolution improved in the decay dimension. It is explained how the standard one-dimensional regularized Laplace inversion can be extended quite simply in order to include regularization in the series dimension. Obvious improvements compared with series of one-dimensional inversions are presented for simulated as well as experimental data. For the latter, comparison with multiexponential fitting is performed.

Localized and Collective Motions in HET-s(218-289) Fibrils from Combined NMR Relaxation and MD Simulation

Nuclear magnetic resonance (NMR) relaxation data and molecular dynamics (MD) simulations are combined to characterize the dynamics of the fungal prion HET-s(218-289) in its amyloid form. NMR data is analyzed with the dynamics detector method, which yields timescale-specific information. An analogous analysis is performed on MD trajectories. Because specific MD predictions can be verified as agreeing with the NMR data, MD was used for further interpretation of NMR results: for the different timescales, cross-correlation coefficients were derived to quantify the correlation of the motion between different residues. Short timescales are the result of very local motions, while longer timescales are found for longer-range correlated motion. Similar trends on ns- and μs-timescales suggest that μs motion in fibrils is the result of motion correlated over many fibril layers.

Characterization of Internal Protein Dynamics and Conformational Entropy by NMR Relaxation

Recent studies suggest that the fast timescale motion of methyl-bearing side chains may play an important role in mediating protein activity. These motions have been shown to encapsulate the residual conformational entropy of the folded state that can potentially contribute to the energetics of protein function. Here, we provide an overview of how to characterize these motions using nuclear magnetic resonance (NMR) spin relaxation methods. The strengths and limitations of several techniques are highlighted in order to assist with experimental design. Particular emphasis is placed on the practical aspects of sample preparation, data collection, data fitting, and statistical analysis. Additionally, discussion of the recently refined "entropy meter" is presented and its use in converting NMR observables to conformational entropy is illustrated. Taken together, these methods should yield new insights into the complex interplay between structure and dynamics in protein function.

Direct Correlation between Adsorption Energetics and Nuclear Spin Relaxation in a Liquid-saturated Catalyst Material

The ratio of NMR relaxation time constants <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow><mml:msub><mml:mi>T</mml:mi> <mml:mn>1</mml:mn></mml:msub> <mml:mo>/</mml:mo> <mml:msub><mml:mi>T</mml:mi> <mml:mn>2</mml:mn></mml:msub> </mml:mrow> </mml:math> provides a non-destructive indication of the relative surface affinities exhibited by adsorbates within liquid-saturated mesoporous catalysts. In the present work we provide supporting evidence for the existence of a quantitative relationship between such measurements and adsorption energetics. As a prototypical example with relevance to green chemical processes we examine and contrast the relaxation characteristics of primary alcohols and cyclohexane within an industrial silica catalyst support. <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow><mml:msub><mml:mi>T</mml:mi> <mml:mn>1</mml:mn></mml:msub> <mml:mo>/</mml:mo> <mml:msub><mml:mi>T</mml:mi> <mml:mn>2</mml:mn></mml:msub> </mml:mrow> </mml:math> values obtained at intermediate magnetic field strength are in good agreement with DFT adsorption energy calculations performed on single molecules interacting with an idealised silica surface. Our results demonstrate the remarkable ability of this metric to quantify surface affinities within systems of relevance to liquid-phase heterogeneous catalysis, and highlight NMR relaxation as a powerful method for the determination of adsorption phenomena within mesoporous solids.

Functionally specific binding regions of microtubule-associated protein 2c exhibit distinct conformations and dynamics

Microtubule-associated protein 2c (MAP2c) is a 49-kDa intrinsically disordered protein regulating the dynamics of microtubules in developing neurons. MAP2c differs from its sequence homologue Tau in the pattern and kinetics of phosphorylation by cAMP-dependent protein kinase (PKA). Moreover, the mechanisms through which MAP2c interacts with its binding partners and the conformational changes and dynamics associated with these interactions remain unclear. Here, we used NMR relaxation and paramagnetic relaxation enhancement techniques to determine the dynamics and long-range interactions within MAP2c. The relaxation rates revealed large differences in flexibility of individual regions of MAP2c, with the lowest flexibility observed in the known and proposed binding sites. Quantitative conformational analyses of chemical shifts, small-angle X-ray scattering (SAXS), and paramagnetic relaxation enhancement measurements disclosed that MAP2c regions interacting with important protein partners, including Fyn tyrosine kinase, plectin, and PKA, adopt specific conformations. High populations of polyproline II and α-helices were found in Fyn- and plectin-binding sites of MAP2c, respectively. The region binding the regulatory subunit of PKA consists of two helical motifs bridged by a more extended conformation. Of note, although MAP2c and Tau did not differ substantially in their conformations in regions of high sequence identity, we found that they differ significantly in long-range interactions, dynamics, and local conformation motifs in their N-terminal domains. These results highlight that the N-terminal regions of MAP2c provide important specificity to its regulatory roles and indicate a close relationship between MAP2c's biological functions and conformational behavior.