Nuclear Magnetic Resonance Relaxation Dispersion Research Articles

Theory and modeling of molecular modes in the NMR relaxation of fluids

Traditional theories of the nuclear magnetic resonance (NMR) autocorrelation function for intra-molecular dipole pairs assume a single-exponential decay, yet the calculated autocorrelation of realistic systems displays a rich, multi-exponential behavior, resulting in anomalous NMR relaxation dispersion (i.e., frequency dependence). We develop an approach to model and interpret the multi-exponential intra-molecular autocorrelation using simple, physical models within a rigorous statistical mechanical development that encompasses both rotational diffusion and translational diffusion in the same framework. We recast the problem of evaluating the autocorrelation in terms of averaging over a diffusion propagator whose evolution is described by a Fokker–Planck equation. The time-independent part admits an eigenfunction expansion, allowing us to write the propagator as a sum over modes. Each mode has a spatial part that depends on the specified eigenfunction and a temporal part that depends on the corresponding eigenvalue (i.e., correlation time) with a simple, exponential decay. The spatial part is a probability distribution of the dipole pair, analogous to the stationary states of a quantum harmonic oscillator. Drawing inspiration from the idea of inherent structures in liquids, we interpret each of the spatial contributions as a specific molecular mode. These modes can be used to model and predict the NMR dipole–dipole relaxation dispersion of fluids by incorporating phenomena on the molecular level. We validate our statistical mechanical description of the distribution in molecular modes with molecular dynamics simulations interpreted without any relaxation models or adjustable parameters: the most important poles in the Padé–Laplace transform of the simulated autocorrelation agree with the eigenvalues predicted by the theory.

Evolutionary Role of Water-Accessible Cavities in Src Homology 2 (SH2) Domains.

Protein excited states are fundamental in the understanding of biological function, despite the fact they are hardly observed using traditional biophysical methodologies. Pressure perturbation coupled with nuclear magnetic resonance (NMR) spectroscopy is a powerful physicochemical tool to glance at these low-populated high-energy states on a residue-by-residue basis and underpin mechanistic insights into protein functionalities. Here we performed pressure titrations using NMR spectroscopy and relaxation dispersion experiments to identify the low-lying energetic states of the c-Abl SH2 domain. By showing that the SH2 excited state contains a hydrated hydrophobic cavity, fast-exchange motions, and highly conserved residues facing the water-accessible hole, we discuss the implications of water-protein interactions in SH2 modules achieving high-affinity binding and promiscuous phospho-Tyr peptide recognition.

A litmus test for classifying recognition mechanisms of transiently binding proteins

Partner recognition in protein binding is critical for all biological functions, and yet, delineating its mechanism is challenging, especially when recognition happens within microseconds. We present a theoretical and experimental framework based on straight-forward nuclear magnetic resonance relaxation dispersion measurements to investigate protein binding mechanisms on sub-millisecond timescales, which are beyond the reach of standard rapid-mixing experiments. This framework predicts that conformational selection prevails on ubiquitin’s paradigmatic interaction with an SH3 (Src-homology 3) domain. By contrast, the SH3 domain recognizes ubiquitin in a two-state binding process. Subsequent molecular dynamics simulations and Markov state modeling reveal that the ubiquitin conformation selected for binding exhibits a characteristically extended C-terminus. Our framework is robust and expandable for implementation in other binding scenarios with the potential to show that conformational selection might be the design principle of the hubs in protein interaction networks.

TAPBPR employs a ligand-independent docking mechanism to chaperone MR1 molecules.

Chaperones tapasin and transporter associated with antigen processing (TAP)-binding protein related (TAPBPR) associate with the major histocompatibility complex (MHC)-related protein 1 (MR1) to promote trafficking and cell surface expression. However, the binding mechanism and ligand dependency of MR1/chaperone interactions remain incompletely characterized. Here in vitro, biochemical and computational studies reveal that, unlike MHC-I, TAPBPR recognizes MR1 in a ligand-independent manner owing to the absence of major structural changes in the MR1 α2-1 helix between empty and ligand-loaded molecules. Structural characterization using paramagnetic nuclear magnetic resonance experiments combined with restrained molecular dynamics simulations reveals that TAPBPR engages conserved surfaces on MR1 to induce similar adaptations to those seen in MHC-I/TAPBPR co-crystal structures. Finally, nuclear magnetic resonance relaxation dispersion experiments using 19F-labeled diclofenac show that TAPBPR can affect the exchange kinetics of noncovalent metabolites with the MR1 groove, serving as a catalyst. Our results support a role of chaperones in stabilizing nascent MR1 molecules to enable loading of endogenous or exogenous cargo.

Conformational Dynamics of the Hepatitis B Virus Pre-genomic RNA on Multiple Time Scales: Implications for Viral Replication

Human hepatitis B virus (HBV) replication is initiated by the binding of the viral polymerase (P) to epsilon (ε), an ≈85-nucleotide (nt) cis-acting regulatory stem-loop RNA located at the 5′-end of the pre-genomic RNA (pgRNA). This interaction triggers P and pgRNA packaging and protein-primed reverse transcription and is therefore an attractive therapeutic target. Our recent nuclear magnetic resonance (NMR) structure of ε provides a useful starting point toward a detailed understanding of HBV replication, and hints at the functional importance of ε dynamics. Here, we present a detailed description of ε motions on the ps to ns and μs to ms time scales by NMR spin relaxation and relaxation dispersion, respectively. We also carried out molecular dynamics simulations to provide additional insight into ε conformational dynamics. These data outline a series of complex motions on multiple time scales within ε. Moreover, these motions occur in mostly conserved nucleotides from structural regions (i.e., priming loop, pseudo-triloop, and U43 bulge) that biochemical and mutational studies have shown to be essential for P binding, P-pgRNA packaging, protein-priming, and DNA synthesis. Taken together, our work implicates RNA dynamics as an integral feature that governs HBV replication.

Functional Dynamics of Deubiquitinase A

Deubiquitinase A (DUBA) is an isopeptidase that cleaves K63‐linked and K48‐linked ubiquitin chains from substrate proteins. DUBA belongs to the ovarian tumor (OTU) subfamily of deubiquitinases (DUBs) and was initially identified as a negative regulator of the production of type I interferons. DUBA is also known to regulate the production of several other cytokines in both innate and adaptive immune cells. More recently, its role in regulation of the stability of chromatin regulators essential for human development has been revealed. DUBA is a model system for understanding how the activity and substrate specificity of DUBs are regulated by post‐translation modifications (PTMs) through modulation of the conformational ensemble that pre‐exists in the apo form of the enzyme. We have previously identified changes in the conformational ensemble of DUBA upon phosphorylation, which is essential for DUBA activity, using solution nuclear magnetic resonance (NMR) spectroscopy and activity assays. We have also characterized the conformational dynamics on the microsecond‐to‐millisecond timescales using NMR relaxation dispersion experiments. We will present NMR and activity data on several mutants of DUBA, which allowed us to identify the structural determinants of the previously observed conformational dynamics and to understand the functional roles of motions in DUBA. We will also present NMR data on the enzyme‐substrate complex, which shed light on the mechanism for the specificity of DUBA for the K63‐linked ubiquitin chain. Overall, our data suggest that the conformational dynamics of DUBA can be modulated by phosphorylation and are essential for the function of DUBA. Our study highlights the functional importance of conformational dynamics in the DUB family and the need to define dynamic properties of DUBs in order to fully understand how activity and substrate specificity can both be modulated by PTMs.

Analysis of protein-ligand interactions from titrations and nuclear magnetic resonance relaxation dispersions.

We present PLIS, a publicly available, open‐source software for the determination of protein–ligand dissociation constants that can be used to characterize biological processes or to shed light on biophysical aspects of interactions. PLIS can analyze data from titration experiments monitored by for instance fluorescence spectroscopy or from nuclear magnetic resonance relaxation dispersion experiments. In addition to analysis of experimental data, PLIS includes functionality for generation of synthetic data, useful for understanding how different parameters effect the data in order to better analyze experiments.

Hydrogen/Deuterium Exchange and Nuclear Magnetic Resonance Spectroscopy Reveal Dynamic Allostery on Multiple Time Scales in the Serine Protease Thrombin.

A deeper understanding of how hydrogen/deuterium exchange mass spectrometry (HDX-MS) reveals allostery is important because HDX-MS can reveal allostery in systems that are not amenable to nuclear magnetic resonance (NMR) spectroscopy. We were able to study thrombin and its complex with thrombomodulin, an allosteric regulator, by both HDX-MS and NMR. In this Perspective, we compare and contrast the results from both experiments and from molecular dynamics simulations. NMR detects changes in the chemical environment around the protein backbone N-H bond vectors, providing residue-level information about the conformational exchange between distinct states. HDX-MS detects changes in amide proton solvent accessibility and H-bonding. Taking advantage of NMR relaxation dispersion measurements of the time scale of motions, we draw conclusions about the motions reflected in HDX-MS experiments. Both experiments detect allostery, but they reveal different components of the allosteric transition. The insights gained from integrating NMR and HDX-MS into thrombin dynamics enable a clearer interpretation of the evidence for allostery revealed by HDX-MS in larger protein complexes and assemblies that are not amenable to NMR.

Molecular Dynamics in Ionic Liquid/Radical Systems.

Molecular dynamics of the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethyl sulfonyl)imide (Emim-Tf2N) with either of the four organic stable radicals, TEMPO, 4-benzoyloxy-TEMPO, BDPA, and DPPH, is studied by using Nuclear Magnetic Resonance (NMR) and Dynamic Nuclear Polarization (DNP). In complex fluids at ambient temperature, NMR signal enhancement by DNP is frequently obtained by a combination of several mechanisms, where the Overhauser effect and solid effect are the most common. Understanding the interactions of free radicals with ionic liquid molecules is of particular significance due to their complex dynamics in these systems, influencing the properties of the ion-radical interaction. A combined analysis of EPR, DNP, and NMR relaxation dispersion is carried out for cations and anions containing, respectively, the NMR active nuclei 1H or 19F. Depending on the size and the chemical properties of the radical, different interaction processes are distinguished, namely, the Overhauser effect and solid effect, driven by dominating dipolar or scalar interactions. The resulting NMR relaxation dispersion is decomposed into rotational and translational contributions, allowing the identification of the corresponding correlation times of motion and interactions. The influence of electron relaxation time and electron-nuclear spin hyperfine coupling is discussed.

Self-diffusion micromechanism in Nafion studied by 2H NMR relaxation dispersion.

Field Cycling (FC) 2H nuclear magnetic resonance (NMR) relaxometry was applied to study dynamics in Nafion NR 212 in the temperature range from 300 K to 190 K and water content of λ = 8.2. The sensitive time window of FC was extended up to eight decades using the temperature-frequency superposition principle and master curve. The rotational correlation times obtained from 2H FC NMR coincide with translational correlation times gained from static field 2H NMR diffusometry in the temperature range applied. This fact means that a long-range mass transport in Nafion is coupled to molecular rotations. It is assumed that confined water in Nafion has more ordered oxygen sublattices as compared with bulk water, on a short range is similar to ice. We discuss the possible role of D and L defects, typical for the ordered ice structure and using this concept to describe the processes of self-diffusion of confined water in Nafion, as well as the similarity of temperature and humidity dependence of self-diffusion and proton conductivity.

Conformational Dynamics of Deubiquitinase A and Functional Implications.

Deubiquitinase A (DUBA) belongs to the ovarian tumor family of deubiquitinating enzymes and was initially identified as a negative regulator of type I interferons, whose overproduction has been linked to autoimmune diseases. The deubiquitinating activity of DUBA is positively regulated by phosphorylation at a single serine residue, S177, which results in minimal structural changes. We have previously shown that phosphorylation induces a two-state conformational equilibrium observed only in the active form of DUBA, highlighting the functional importance of DUBA dynamics. Here, we report the conformational dynamics of DUBA on the microsecond-to-millisecond time scales characterized by nuclear magnetic resonance relaxation dispersion experiments. We found that motions on these time scales are highly synchronized in the phosphorylated and nonphosphorylated DUBA. Despite the overall similarity of these two forms, different dynamic properties were observed in helix α1 and the neighboring regions, including residue S177, which likely contribute to the activation of DUBA by phosphorylation. Moreover, our data suggest that transient unfolding of helix α6 drives the global conformational process and that mutations can be introduced to modulate this process, which provides a basis for future studies to define the exact functional roles of motions in DUBA activation and substrate specificity.

An ultraweak interaction in the intrinsically disordered replication machinery is essential for measles virus function.

Measles virus genome encapsidation is essential for viral replication and is controlled by the intrinsically disordered phosphoprotein (P) maintaining the nucleoprotein in a monomeric form (N) before nucleocapsid assembly. All paramyxoviruses harbor highly disordered amino-terminal domains (PNTD) that are hundreds of amino acids in length and whose function remains unknown. Using nuclear magnetic resonance (NMR) spectroscopy, we describe the structure and dynamics of the 90-kDa N0PNTD complex, comprising 450 disordered amino acids, at atomic resolution. NMR relaxation dispersion reveals the existence of an ultraweak N-interaction motif, hidden within the highly disordered PNTD, that allows PNTD to rapidly associate and dissociate from a specific site on N while tightly bound at the amino terminus, thereby hindering access to the surface of N. Mutation of this linear motif quenches the long-range dynamic coupling between the two interaction sites and completely abolishes viral transcription/replication in cell-based minigenome assays comprising integral viral replication machinery. This description transforms our understanding of intrinsic conformational disorder in paramyxoviral replication. The essential mechanism appears to be conserved across Paramyxoviridae, opening unique new perspectives for drug development against this family of pathogens.

Analysis of Artifacts Caused by Pulse Imperfections in CPMG Pulse Trains in NMR Relaxation Dispersion Experiments

Nuclear magnetic resonance relaxation dispersion (rd) experiments provide kinetics and thermodynamics information of molecules undergoing conformational exchange. Rd experiments often use a Carr-Purcell-Meiboom-Gill (CPMG) pulse train equally separated by a spin-state selective inversion element (U-element). Even with measurement parameters carefully set, however, parts of 1H–15N correlations sometimes exhibit large artifacts that may hamper the subsequent analyses. We analyzed such artifacts with a combination of NMR measurements and simulation. We found that particularly the lowest CPMG frequency (νcpmg) can also introduce large artifacts into amide 1H–15N and aromatic 1H–13C correlations whose 15N/13C resonances are very close to the carrier frequencies. The simulation showed that the off-resonance effects and miscalibration of the CPMG π pulses generate artifact maxima at resonance offsets of even and odd multiples of νcpmg, respectively. We demonstrate that a method once introduced into the rd experiments for molecules having residual dipolar coupling significantly reduces artifacts. In the method the 15N/13C π pulse phase in the U-element is chosen between x and y. We show that the correctly adjusted sequence is tolerant to miscalibration of the CPMG π pulse power as large as ±10% for most amide 15N and aromatic 13C resonances of proteins.

Recent advances in measuring the kinetics of biomolecules by NMR relaxation dispersion spectroscopy

Protein function can be modulated or dictated by the amplitude and timescale of biomolecular motion, therefore it is imperative to study protein dynamics. Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful technique capable of studying timescales of motion that range from those faster than molecular reorientation on the picosecond timescale to those that occur in real-time. Across this entire regime, NMR observables can report on the amplitude of atomic motion, and the kinetics of atomic motion can be ascertained with a wide variety of experimental techniques from real-time to milliseconds and several nanoseconds to picoseconds. Still a four orders of magnitude window between several nanoseconds and tens of microseconds has remained elusive. Here, we highlight new relaxation dispersion NMR techniques that serve to cover this “hidden-time” window up to hundreds of nanoseconds that achieve atomic resolution while studying the molecule under physiological conditions.

Cation Dynamics in Supercooled and Solid Alkyl Methylimidazolium Bromide Ionic Liquids

The molecular dynamics of alkyl methylimidazolium bromide ionic liquids with different side groups of the cation are studied over a wide range of temperatures, covering the supercooled and crystalline states. Nuclear magnetic resonance relaxation dispersion (NMRD) at different magnetic field strengths was combined with NMR pulsed field gradient (PFG) diffusion measurements in order to obtain a description of the temperature dependence of the cationic mobility. While an Arrhenius dependence of the correlation times was found at high temperatures, a deviation is observed below a critical temperature of Tdyn ∼ 275 K which corresponds to about 1.25 Tg for two of the substances. The macroscopic diffusion coefficient, on the other hand, is best described by a VFT dependence down to a similar temperature, and a much weaker temperature dependence below. Measurements carried out in the crystalline state of 1-butyl-3-methylimidazolium bromide (Bmim Br) exhibit a dramatically increased self-diffusion coefficient in agreement with earlier reports of strong dynamic heterogeneity in the presence of minute amounts of water.

Role of Watson-Crick-Like Mismatches in DNA Replication Fidelity

DNA replication, transcription, and translation rely on the strict Watson-Crick base pairing rules to ensure faithful transmission of genetic information. The Watson-Crick pairing rules are determined by the predominant neutral tautomeric forms of the nucleic acid bases. Incorrect base pairing during replication, if left unrepaired, leads to transition or transversion point mutations. Spontaneous mutagenesis from replication errors is believed to be a prominent source of base substitution errors in tumor suppressor genes in multiple forms of cancer. Rare tautomeric and ionized nucleotide bases can form mismatches that conform to the Watson-Crick like geometry, subverting proof reading mechanisms. These tautomeric and anionic mismatches have long been suspected to contribute to spontaneous replication errors; they have proved difficult to visualize as the conformational changes are subtle and involve the rearmament of protons. Nuclear magnetic resonance relaxation dispersion techniques have allowed for the characterization of a highly sequence-dependent kinetic network connecting the wobble dG·dT mismatch to multiple Watson-Crick-like tautomeric and anionic dG·dT mismatch ‘excited states’. We have obtained evidence in support of a kinetic model for misincorporation which introduces a rate-limiting on-pathway tautomerization or ionization step that leads to Watson-Crick-like mismatches prior to incorporation through the canonical synthesis pathway. This kinetic model can account for i) the three orders of magnitude difference seen in vitro between rates of correct and incorrect nucleotide incorporations, ii) nucleotide selectivity fidelity as low as 10−6, and iii) the poorly understood sequence dependence of polymerization errors.

The Dynamic Landscape of the Full-Length HIV-1 Transactivator of Transcription.

The type 1 human immunodeficiency virus (HIV-1) transactivator of transcription (Tat) is a small RNA-binding protein essential for viral gene expression and replication. It has also been shown to bind to a large number of human proteins and to modulate many different cellular activities. We have used nuclear magnetic resonance (NMR) spectroscopy and hydrogen exchange chemistry to measure backbone dynamics over the millisecond to picosecond time scales. Sequential backbone assignment was facilitated by several isotope labeling schemes, including uniform labeling, site-specific labeling, and unlabeling. (15)N NMR relaxation parameters were measured and analyzed by reduced spectral density mapping and the Lipari-Szabo Model-Free approach to characterize the backbone dynamics on the picosecond to nanosecond time scale. The results indicate that the protein exists in an extended disordered conformational ensemble. NMR relaxation dispersion profiles show that on the millisecond time scale no conformational exchange is detected for any of the residues, supporting the model of a disordered backbone. NMR chemical shift differences from random coil values suggest that some segments of the protein have a modest propensity to fold; comparison to X-ray diffraction structures of Tat complexes indicates that some segments of the protein function through an induced-fit mechanism whereas other segments likely operate by conformational selection. Surprisingly, measured hydrogen exchange rates are higher than predicted for a disordered polymer, but this is explained as being caused by the high net charge on the protein that enhances base-catalyzed hydrogen exchange. The dynamics results provide a deeper understanding of the protein conformational ensemble and form a foundation for future studies of the conformational changes that accompany the formation of the superelongation complex that activates viral transcription.

Parsimony in Protein Conformational Change

Protein conformational change is analyzed by finding the minimalist backbone torsion angle rotations that superpose crystal structures within experimental error. Of several approaches for enforcing parsimony during flexible least-squares superposition, an ℓ(1)-norm restraint provided greatest consistency with independent indications of flexibility from nuclear magnetic resonance relaxation dispersion and chemical shift perturbation in arginine kinase and four previously studied systems. Crystallographic cross-validation shows that the dihedral parameterization describes conformational change more accurately than rigid-group approaches. The rotations that superpose the principal elements of structure constitute a small fraction of the raw (φ, ψ) differences that also reflect local conformation and experimental error. Substantial long-range displacements can be mediated by modest dihedral rotations, accommodated even within α helices and β sheets without disruption of hydrogen bonding at the hinges. Consistency between ligand-associated and intrinsic motions (in the unliganded state) implies that induced changes tend to follow low-barrier paths between conformational sub-states that are in intrinsic dynamic equilibrium.

Dynamics of the ionic liquid 1-butyl-3-methylimidazolium bis(trifluoromethylsulphonyl)imide studied by nuclear magnetic resonance dispersion and diffusion.

The dynamics of the imidazolium based room temperature ionic liquid Bmim Tf2N was investigated by means of nuclear magnetic resonance relaxation dispersion (NMRD) and nuclear magnetic resonance pulsed field gradient (NMR-PFG) diffusion experiments on the bulk liquid in a wide range of temperatures. Relaxation and diffusion properties were determined for anions and cations individually, giving evidence of heterogeneities in the dynamics of the ionic liquid. The relevant NMR relaxation mechanisms are the inter- and intramolecular dipolar interactions between the molecular ions reflecting the molecular translational and rotational diffusion. Rotational and translational correlation times could be obtained and showed different dependences on temperature. The experimental diffusion values follow the Vogel-Fulcher-Tammann (VFT) relation above a transition temperature Tc∼ 1.26 Tg, below which a deviation was observed. Differential scanning calorimetry experiments show a transition at the same temperature.

Functional Unfolding in E. coli Adenylate Kinase

It has become increasingly clear that proteins have evolved for their entire energy landscape including excited states that are important for their biological functions. However, excited state conformations are difficult to study due to their low population and transient nature. One such excited state has been stabilized in E. coli adenylate kinase (AK) using an entropy-enhancing mutation scheme. Mutating solvent exposed residues from valine to glycine has preferentially stabilized a locally unfolded (LU) excited state in the LID domain of AK while maintaining the same ground-state structure. Nuclear magnetic resonance (NMR) measurements of these variants demonstrate direct evidence of the LU state and verify previous thermodynamic data. Furthermore, NMR relaxation dispersion experiments give access to the kinetics of the local unfolding transition, which in conjunction with entropy-enhancing variants that modulate the enzymatic activity of AK, should allow insight into the protein dynamics that drive enzymatic activity. These studies illuminate the ensemble nature of the native state and provide insight on how conformational excursions can tune biological activity in other systems.