Improved measurement of (15)N-[(1)H] NOEs in the presence of H(N)-water proton chemical exchange

Dynamic 15N{1H} NOE measurements: a tool for studying protein dynamics

Intramolecular motions in proteins are one of the important factors that determine their biological activity and interactions with molecules of biological importance. Magnetic relaxation of 15N amide nuclei allows one to monitor motions of protein backbone over a wide range of time scales. 15N{1H} nuclear Overhauser effect is essential for the identification of fast backbone motions in proteins. Therefore, exact measurements of NOE values and their accuracies are critical for determining the picosecond time scale of protein backbone. Measurement of dynamic NOE allows for the determination of NOE values and their probable errors defined by any sound criterion of nonlinear regression methods. The dynamic NOE measurements can be readily applied for non-deuterated or deuterated proteins in both HSQC and TROSY-type experiments. Comparison of the dynamic NOE method with commonly implied steady-state NOE is presented in measurements performed at three magnetic field strengths. It is also shown that improperly set NOE measurement cannot be restored with correction factors reported in the literature.

NMR Methods for Characterizing the Basic Side Chains of Proteins: Electrostatic Interactions, Hydrogen Bonds, and Conformational Dynamics

NMR spectroscopy is a powerful tool for studying protein dynamics. Conventionally, NMR studies on protein dynamics have probed motions of protein backbone NH, side-chain aromatic, and CH₃ groups. Recently, there has been remarkable progress in NMR methodologies that can characterize motions of cationic groups in protein side chains. These NMR methods allow investigations of the dynamics of positively charged lysine (Lys) and arginine (Arg) side chains and their hydrogen bonds as well as their electrostatic interactions important for protein function. Here, describing various practical aspects, we provide an overview of the NMR methods for dynamics studies of Lys and Arg side chains. Some example data on protein-DNA complexes are shown. We will also explain how molecular dynamics (MD) simulations can facilitate the interpretation of the NMR data on these basic side chains. Studies combining NMR and MD have revealed the highly dynamic nature of short-range electrostatic interactions via ion pairs, especially those involving Lys side chains.

Imaging human teeth by phosphorus magnetic resonance with nuclear Overhauser enhancement

Three-dimensional phosphorus MR images ((31)P MRI) of teeth are obtained at a nominal resolution of 0.5 mm in less than 15 minutes using acquisition pulse sequences sensitive to ultra-short transversal relaxation times. The images directly reflect the spatially resolved phosphorus content of mineral tissue in dentin and enamel; they show a lack of signal from pulp tissue and reduced signal from de-mineralized carious lesions. We demonstrate for the first time that the signal in (31)P MR images of mineralized tissue is enhanced by a (1)H-(31)P nuclear Overhauser effect (NOE). Using teeth as a model for imaging mineralized human tissue, graded differences in signal enhancement are observed that correlate well with known mineral content. From solid-state NMR experiments we conclude that the NOE is facilitated by spin diffusion and that the NOE difference can be assigned to a higher water content and a different micro-structure of dentin. Thus, a novel method for imaging mineral content without ionizing radiation is proposed. This method has potential use in the assessment of de-mineralization states in humans, such as caries of teeth and osteoporosis of bones.

NMR studies on the dynamics of hydrogen bonds and ion pairs involving lysine side chains of proteins

Hydrogen bonds and ion pairs involving side chains play vital roles in protein functions such as molecular recognition and catalysis. Despite the wealth of structural information about hydrogen bonds and ion pairs at functionally crucial sites on proteins, the dynamics of these fundamental chemical interactions are not well understood largely due to the lack of suitable experimental tools in the past. NMR spectroscopy is a powerful tool for investigations of protein dynamics, but the vast majority of NMR methods had been applicable only to the backbone or methyl groups. Recently, a substantial progress has been made in the research on the dynamics of hydrogen bonds and ion pairs involving lysine side-chain NH3+ groups. Together with computational/theoretical approaches, the new NMR methods provide unique insights into the dynamics of hydrogen bonds and ion pairs involving lysine side chains. Here, the methodology and its applications are reviewed.

A study on the influence of fast amide exchange on the accuracy of (15)N relaxation rate constants

(15)N relaxation rates of amide moieties provide insight both into global as well as local backbone dynamics of peptides and proteins. As the differences in the relaxation rates in general are small, their accurate determination is of prime importance. One potential source of error is fast amide exchange. It is well known that in its presence the effects of saturation transfer and H/D exchange may result in erroneous apparent relaxation rates R (1) and R (2). Here, the extent of these errors is rigorously examined. Theoretical considerations reveal that even when saturation effects are absent, H/D exchange will easily result in significant deviations from the true values. In particular overestimations of up to 10 % in R (1) and up to 5 % in R (2) are observed. An alternative scheme for fitting the relaxation data to the corresponding exponentials is presented that in the best cases not only delivers more accurate relaxation rates but also allows extracting estimates for the exchange rates. The theoretical computations were tested and verified for the case of ubiquitin.

Dynamics of lysine side-chain amino groups in a protein studied by heteronuclear 1H−15N NMR spectroscopy

Despite their importance in macromolecular interactions and functions, the dynamics of lysine side-chain amino groups in proteins are not well understood. In this study, we have developed the methodology for the investigations of the dynamics of lysine NH3(+) groups by NMR spectroscopy and computation. By using 1H−15N heteronuclear correlation experiments optimized for 15NH3(+) moieties, we have analyzed the dynamic behavior of individual lysine NH3(+) groups in human ubiquitin at 2 °C and pH 5. We modified the theoretical framework developed previously for CH3 groups and used it to analyze 15N relaxation data for the NH3(+) groups. For six lysine NH3(+) groups out of seven in ubiquitin, we have determined model-free order parameters, correlation times for bond rotation, and reorientation of the symmetry axis occurring on a pico- to nanosecond time scale. From CPMG relaxation dispersion experiment for lysine NH3(+) groups, slower dynamics occurring on a millisecond time scale have also been detected for Lys27. The NH3(+) groups of Lys48, which plays a key role as the linkage site in ubiquitination for proteasomal degradation, was found to be highly mobile with the lowest order parameter among the six NH3(+) groups analyzed by NMR. We compared the experimental order parameters for the lysine NH3(+) groups with those from a 1 μs molecular dynamics simulation in explicit solvent and found good agreement between the two. Furthermore, both the computer simulation and the experimental correlation times for the bond rotations of NH3(+) groups suggest that their hydrogen bonding is highly dynamic with a subnanosecond lifetime. This study demonstrates the utility of combining NMR experiment and simulation for an in-depth characterization of the dynamics of these functionally most important side-chains of ubiquitin.

Compensating increases in protein backbone flexibility occur when the Dead ringer AT-rich interaction domain (ARID) binds DNA: a nitrogen-15 relaxation study

AT-rich interaction domains (ARIDs) are found in a large number of eukaryotic transcription factors that regulate cell proliferation, differentiation, and development. Previously we elucidated how ARIDs recognize DNA by determining the solution structure of the Drosophila melanogaster Dead ringer protein in both its DNA-free and -bound states. In order to quantitatively determine how ARIDs alter their mobility to recognize DNA, we have measured the relaxation parameters of the backbone nitrogen-15 nuclei of Dead ringer in its free and bound forms, and interpreted these data using the model-free approach. We show that Dead ringer undergoes significant changes in its mobility upon binding, with residues in the loop connecting helices H5 and H6 becoming immobilized in the major groove and contacts to the minor groove slowing down the motion of residues at the C terminus. A DNA-induced rotation and displacement of the N-terminal subdomain of the protein increases the mobility of helix H1 located distal to the DNA interface and may partially negate the entropic cost of immobilizing interfacial residues. Elevated motions on the micro- to millisecond timescale in the N-terminal domain prior to DNA binding appear to foreshadow the DNA-induced conformation change.

Protein dynamics using frequency-dependent order parameters from analysis of NMR relaxation data

A novel approach is described to analyze NMR relaxation data on proteins. This method introduces the frequency-dependent order parameter, S(2)(omega), in order to estimate contributions to the generalized order parameter S(2) from different motional frequencies occurring on the picosecond to nanosecond time scales. S(2)(omega) is defined as the sum of a specified set of weighting coefficients from the Lorentzian expansion of the spectral density function. 15N NMR relaxation data (500, 600, and 800 MHz) on protein GB1 exemplify the method. Using this approach provides information on motional restrictions over specific frequency or time scale ranges and provides a normalized comparison of motional restrictions between proteins having different overall tumbling correlation times.

Heat capacities and a snapshot of the energy landscape in protein GB1 from the pre-denaturation temperature dependence of backbone NH nanosecond fluctuations

Protein stability is usually characterized calorimetrically by a melting temperature and related thermodynamic parameters. Despite its importance, the microscopic origin of the melting transition and the relationship between thermodynamic stability and dynamics remains a mystery. Here, NMR relaxation parameters were acquired for backbone 15NH groups of the 56 residue immunoglobulin-binding domain of streptococcal protein G over a pre-denaturation temperature range of 5-50 degrees C. Relaxation data were analyzed using three methods: the standard three-Lorentzian model free approach; the F(omega)=2omegaJ(omega) spectral density approach that yields motional correlation time distributions, and a new approach that determines frequency-dependent order parameters. Regardless of the method of analysis, the temperature dependence of internal motional correlation times and order parameters is essentially the same. Nanosecond time-scale internal motions are found for all NHs in the protein, and their temperature dependence yields activation energies ranging up to about 33kJ/mol residue. NH motional barrier heights are structurally correlated, with the largest energy barriers being found for residues in the most "rigid" segments of the fold: beta-strands 1 and 4 and the alpha-helix. Trends in this landscape also parallel the free energy of folding-unfolding derived from hydrogen-deuterium (H-D) exchange measurements, indicating that the energetics for internal motions occurring on the nanosecond time-scale mirror those occurring on the much slower time-scale of H-D exchange. Residual heat capacities, derived from the temperature dependence of order parameters, range from near zero to near 100J/mol K residue and correlate with this energy landscape. These results provide a unique picture of this protein's energy landscape and a relationship between thermodynamic stability and dynamics that suggests thermosensitive regions in the fold that could initiate the melting process.

Temperature dependence of the internal dynamics of a calmodulin-peptide complex

The temperature dependence of the fast internal dynamics of calcium-saturated calmodulin in complex with a peptide corresponding to the calmodulin-binding domain of the smooth muscle myosin light chain kinase is examined using 15N and 2H NMR relaxation methods. NMR relaxation studies of the complex were carried out at 13 temperatures that span 288-346 K. The dynamics of the backbone and over four dozen methyl-bearing side chains, distributed throughout the calmodulin molecule, were probed. The side chains show a much more variable and often considerably larger response to temperature than the backbone. A significant variation in the temperature dependence of the amplitude of motion of individual side chains is seen. The amplitude of motion of some side chains is essentially temperature-independent while many show a simple roughly linear temperature dependence. In a few cases, angular order increases with temperature, which is interpreted as arising from interactions with neighboring residues. In addition, a number of side chains display a nonlinear temperature dependence. The significance of these and other results is illuminated by several simple interpretative models. Importantly, analysis of these models indicates that changes in generalized order parameters can be robustly related to corresponding changes in residual entropy. A simple cluster model that incorporates features of cooperative or conditional motion reproduces many of the unusual features of the experimentally observed temperature dependence and illustrates that side chain interactions result in a dynamically changing environment that significantly influences the motion of internal side chains. This model also suggests that the intrinsic entropy of interacting clusters of side chains is only modestly reduced from that of independent side chain motion. Finally, estimates of protein heat capacity support the view that the major contribution to the heat capacity of protein solutions largely arises from local bond vibrations and solvent interactions and not from torsional oscillations of side chains.