The effects of dissolved oxygen upon amide proton relaxation and chemical shift in a perdeuterated protein

Nuclear magnetic resonance-based determination of dioxygen binding sites in protein cavities

The location and ligand accessibility of internal cavities in cysteine-free wild-type T4 lysozyme was investigated using O₂ gas-pressure NMR spectroscopy and molecular dynamics (MD) simulation. Upon increasing the concentration of dissolved O₂ in solvent to 8.9 mM, O₂ -induced paramagnetic relaxation enhancements (PREs) to the backbone amide and side chain methyl protons were observed, specifically around two cavities in the C-terminal domain. To determine the number of O₂ binding sites and their atomic coordinates from the 1/r⁶ distance dependence of the PREs, we established an analytical procedure using Akaike's Information Criterion, in combination with a grid-search. Two O₂ -accessible sites were identified in internal cavities: One site was consistent with the xenon-binding site in the protein in crystal, and the other site was established to be a novel ligand-binding site. MD simulations performed at 10 and 100 mM O₂ revealed dioxygen ingress and egress as well as rotational and translational motions of O₂ in the cavities. It is therefore suggested that conformational fluctuations within the ground-state ensemble transiently develop channels for O₂ association with the internal protein cavities.

Analysis of O2-binding Sites in Proteins Using Gas-Pressure NMR Spectroscopy: Outer Surface Protein A

Internal cavities in proteins produce conformational fluctuations and enable the binding of small ligands. Here, we report a NMR analysis of O₂-binding sites by O₂-induced paramagnetic relaxation enhancements (PREs) on amide groups of proteins in solution. Outer surface protein A contains a nonglobular single-layer β-sheet that connects the N- and C-terminal globular domains. Several cavities have been observed in both domains of the crystallized protein structure. The receptor-binding sites are occluded and line the largest cavity of the C-terminal domain. We observed significant O₂-induced PREs for amide protons located around the largest cavity and at the central β-sheet. We suggested three potential O₂-accessible sites in the protein based on the 1/r⁶ distance dependence of the PRE. Two sites were in or close to the largest cavity and the third site was in the surface crevice of the central β-sheet. These results provide, to our knowledge, the first evidence of ligand binding to the surface crevice and cavity of the protein in solution. Because O₂ generally binds more specifically to hydrophobic rather than hydrophilic cavities within a protein, the results also indicated that the receptor-binding sites lining the largest cavity were in the hydrophobic environment in the ground-state conformation. Molecular dynamics simulations permitted the visualization of the rotational and translational motions of O₂ within the largest cavity, egress of O₂ from the cavity, and ingress of O₂ in the surface crevice of the β-sheet. These molecular dynamics simulation results qualitatively explained the O₂-induced changes in NMR observations. Exploring cavities that are sufficiently dynamic to enable access by small molecules can be a useful strategy for the design of stable proteins and their ligands.

Detecting O2 binding sites in protein cavities

Internal cavities are important elements in protein structure, dynamics, stability and function. Here we use NMR spectroscopy to investigate the binding of molecular oxygen (O₂) to cavities in a well-studied model for ligand binding, the L99A mutant of T4 lysozyme. On increasing the O₂ concentration to 8.9 mM, changes in ¹H, ¹⁵N, and ¹³C chemical shifts and signal broadening were observed specifically for backbone amide and side chain methyl groups located around the two hydrophobic cavities of the protein. O₂-induced longitudinal relaxation enhancements for amide and methyl protons could be adequately accounted for by paramagnetic dipolar relaxation. These data provide the first experimental demonstration that O₂ binds specifically to the hydrophobic, and not the hydrophilic cavities, in a protein. Molecular dynamics simulations visualized the rotational and translational motions of O₂ in the cavities, as well as the binding and egress of O₂, suggesting that the channel consisting of helices D, E, G, H, and J could be the potential gateway for ligand binding to the protein. Due to strong paramagnetic relaxation effects, O₂ gas-pressure NMR measurements can detect hydrophobic cavities when populated to as little as 1%, and thereby provide a general and highly sensitive method for detecting oxygen binding in proteins.

Dioxygen transmembrane distributions and partitioning thermodynamics in lipid bilayers and micelles

Cellular respiration, mediated by the passive diffusion of oxygen across lipid membranes, is key to many basic cellular processes. In this work, we report the detailed distribution of oxygen across lipid bilayers and examine the thermodynamics of oxygen partitioning via NMR studies of lipids in a small unilamellar vesicle (SUV) morphology. Dissolved oxygen gives rise to paramagnetic chemical shift perturbations and relaxation rate enhancements, both of which report on local oxygen concentration. From SUVs containing the phospholipid sn-2-perdeuterio-1-myristelaidoyl, 2-myristoyl-sn-glycero-3-phosphocholine (MLMPC), an analogue of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), we deduced the complete trans-bilayer oxygen distribution by measuring (13)C paramagnetic chemical shifts perturbations for 18 different sites on MLMPC arising from oxygen at a partial pressure of 30 bar. The overall oxygen solubility at 45 °C spans a factor of 7 between the bulk water (23.7 mM) and the bilayer center (170 mM) and is lowest in the vicinity of the phosphocholine headgroup, suggesting that oxygen diffusion across the glycerol backbone should be the rate-limiting step in diffusion-mediated passive transport of oxygen across the lipid bilayer. Lowering of the temperature from 45 to 25 °C gave rise to a slight decrease of the oxygen solubility within the hydrocarbon interior of the membrane. An analysis of the temperature dependence of the oxygen solubility profile, as measured by (1)H paramagnetic relaxation rate enhancements, reveals that oxygen partitioning into the bilayer is entropically favored (ΔS° = 54 ± 3 J K(-1) mol(-1)) and must overcome an enthalpic barrier (ΔH° = 12.0 ± 0.9 kJ mol(-1)).

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

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

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

BACKGROUND

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

METHOD

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

RESULTS

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

CONCLUSIONS

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

GENERAL SIGNIFICANCE

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

Transient NOE-exchange-relay experiment: application to ligand-protein binding under slow exchange conditions

A new version of one-dimensional (1)H experiment has been developed to probe ligand binding to macromolecular targets. The experiment, called transient NOE-exchange relay, is similar to the 'reverse NOE pumping' technique [A. Chen, M.J. Shapiro, J. Am. Chem. Soc. 122 (2000) 414-415]. The T(2) filter is used to erase protein magnetization, and the saturation then spreads from protein to bound ligand (via NOE) and further to a free ligand (via on-off exchange). The ligand signals, monitored as a function of mixing time, present a familiar 'dip' pattern characteristic of transient NOE or transient exchange experiments. In addition to the T(2) filter, we have also implemented a T(1) filter which makes use of the fact that the selective T(1)(-1) rates in macromolecules are much higher than those in small ligands. To model the experiment, complete relaxation and exchange matrix analysis has been invoked. This formalism was further used as a starting point to develop a simplified treatment where the relaxation and exchange components are represented by 2x2 matrix and, in addition, there is a special term responsible for coupling of ligand magnetization to the protein spin bath. The proposed experimental scheme has been tested on a system of peanut agglutinin complexed with Me-beta-D-galactopyranoside, which is known to be in a slow exchange regime. The results suggest that the NOE-exchange-relay experiment can be used at the advanced stages of the drug development process to confirm high-affinity ligand binding.

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

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

A Combined NMR and Molecular Dynamics Study of the Transmembrane Solubility and Diffusion Rate Profile of Dioxygen in Lipid Bilayers

The transmembrane profile of oxygen solubility and diffusivity in a lipid bilayer was assessed by (13)C NMR of the resident lipids (sn-2-perdeuterio-1-myristelaidoyl-2-myristoyl-sn-glycero-3-phosphocholine) in combination with molecular dynamics (MD) simulations. At an oxygen partial pressure of 50 atm, distinct chemical shift perturbations of a paramagnetic origin were observed, spanning a factor of 3.2 within the sn-1 chain and an overall factor of 10 from the headgroup to the hydrophobic interior. The distinguishing feature of the (13)C NMR shift perturbation measurements, in comparison to ESR and fluorescence quenching measurements, is that the local accessibility of oxygen is achieved for nearly all carbon atoms in a single experiment with atomic resolution and without the use of a probe molecule. MD simulations of an oxygenated and hydrated lipid bilayer provided an immersion depth distribution of all carbon nuclei, in addition to the distribution of oxygen concentration and diffusivity with immersion depth. All oxygen-induced (13)C NMR chemical shift perturbations could be reasonably approximated by simply accounting for the MD-derived immersion depth distribution of oxygen in the bilayer, appropriately averaged according to the immersion depth distribution of the (13)C nuclei. Second-order effects in the paramagnetic shift are attributed to the collisionally accessible solid angle or to the propensity of the valence electrons in the vicinity of a given nuclear spin to be polarized or delocalized by oxygen. A method is presented to measure such effects. The excellent agreement between MD and NMR provides an important cross-validation of the two techniques.

An NMR Method for the Determination of Protein-Binding Interfaces Using Dioxygen-Induced Spin−Lattice Relaxation Enhancement

Using oxygen as a paramagnetic probe, researchers can routinely study topologies and protein-binding interfaces by NMR. The paramagnetic contribution to the amide (1)H spin-lattice relaxation rates (R(1)(P)) have been studied for uniformly (2)H,(15)N-labeled FB protein, a 60-residue three-helix bundle, constituting the B domain of protein A. Through TROSY versions of inversion-recovery experiments, R(1)(P) could be determined. R(1)(P) was then measured in the presence of a stoichiometric equivalent of an unlabeled Fc fragment of immunoglobulin (Ig) G, and the ratio of R(1)(P) of the FB-Fc complex to that of free FB [i.e., R(1)(P)(complex)/R(1)(P)(free)] was determined for each observable residue. Regions of helix I and helix II, which were previously known to interact with Fc, were readily identified as belonging to the binding interface by their characteristically reduced values of R(1)(P)(complex)/R(1)(P)(free). The method of comparing oxygen-induced spin-lattice relaxation rates of free protein and protein-protein complexes, to detect binding interfaces, offers greater sensitivity than chemical shift perturbation, while it is not necessary to heavily deuterate the labeled protein, as is the case in cross saturation experiments.

Probing protein-peptide binding surfaces using charged stable free radicals and transverse paramagnetic relaxation enhancement (PRE)

Nitroxide species, which have an unpaired electron localized on a nitrogen atom, can be useful as NMR probes to identify areas of the surface of a protein involved in the formation of a complex. The proximity of an electron spin leads to higher NMR relaxation rates for protein nuclei. If a protein-ligand complex is formed the radical is excluded from certain sites on the protein surface, protecting them from relaxation effects. We show here that charged nitroxide species can be helpful for identifying regions of the surface of the 4F1(5)F1 module pair from human fibronectin involved in peptide binding.

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

Due to its depth-dependent solubility, oxygen exerts paramagnetic effects which become progressively greater toward the hydrophobic interior of micelles, and lipid bilayer membranes. This paramagnetic gradient, which is manifested as contact shift perturbations (19F and 13C NMR) and spin-lattice relaxation enhancement (19F and 1H NMR), has been shown to be useful for precisely determining immersion depth, membrane protein secondary structure, and overall topology of membrane proteins. We have investigated the influence of oxygen on 19F and 13C NMR spectra and spin-lattice relaxation rates of a semiperfluorinated detergent, (8,8,8)-trifluoro (3,3,4,4,5,5,6,6,7,7)-difluoro octylmaltoside (TFOM) in a model membrane system, to determine the dominant paramagnetic spin-lattice relaxation and shift-perturbation mechanism. Based on the ratio of paramagnetic spin-lattice relaxation rates of 19F and directly bonded 13C nuclei, we conclude that the dominant relaxation mechanism must be dipolar. Furthermore, the temperature dependence of oxygen-induced chemical shift perturbations in 9F NMR spectra suggests a contact interaction is the dominant shift mechanism. The respective hyperfine coupling constants for 19F and 13C nuclei can then be estimated from the contact shifts <(deltav/v0)19F> and <(deltav/v0)13C>, allowing us to estimate the relative contribution of scalar and dipolar relaxation to 19F and 13C nuclei. We conclude that the contribution to spin-lattice relaxation from the oxygen induced paramagnetic scalar mechanism is negligible.

Amide proton relaxation measurements employing a highly deuterated protein

Proton NMR longitudinal and transverse relaxation rates of unlabelled proteins are generally dominated by the many 1H-1H dipolar interactions so that spin diffusion, rather than molecular or internal motions, governs longitudinal relaxation. Here, relaxation measurements of backbone amide proton (1H(N)) magnetisations have been carried out employing the 99% 2H, 98% 15N labelled, small 2F2 protein domain in 10%/90% H(2)O/D(2)O solution. Under these conditions, the longitudinal relaxation rates exhibit time constants, T(1)*=1/R(1)* if described by a mono-exponential, within the range of 3.0 to 18.7s-a wide range which indicates that the phenomenon of spin diffusion has been greatly reduced. The majority of 1H(N) nuclei in this sample (pH 4.0 and 5 degrees C) exhibit chemical exchange with solvent that couples their longitudinal relaxation to that of the solvent. For the subset of 1H(N) nuclei not undergoing detectable solvent chemical exchange, the R(1)* rates correlate well with their individual 1H(N,O)/2H(N,O) structural environments. The correlation for corresponding transverse relaxation rates, R(2)* was found to be less good. Longitudinal relaxation measurements in 1%/99% H(2)O/D(2)O solution identify a further subset of 1H(N) nuclei which exhibit essentially indistinguishable R(1)* rates in both 1% and 10% H(2)O, implying that averaging of rates from spin diffusion processes and different 2F2 isotopomer populations are negligible for these 1H(N) sites. In addition to a high sensitivity to structural parameters, model calculations predict 1H(N) relaxation rates to exhibit pronounced sensitivity to internal dynamics.