Phospholipids in Motion: High-Resolution 31P NMR Field Cycling Studies

Diverse phospholipid motions are key to membrane function but can be quite difficult to untangle and quantify. High-resolution field cycling ³¹P NMR spin-lattice relaxometry, where the sample is excited at high field, shuttled in the magnet bore for low-field relaxation, then shuttled back to high field for readout of the residual magnetization, provides data on phospholipid dynamics and structure. This information is encoded in the field dependence of the ³¹P spin-lattice relaxation rate (R₁). In the field range from 11.74 down to 0.003 T, three dipolar nuclear magnetic relaxation dispersions (NMRDs) and one due to ³¹P chemical shift anisotropy contribute to R₁ of phospholipids. Extraction of correlation times and maximum relaxation amplitudes for these NMRDs provides (1) lateral diffusion constants for different phospholipids in the same bilayer, (2) estimates of how additives alter the motion of the phospholipid about its long axis, and (3) an average ³¹P-¹H angle with respect to the bilayer normal, which reveals that polar headgroup motion is not restricted on a microsecond timescale. Relative motions within a phospholipid are also provided by comparing ³¹P NMRD profiles for specifically deuterated molecules as well as ¹³C and ¹H field dependence profiles to that of ³¹P. Although this work has dealt exclusively with phospholipids in small unilamellar vesicles, these same NMRDs can be measured for phospholipids in micelles and nanodisks, making this technique useful for monitoring lipid behavior in a variety of structures and assessing how additives alter specific lipid motions.

Enzyme-Substrate-Cofactor Dynamical Networks Revealed by High-Resolution Field Cycling Relaxometry

The remarkable power and specificity of enzyme catalysis rely on the dynamic alignment of the enzyme, substrates, and cofactors, yet the role of dynamics has usually been approached from the perspective of the protein. We have been using an underappreciated NMR technique, subtesla high-resolution field cycling 31P NMR relaxometry, to investigate the dynamics of the enzyme-bound substrates and cofactor on guanosine-5'-monophosphate reductase (GMPR). GMPR forms two dead end, yet catalytically competent, complexes that mimic distinct steps in the catalytic cycle: E·IMP·NADP+ undergoes a partial hydride transfer reaction, while E·GMP·NADP+ undergoes a partial deamination reaction. A different cofactor conformation is required for each partial reaction. Here we report the effects of mutations designed to perturb cofactor conformation and ammonia binding with the goal of identifying the structural features that contribute to the distinct dynamic signatures of the hydride transfer and deamination complexes. These experiments suggest that Asp129 is a central cog in a dynamic network required for both hydride transfer and deamination. In contrast, Lys77 modulates the conformation and mobility of substrates and cofactors in a reaction-specific manner. Thr105 and Tyr318 are part of a deamination-specific dynamic network that includes the 2'-OH of GMP. These residues have comparatively little effect on the dynamic properties of the hydride transfer complex. These results further illustrate the potential of high-resolution field cycling NMR relaxometry for the investigation of ligand dynamics. In addition, exchange experiments indicate that NH3/NH4+ has a high affinity for the deamination complex but a low affinity for the hydride transfer complex, suggesting that the movement of ammonia may gate the cofactor conformational change. Collectively, these experiments reinforce the view that the enzyme, substrates, and cofactor are linked in intricate, reaction-specific, dynamic networks and demonstrate that distal portions of the substrates and cofactors are critical features in these networks.

Dynamic Characteristics of Guanosine-5'-monophosphate Reductase Complexes Revealed by High-Resolution 31P Field-Cycling NMR Relaxometry

The ability of enzymes to modulate the dynamics of bound substrates and cofactors is a critical feature of catalysis, but the role of dynamics has largely been approached from the perspective of the protein. Here, we use an underappreciated NMR technique, subtesla high-resolution field-cycling ³¹P NMR relaxometry, to interrogate the dynamics of enzyme bound substrates and cofactors in guanosine-5'-monophosphate reductase (GMPR). These experiments reveal distinct binding modes and dynamic profiles associated with the ³¹P nuclei in the Michaelis complexes for the deamination and hydride transfer steps of the catalytic cycle. Importantly, the substrate is constrained and the cofactor is more dynamic in the deamination complex E·GMP·NADP⁺, whereas the substrate is more dynamic and the cofactor is constrained in the hydride transfer complex E·IMP·NADP⁺. The presence of D₂O perturbed the relaxation of the ³¹P nuclei in E·IMP·NADP⁺ but not in E·GMP·NADP⁺, providing further evidence of distinct binding modes with different dynamic properties. dIMP and dGMP are poor substrates, and the dynamics of the cofactor complexes of dGMP/dIMP are disregulated relative to GMP/IMP. The substrate 2'-OH interacts with Asp219, and mutation of Asp219 to Ala decreases the value of V_max by a factor of 30. Counterintuitively, loss of Asp219 makes both substrates and cofactors less dynamic. These observations suggest that the interactions between the substrate 2'-OH and Asp219 coordinate the dynamic properties of the Michaelis complexes, and these dynamics are important for progression through the catalytic cycle.

Substrate and Cofactor Dynamics on Guanosine Monophosphate Reductase Probed by High Resolution Field Cycling 31P NMR Relaxometry

Guanosine-5'-monophosphate reductase (GMPR) catalyzes the reduction of GMP to IMP and ammonia with concomitant oxidation of NADPH. Here we investigated the structure and dynamics of enzyme-bound substrates and cofactors by measuring 31P relaxation rates over a large magnetic field range using high resolution field cycling NMR relaxometry. Surprisingly, these experiments reveal differences in the low field relaxation profiles for the monophosphate of GMP compared with IMP in their respective NADP+ complexes. These complexes undergo partial reactions that mimic different steps in the overall catalytic cycle. The relaxation profiles indicate that the substrate monophosphates have distinct interactions in E·IMP·NADP+ and E·GMP·NADP+ complexes. These findings were not anticipated by x-ray crystal structures, which show identical interactions for the monophosphates of GMP and IMP in several inert complexes. In addition, the motion of the cofactor is enhanced in the E·GMP·NADP+ complex. Last, the motions of the substrate and cofactor are coordinately regulated; the cofactor has faster local motions than GMP in the deamination complex but is more constrained than IMP in that complex, leading to hydride transfer. These results show that field cycling can be used to investigate the dynamics of protein-bound ligands and provide new insights into how portions of the substrate remote from the site of chemical transformation promote catalysis.

Phospholipid-binding sites of phosphatase and tensin homolog (PTEN): exploring the mechanism of phosphatidylinositol 4,5-bisphosphate activation

The lipid phosphatase activity of the tumor suppressor phosphatase and tensin homolog (PTEN) is enhanced by the presence of its biological product, phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). This enhancement is suggested to occur via the product binding to the N-terminal region of the protein. PTEN effects on short-chain phosphoinositide (31)P linewidths and on the full field dependence of the spin-lattice relaxation rate (measured by high resolution field cycling (31)P NMR using spin-labeled protein) are combined with enzyme kinetics with the same short-chain phospholipids to characterize where PI(4,5)P2 binds on the protein. The results are used to model a discrete site for a PI(4,5)P2 molecule close to, but distinct from, the active site of PTEN. This PI(4,5)P2 site uses Arg-47 and Lys-13 as phosphate ligands, explaining why PTEN R47G and K13E can no longer be activated by that phosphoinositide. Placing a PI(4,5)P2 near the substrate site allows for proper orientation of the enzyme on interfaces and should facilitate processive catalysis.

Cytotoxic amphiphiles and phosphoinositides bind to two discrete sites on the Akt1 PH domain

The mechanism of binding of two promising anticancer agents (the cytotoxic alkylphospholipids perifosine and miltefosine) to the Akt PH domain is investigated by high-resolution field-cycling (31)P nuclear magnetic resonance (NMR) spectroscopy using a spin-labeled recombinant PH domain. These results strongly indicate that there are two discrete amphiphile binding sites on the domain: (i) the cationic site that binds phosphoinositides and some alkylphospholipids and (ii) a second site that is occupied by only the alkylphospholipids. The identification of this second site for amphiphiles on the Akt1 PH domain provides a new target for drug development as well as insights into the regulation of the activity of the intact Akt1 protein. The field-cycling NMR methodology could be used to define discrete phospholipid or amphiphile binding sites on a wide variety of peripheral membrane proteins.

High-resolution NMR field-cycling device for full-range relaxation and structural studies of biopolymers on a shared commercial instrument

Improvements are described in a shuttling field-cycling device (Redfield in Magn Reson Chem 41:753-768, 2003), designed to allow widespread access to this useful technique by configuring it as a removable module to a commercial 500 MHz NMR instrument. The main improvements described here, leading to greater versatility, high reliability and simple construction, include: shuttling provided by a linear motor driven by an integrated-control servomotor; provision of automated bucking magnets to allow fast two-stage cycling to nearly zero field; and overall control by a microprocessor. A brief review of history and publications that have used the system is followed by a discussion of topics related to such a device including discussion of some future applications. A description of new aspects of the shuttling device follows. The minimum round trip time to 1T and above is less than 0.25 s and to 0.002 T is 0.36 s. Commercial probes are used and sensitivity is that of the host spectrometer reduced only by relaxation during travel. A key element is development of a linkage that prevents vibration of the linear motor from reaching the probe.

Defining specific lipid binding sites for a peripheral membrane protein in situ using subtesla field-cycling NMR

Despite the profound physiological consequences associated with peripheral membrane protein localization, only a rudimentary understanding of the interactions of proteins with membrane surfaces exists because these questions are inaccessible by commonly used structural techniques. Here, we combine high resolution field-cycling (31)P NMR relaxation methods with spin-labeled proteins to delineate specific interactions of a bacterial phospholipase C with phospholipid vesicles. Unexpectedly, discrete binding sites for both a substrate analogue and a different phospholipid (phosphatidylcholine) known to activate the enzyme are observed. The lifetimes for the occupation of these sites (when the protein is anchored transiently to the membrane) are >1-2 micros (but <1 ms), which represents the first estimate of an off-rate for a lipid dissociating from a specific site on the protein and returning to the bilayer. Furthermore, analyses of the spin-label induced NMR relaxation corroborates the presence of a discrete tyrosine-rich phosphatidylcholine binding site whose location is consistent with that suggested by modeling studies. The methodology illustrated here may be extended to a wide range of peripheral membrane proteins.

Phospholipid reorientation at the lipid/water interface measured by high resolution 31P field cycling NMR spectroscopy

The magnetic field dependence of the 31P spin-lattice relaxation rate, R1, of phospholipids can be used to differentiate motions for these molecules in a variety of unilamellar vesicles. In particular, internal motion with a 5- to 10-ns correlation time has been attributed to diffusion-in-a-cone of the phosphodiester region, analogous to motion of a cylinder in a liquid hydrocarbon. We use the temperature dependence of 31P R1 at low field (0.03-0.08 T), which reflects this correlation time, to explore the energy barriers associated with this motion. Most phospholipids exhibit a similar energy barrier of 13.2 +/- 1.9 kJ/mol at temperatures above that associated with their gel-to-liquid-crystalline transition (Tm); at temperatures below Tm, this barrier increases dramatically to 68.5 +/- 7.3 kJ/mol. This temperature dependence is broadly interpreted as arising from diffusive motion of the lipid axis in a spatially rough potential energy landscape. The inclusion of cholesterol in these vesicles has only moderate effects for phospholipids at temperatures above their Tm, but significantly reduces the energy barrier (to 17 +/- 4 kJ/mol) at temperatures below the Tm of the pure lipid. Very-low-field R1 data indicate that cholesterol inclusion alters the averaged disposition of the phosphorus-to-glycerol-proton vector (both its average length and its average angle with respect to the membrane normal) that determines the 31P relaxation.

Enzymology with a spin-labeled phospholipase C: soluble substrate binding by 31P NMR from 0.005 to 11.7 T

31P NMR relaxation studies from 0.005 to 11.7 T are used to monitor water-soluble inositol 1,2-(cyclic) phosphate (cIP) binding to phosphatidylinositol-specific phospholipase C spin-labeled at H82C, a position near the active site of the enzyme, and to determine how activating phosphatidylcholine (PC) molecules affect this interaction. We show that, in the absence of an interface, cIP binding to the protein is not rate-limiting, and that lower activation by PC vesicles as opposed to micelles is likely due to hindered product release. The methodology is general and could be used for determining distances in other weakly binding small molecule ligand-protein interactions.

Phosphatidylcholine "wobble" in vesicles assessed by high-resolution 13C field cycling NMR spectroscopy

High resolution (13)C NMR field cycling (covering 11.7 down to 0.002 T) relaxation studies of the sn-2 carbonyl of phosphatidylcholines in vesicles provide a detailed look at the dynamics of this position of the phospholipid in vesicles. The spin-lattice relaxation rate, R(1), observed down to 0.05 T is the result of dipolar and CSA relaxation components characterized by a single correlation time tau(c), with a small contribution from a faster motion contributing to CSA relaxation. At lower fields, R(1) increases further with a correlation time consistent with vesicle tumbling. The tau(c) is particularly interesting since it is 2-3 times slower than what is observed for (31)P of the same phospholipid. However, cholesterol increases the tau(c) for both (31)P and (13)C sites to the same value, approximately 25 ns. These observations suggest faster local motion dominates the dipolar relaxation of the (31)P, while a slower rotation or wobble dominates the relaxation of the carbonyl carbon by the alpha-CH(2) group. The faster motion must be damped with the sterol present. As a general methodology, high resolution (13)C field cycling may be useful for quantifying dynamics in other complex systems as long as a (13)C label (without attached protons) can be introduced.

Modulation of Bacillus thuringiensis phosphatidylinositol-specific phospholipase C activity by mutations in the putative dimerization interface

Cleavage of phosphatidylinositol (PI) to inositol 1,2-(cyclic)-phosphate (cIP) and cIP hydrolysis to inositol 1-phosphate by Bacillus thuringiensis phosphatidylinositol-specific phospholipase C are activated by the enzyme binding to phosphatidylcholine (PC) surfaces. Part of this reflects improved binding of the protein to interfaces. However, crystallographic analysis of an interfacially impaired phosphatidylinositol-specific phospholipase (W47A/W242A) suggested protein dimerization might occur on the membrane. In the W47A/W242A dimer, four tyrosine residues from one monomer interact with the same tyrosine cluster of the other, forming a tight dimer interface close to the membrane binding regions. We have constructed mutant proteins in which two or more of these tyrosine residues have been replaced with serine. Phospholipid binding and enzymatic activity of these mutants have been examined to assess the importance of these residues to enzyme function. Replacing two tyrosines had small effects on enzyme activity. However, removal of three or four tyrosine residues weakened PC binding and reduced PI cleavage by the enzyme as well as PC activation of cIP hydrolysis. Crystal structures of Y247S/Y251S in the absence and presence of myo-inositol as well as Y246S/Y247S/Y248S/Y251S indicate that both mutant proteins crystallized as monomers, were very similar to one another, and had no change in the active site region. Kinetic assays, lipid binding, and structural results indicate that either (i) a specific PC binding site, critical for vesicle activities and cIP activation, has been impaired, or (ii) the reduced dimerization potential for Y246S/Y247S/Y248S and Y246S/Y247S/Y248S/Y251S is responsible for their reduced catalytic activity in all assay systems.

Correlation of vesicle binding and phospholipid dynamics with phospholipase C activity: insights into phosphatidylcholine activation and surface dilution inhibition

The enzymatic activity of the peripheral membrane protein, phosphatidylinositol-specific phospholipase C (PI-PLC), is increased by nonsubstrate phospholipids with the extent of enhancement tuned by the membrane lipid composition. For Bacillus thuringiensis PI-PLC, a small amount of phosphatidylcholine (PC) activates the enzyme toward its substrate PI; above 0.5 mol fraction PC (XPC), enzyme activity decreases substantially. To provide a molecular basis for this PC-dependent behavior, we used fluorescence correlation spectroscopy to explore enzyme binding to multicomponent lipid vesicles composed of PC and anionic phospholipids (that bind to the active site as substrate analogues) and high resolution field cycling 31P NMR methods to estimate internal correlation times (tauc) of phospholipid headgroup motions. PI-PLC binds poorly to pure anionic phospholipid vesicles, but 0.1 XPC significantly enhances binding, increases PI-PLC activity, and slows nanosecond rotational/wobbling motions of both phospholipid headgroups, as indicated by increased tauc. PI-PLC activity and phospholipid tauc are constant between 0.1 and 0.5 XPC. Above this PC content, PI-PLC has little additional effect on the substrate analogue but further slows the PC tauc, a motional change that correlates with the onset of reduced enzyme activity. For PC-rich bilayers, these changes, together with the reduced order parameter and enhanced lateral diffusion of the substrate analogue in the presence of PI-PLC, imply that at high XPC, kinetic inhibition of PI-PLC results from intravesicle sequestration of the enzyme from the bulk of the substrate. Both methodologies provide a detailed view of protein-lipid interactions and can be readily adapted for other peripheral membrane proteins.

Insights into the structural specificity of the cytotoxicity of 3-deoxyphosphatidylinositols

D-3-deoxyphosphatidylinositol (D-3-deoxy-PI) derivatives have cytotoxic activity against various human cancer cell lines. These phosphatidylinositols have a potentially wide array of targets in the phosphatidylinositol-3-kinase (PI3K)/Akt signaling network. To explore the specificity of these types of molecules, we have synthesized D-3-deoxydioctanoylphosphatidylinositol (D-3-deoxy-diC8PI), D-3,5-dideoxy-diC8PI, and D-3-deoxy-diC8PI-5-phosphate and their enantiomers, characterized their aggregate formation by novel high-resolution field cycling (31)P NMR, and examined their susceptibility to phospholipase C (PLC), their effects on the catalytic activities of PI3K and PTEN against diC8PI and diC8PI-3-phosphate substrates, respectively, and their ability to induce the death of U937 human leukemic monocyte lymphoma cells. Of these molecules, only D-3-deoxy-diC8PI was able to promote cell death; it did so with a median inhibitory concentration of 40 microM, which is much less than the critical micelle concentration of 0.4 mM. Under these conditions, little inhibition of PI3K or PTEN was observed in assays of recombinant enzymes, although the complete series of deoxy-PI compounds did provide insights into ligand binding by PTEN. D-3-deoxy-diC8PI was a poor substrate and not an inhibitor of the PLC enzymes. The in vivo results are consistent with the current thought that the PI analogue acts on Akt1, since the transcription initiation factor eIF4e, which is a downstream signaling target of the PI3K/Akt pathway, exhibited reduced phosphorylation on Ser209. Phosphorylation of Akt1 on Ser473 but not Thr308 was reduced. Since the potent cytotoxicity for U937 cells was completely lost when L-3-deoxy-diC8PI was used as well as when the hydroxyl group at the inositol C5 in D-3-deoxy-diC8PI was modified (by either replacing this group with a hydrogen or phosphorylating it), both the chirality of the phosphatidylinositol moiety and the hydroxyl group at C5 are major determinants of the binding of 3-deoxy-PI to its target in cells.

Phospholipid bilayer surface configuration probed quantitatively by (31)P field-cycling NMR

(31)P relaxation of the diester phosphate of phospholipids in unilamellar vesicles has been studied from 0.004 to 11.7 T. Relaxation at very low fields, below 0.1 T, shows a rate increase that reflects a residual dipolar interaction with neighboring protons, probably dominated by the glycerol C3 protons. This interaction is not fully averaged by faster motion such as rotational diffusion perpendicular to the membrane surface. The remaining dipolar interaction, modulated by overall rotational diffusion of the vesicle and lateral diffusion of the lipid molecules, is responsible for the very low-field relaxation. These measurements yield a good estimate of the time-average angle between the membrane surface and the vector connecting the phosphorus to the glycerol C3 protons, based on the classic theory by Woessner. Dynamic information is also obtained. Implications for solid-state NMR and other studies are discussed.

High-resolution 31p field cycling NMR as a probe of phospholipid dynamics

We have used high-resolution field-cycling 31P NMR spectroscopy to measure spin-lattice relaxation rates (R1 = 1/T1) of multicomponent phospholipid vesicle and micelle samples over a large field range, from 0.1 to 11.7 T. The shape of the curve for R1 as a function of field and a model-free analysis were used to extract tauc, a correlation time for each type of phospholipid molecule in the bilayer that is likely to reflect rotation of the molecule about the axis perpendicular to the membrane surface; Sc2, a chemical shift anisotropy (CSA) order parameter; and tauhf, a time constant reflecting faster internal motion. This 31P technique was also used to monitor association of a peripheral membrane protein, Bacillus thuringiensis phosphatidylinositol-specific phospholipase C, with both phosphatidylcholine and phosphatidylmethanol bilayers. Differences in phospholipid dynamics induced by the protein shed light on how zwitterionic phosphatidylcholine, and not the anionic phosphatidylmethanol, activates the enzyme toward its substrate.

High-Resolution Field-Cycling NMR Studies of a DNA Octamer as a Probe of Phosphodiester Dynamics and Comparison with Computer Simulation†

Phosphorus-spin longitudinal relaxation rates of the DNA duplex octamer [d(GGAATTCC)](2) have been measured from 0.1 to 17.6 T by means of conventional and new field-cycling NMR methods. The high-resolution field-cycling method is identical to a conventional relaxation experiment, except that after preparation the sample is moved pneumatically from its usual position at the center of the high-resolution magnet upward to a lower field above its normal position and then returned to the center for readout after it has relaxed for the programmed relaxation delay at the low field. This is the first measurement of all longitudinal relaxation rates R(1) of a nuclear species in a macromolecule over virtually the entire accessible magnetic field range. For detailed analysis, three magnetic field regions can be delineated: (i) dipolar relaxation dominates at fields below 2 T, (ii) chemical shift anisotropy (CSA) relaxation is roughly constant from 2 to 6 T, and (iii) a square-law increasing dependence is seen at fields higher than approximately 6 T due to internal motion CSA relaxation. The analysis provides a rotational correlation time (tau(r) = 4.1 +/- 0.3 ns) for the duplex at both 1.5 and 0.25 mM concentrations (of duplex) at 22 degrees C. For comparison, extraction of tau(r) in the conventional way from the ratio of T(1)/T(2) at 14 T yields 3.2 ns. The tau(r) discrepancy disappears when we exclude the contribution of internal motion from the R(1) in the ratio. The low-field dipolar relaxation provides a weighted inverse sixth power sum of the distances from the phosphorus to the protons responsible for relaxation. This average is similar for all phosphates in the octamer and similar to that in previous B-DNA structures (its inverse sixth root is about 2.40 A for two different concentrations of octamer). The CSA relaxation at intermediate field provides an estimate of the order parameter squared, S(c)(2), for each phosphorus. S(c)(2) is about 0.7-1, clearly different for different phosphate linkages in the octamer duplex. The increasing R(1) at high fields reflects CSA relaxation due to internal motions, for which a correlation time, tau(hf), can be approximately extracted with the aid of additional measurements at 14.0 and 17.6 T. We conclude that tau(hf) values are relatively large, in the range of about 150 ps. Insight into the motions leading to this correlation time was gained by a 28 ns molecular dynamics simulation of the molecule. S(2) and tau(s) (corresponding to tau(hf)) predicted by this simulation were in good agreement with the experimental values from the field-cycling data. Both the effect of Mg(2+) on the dynamic parameters extracted from (31)P relaxation rates and the field dependence of relaxation rates for several protons of the octamer were measured. High-resolution field cycling opens up the possibility of monitoring residue-specific dipolar interactions and dynamics for the phosphorus nuclei of diverse oligonucleotides.

Field-cycling method with central transition readout for pure quadrupole resonance detection in dilute systems

We present a modification of a field-cycling method which uses the NMR signal of the central transition at high field to indirectly detect zero-field quadrupole transitions. The quadrupole transitions at zero-field are detected as changes in the overall intensity of the central transition signal after the field cycle, and the method is relatively immune to lineshape distortions of the central transition caused by receiver dead time, frequency response of the probe, longer pulse lengths, etc. Cross-polarization with protons is used to enhance the central-transition signal and to increase the recycling rate of the experiment. The technique is especially useful when mixtures of several species are present. In a frozen solution of phenylboronic acid, 11B quadrupole signals of the tetrahedral species at 600 kHz and planar-trigonal species at 1450 kHz are clearly resolved. The field-cycling approach allows high-sensitivity detection of low-frequency quadrupole transitions; the experiment is sensitive enough to study boronic-acid protease inhibitors bound to proteins and may possibly be extended to lower sensitivity nuclei. The experiments are performed using a low-temperature field-cycling apparatus, operated at 10-30 K, capable of pneumatically moving the sample from the high field of a commercial 500 MHz magnet to the area above the top of the magnet where the low field is controlled by a pair of Helmholz coils.

Boron-11 pure quadrupole resonance investigation of peptide boronic acid inhibitors bound to alpha-lytic protease

Pure quadrupole resonance is a potentially useful spectroscopic approach to study the coordination of quadrupolar nuclei in biological systems. We used a field-cycling NMR method to observe boron pure quadrupole resonance of two peptide boronic acid inhibitors bound to alpha-lytic protease. The method is similar to our earlier field-cycling experiment [Ivanov, D., and Redfield, A. R. (1998) Z. Naturforsch. A 53, 269-272] but uses a simple Hartmann-Hahn transfer from proton to (11)B before field cycle and direct (11)B observe after it. Pure quadrupole resonance is sensitive to the boron coordination geometry. For example, trigonal boron in neutral phenylboronic acid, which was used as a model compound, resonates at 1450 kHz, while the resonance of the tetrahedral phenylboronic acid anion appears at approximately 600 kHz. In the complex of the MeOSuc-Ala-Ala-Pro-boroVal inhibitor with the enzyme the quadrupole resonance signal was observed at 600-650 kHz, which indicates tetrahedral boron coordination in the active site. The quadrupole frequency of the MeOSuc-Ala-Ala-Pro-boroPhe enzyme-inhibitor complex, in which a boron-histidine bond is known to be formed, was found to be the same within experimental error as in the MeOSuc-Ala-Ala-Pro-boroVal enzyme-inhibitor adduct, suggesting that the boron coordination geometry in the enzyme-MeOSuc-Ala-Ala-Pro-boroPhe adduct is also close to tetrahedral.

Analog filtering of large solvent signals for improved dynamic range in high-resolution NMR

The large solvent signal from samples in H2O solvent still challenges the dynamic range capability of any spectrometer. The solvent signal can be largely removed with a pair of simple resistor-capacitor (RC) high-pass filters when the solvent frequency is set at center band (zero frequency) using quadrature detection, with RC approximately 0.5 ms. However, an approximately 0.5-ms transient remains at initial time, which we reduce fourfold for a short time only, just before the A/D converter, by means of a variable-gain amplifier, and later restore with software. This modification can result in a nearly fourfold increase in dynamic range. When we converted to a frequency-shifted mode (A. G. Redfield and S. D. Kunz, 1994, J. Magn. Reson. A 108, 234-237) we replaced the RC high-pass filter with a quadrature feedback notch filter tuned to the solvent frequency (5.06 kHz). This filter is an example of a class of two-input/two-output filters which maintain the spectral integrity (image-free character) of quadrature signals. Digital filters of the same type are also considered briefly. We discuss the implications of these ideas for spectrometer input design, including schemes for elimination of radiation damping, and effects of probe bandwidth on extreme oversampling.

Conformational and dynamic differences between N-ras P21 bound to GTPgammaS and to GMPPNP as studied by NMR

Heteronuclear-edited proton-detected NMR methods are used to study the nucleotide-dependent conformational changes between the GMPPNP form of human N-ras P21 as compared to GDP and GTPgammaS forms. Full-length N-ras P21 was also compared with protein truncated beyond residue 167, to search for interaction points between the more invariant part of the protein and the variable C-terminal section. In both cases, the reporter was the 15N-H 2D spectrum of aspartate amide groups labeled with 15N. Small truncation-induced changes were seen in the spectrum at the resonances of Asp-54, -108, and -109 which are not far from the C-terminal and, surprisingly, at Asp-57 which is more remote. The spectrum obtained for the GMPPNP-ligated form is similar to that of the GTPgammaS form, except that peaks of several residues are weak at low temperature, and strongly temperature-dependent in their intensity, and a new resonance appears at 15 degrees C and above. The observations are discussed in terms of a two-state model for the GMPPNP-ligated protein, previously proposed by Geyer et al. [(1996) Biochemistry 35, 10308-10320].

The effect of 17O on the relaxation of an amide proton within a hydrogen bond

The relaxation rates of the multiple-quantum coherence for the amide hydrogen of Gly13 in ras p21.GDP were determined in the presence and absence of 17O labeling in the beta-phosphate of GDP. No significant difference could be observed between labeled and unlabeled samples, in spite of the fact that the hydrogen bond from the amide group of Gly13 to the beta-phosphate is shorter than is typical, based on its chemical shift. For macromolecules in which an oxygen atom is the acceptor of a hydrogen bond, dipolar coupling between 17O and hydrogen is unlikely to be observable, except for extremely short H-bonds.

Proton exchange and basepair kinetics of yeast tRNA(Phe) and tRNA(Asp1)

Nuclear magnetic resonance measurements of proton exchange were performed on yeast tRNA(Phe) and yeast tRNA(Asp), at temperatures from 20 to 45 degrees C, in the presence of various levels of salt, phosphate, added magnesium, and pH. The dynamical changes of the tRNA molecule were interpreted, with the aid of firmly established assignments and the use of the saturation recovery technique. In tRNA(Phe), the exchange rates in zero magnesium indicated early melting of the acceptor stem, tertiary structure, and D stem. However, in the presence of even low levels of magnesium the D stem remained intact up to high temperature, stabilized by a Mg2+ ion. A similar unfolding sequence was observed in tRNA(Asp). The difference between these two tRNAs was the thermal behavior of the tertiary resonance U8-A14. In tRNA(Phe), this base pair showed sharp rate increases between 32 and 39 degrees C. However, in tRNA(Asp), it remained intact up to 36 degrees C and disappeared at 39 degrees C, even if there was not important kinetic broadening. By measuring the temperature dependence of the exchange rates, we obtained an activation energy of 40-60 kcal/mol for all the imino protons of yeast tRNA(Phe) in zero magnesium. The same activation energy was obtained for tRNA(Phe) with equimolar concentration of magnesium. By investigation of the dependence of the exchange rates of these imino protons on solution conditions, we observed the transition from kop rate limiting in the absence of magnesium to kex rate limiting in the presence of magnesium.

Characterization of the active site of p21 ras by electron spin-echo envelope modulation spectroscopy with selective labeling: comparisons between GDP and GTP forms

Selectively labeled samples of human H- or N-ras p21 ligated to MnIIGDP or MnIIGMPPNP were studied by electron spin-echo envelope modulation spectroscopy in order to define the protein environment around the divalent metal. We incorporated [4-13C]-labeled Asx into p21.MnIIGDP and found that the distance from the carboxyl 13C of Asp57 to MnII is approximately 4.1 A. Our result is consistent with indirect coordination of this residue to the metal. From a [2-2H]Thr-labeled sample, we estimate that the distance from the MnII ion to the 2H of Thr35 is at least 5.8 A. Thus, the only protein or nucleotide ligands to the metal appear to be Ser17 and the beta-phosphate of GDP, as previously reported [Larsen, R. G., Halkides, C. J., Redfield, A. G., & Singel, D. J. (1992b) J. Am. Chem. Soc. 114, 9608-9611]. In the 5'-guanylylimido diphosphate (GMPPNP) form of p21, Thr35 has been reported by X-ray crystallography to be a ligand of the metal via its hydroxyl group, and this residue appears to play a key role in the biologically important conformational change upon nucleotide substitution [Pai, E. F., Krengel, U., Petsko, G., Goody, R. S., Kabsch, W., & Wittinghofer, A. (1990) EMBO J. 9, 2351-2359]. The ESEEM spectrum of p21.MnIIGMPPNP labeled with [2-2H]Thr yields a MnII-2H distance of 4.9 A, a distance inconsistent with strong coordination. A sample of p21 in which the Thr residues were fully labeled with 13C and 15N yielded a value of 5.0 A for the distance from MnII to the amide nitrogen of Thr35, while the 13C signal is much smaller than expected if Thr35 were coordinated. A [15N]serine/glycine-labeled sample gives a distance to the amide 15N of Ser17 of 3.9 A, consistent with the X-ray structure; a [4-13C]-labeled Asx sample of p21 gives a distance of approximately 4 A between MnII and the label of Asp57, again implying indirect coordination. Both of these values are very similar to those found for the GDP form of the protein. The results for Thr35, however, reveal a structural difference between the GDP and GTP forms in the region of Thr35. In addition, the position of this residue is found to be different from the crystal structure and in a manner suggesting that the metal ligation of Thr35 does not drive the conformational change that accompanies nucleotide substitution.

An NMR comparison of the changes produced by different guanosine 5'-triphosphate analogs in wild-type and oncogenic mutant p21ras

We have used nuclear magnetic resonance spectroscopy to compare the conformational changes produced by replacement of bound GDP by the GTP analogs guanosine 5'-O-(3-thiotriphosphate) (GTP gamma S) and guanylyl (beta, gamma-imido)diphosphate (GMPPNP) in wild-type p21ras as well as the oncogenic mutant (G12D)p21ras. We have used isotope-edited nuclear magnetic resonance spectroscopy to observe the amide resonances of selectively [15N]glycine and [15N]isoleucine labeled p21ras-nucleotide complexes. We find that eight of the nine resonances that respond strongly to GTP gamma S and GMPPNP binding are the same but that the nature of the effect appears different. With GTP gamma S, seven new resonances replace the eight resonances specifically associated with GDP-p21ras, but in GMPPNP-p21ras only two resonances replace the GDP-specific resonances that are lost. The resonance of Gly 60 is clearly shown to be responsive to replacement of GDP by GMPPNP, in addition to glycines 10, 12, 13, 15, and 75 and isoleucines 36, 21, and one other, that were found to respond to GTP gamma S by Miller et al. [Miller, A.-F., Papastavros, M. Z., & Redfield, A.G. (1992) Biochemistry 31, 10208-10216). The two GMPPNP-specific resonances observed appear in positions similar to GTP gamma S-specific resonances, and the GTP gamma S-specific resonances, although not lost altogether, are weaker than the GDP-specific resonances they replace. Thus, the two GTP analogs have similar effects on the spectrum of p21ras, suggesting that the effects are due to features common to both analogs. We propose that active site resonance intensities are specifically attenuated when GTP analogs are bound because interactions with the gamma-phosphate of GTP analogs couple the flexible loops 2 and 4 to the rigid loop 1 of the active site. The conformational heterogeneity and dynamics of loops 2 and 4 would be constrained by loop 1 but also transmitted to it. Coupled conformational exchange on a common intermediate time scale could explain the simultaneous loss of resonances from all three loops in the active site. In our comparison of wild-type and (G12D) GDP-p21ras, we find that the resonance of Ile 36 is not visible in (G12D)p21ras. In (G12D)p21ras, replacement of GDP by GTP gamma S causes the resonances of glycines 10, 13, 15, 60, and 75 and isoleucine 21 and four others to shift from their GDP-specific positions. GTP gamma S-specific resonances are observed for all but two of these.(ABSTRACT TRUNCATED AT 400 WORDS)

Mapping the nucleotide-dependent conformational change of human N-ras p21 in solution by heteronuclear-edited proton-observed NMR methods

Heteronuclear-edited proton-detected NMR methods are used to study the nucleotide-dependent conformational change between GDP- and GTP gamma S-bound forms of human N-ras p21. Amide groups of Asp are used as sensitive probes. When GTP gamma S is substituted for GDP in cellular N-ras p21, the chemical shifts of resonances Asp-47, -126, -154, and Asn-172, as well as Gly-77 and -151, are not sensitive to nucleotide exchange, whereas Asp-30, -33, -38, -54, -57, -69, -92, -105, and -119 are affected. Distinct chemical shift changes of Asp-33, -38, and -69 indicate that substantial structure changes occur in the effector-binding region and the switch II region. Crystallographic studies of H-ras p21 have indicated that the conformational differences are confined to residues 32-38 and 60-76. Our observations indicate that the nucleotide-dependent structural transitions of the protein in solution may not be identical to those in the crystal. They suggest that the peptide beyond Glu-76 participates in a conformational switch, and possibly is involved in effector function. We propose that the region roughly from Asp-92 to -105, and the region of guanine base-binding motif(s), e.g., 116NKXD, are candidate sites recognized by either a GDP/GTP release factor or a GTPase-affected protein.

NMR study of nitrogen-15-labeled Escherichia coli valine transfer RNA

1,3-15N-Labeled uracil was synthesized chemically and used to prepare labeled Escherichia coli tRNA(Val) biosynthetically. 500-MHz measurements of 15N and proton chemical shift were obtained, for all uridine and uridine-related bases, by heteronuclear multiple-quantum coherence spectroscopy. All the uracil NH group resonances were assigned and were in agreement with previous proton-only assignments. The temperature dependence of intensities of resonances was used to infer the relative stability of parts of the molecule. The acceptor stem was the least thermally stable structural feature, while the anticodon and T loop were relatively more stable.

NMR studies of the conformational change in human N-p21ras produced by replacement of bound GDP with the GTP analog GTP gamma S

1H-Detected 15N-edited NMR in solution was used to study the conformational differences between the GDP- and GTP gamma S-bound forms of human N-p21ras. The amide protons of 15N-labeled glycine and isoleucine were observed. Resonances were assigned to residues of particular interest, glycines-60 and -75 and isoleucines-21 and -36, by incorporating various 13C-labeled amino acids in addition to [15N]glycine and [15N]iosleucine and by replacing Mg2+ by Co2+. When GTP gamma S replaced GDP in the active site of p21ras, only 5 of the 14 glycine amide resonances show major shifts, indicating that the conformational effects are fairly localized. Responsive glycines-10, -12, -13, and -15 are in the active site. Gly-75, located at the far end of a conformationally-active loop and helix, also responds to substitution of GTP gamma S for GDP, while Gly-77 does not, supporting a role for Gly-75 as a swivel point for the conformational change. The amide proton resonances of isoleucines-36 and -21 and a third unidentified isoleucine also undergo major shifts upon replacement of GDP by GTP gamma S. Thus, the effector-binding loop containing Ile-36 is confirmed to be involved in the conformational change, and the alpha-helix containing Ile-21 is also shown to be affected.

NMR study of the phosphate-binding loops of Thermus thermophilus elongation factor Tu

The phosphoryl-binding loops in the guanosine diphosphate binding domain of elongation factor Tu were studied by 15N heteronuclear proton-observe NMR methods. Five proton resonances were found below 10.5 ppm. One of these was assigned to the amide group of Lys 24, which is a conserved residue in the phosphoryl-binding concensus loop of purine nucleotide binding proteins. The uncharacteristic downfield proton shift is attributed to a strong hydrogen bond with a phosphate oxygen. The amide protons from the homologous lysines in N-ras p21 [Redfield, A.G., & Papastavros, M.Z. (1990) Biochemistry 29, 3509-3514] and the catalytic domain of Escherichia coli elongation factor Tu [Lowry, D.F., Cool, R.H., Redfield, A.G., & Parmeggiani, A. (1991) Biochemistry 30, 10872-10877] also resonate downfield in similar positions. We propose that the downfield shift of this lysine amide proton is a spectral marker for this class of proteins. We also have studied the temperature dependence of the downfield resonances and find a possible conformation change at 40 degrees C.

NMR study of the phosphate-binding elements of Escherichia coli elongation factor Tu catalytic domain

The phosphoryl-binding elements in the GDP-binding domain of elongation factor Tu were studied by heteronuclear proton observe methods. Five proton resonances were found below 10.5 ppm. Two of these were assigned to the amide groups of Lys 24 and Gly 83. These are conserved residues in each of the consensus sequences. Their uncharacteristic downfield proton shifts are attributed to strong hydrogen bonds to phosphate oxygens as for resonances in N-ras-p21 [Redfield, A. G., & Papastavros, M. Z. (1990) Biochemistry 29, 3509-3514]. The Lys 24 of the EF-Tu G-domain has nearly the same proton and nitrogen shifts as the corresponding Lys 16 in p21. These results suggest that this conserved lysine has a similar structural role in proteins in this class. The tentative Gly 83 resonance has no spectral analogue in p21. A mutant protein with His 84 changed to glycine was fully 15N-labeled and the proton resonance assigned to Gly 83 shifted downfield by 0.3 ppm, thereby supporting the assignment.

Molecular structure of charybdotoxin: retraction

Shortly after our paper of 3 August 1990 on the molecular structure of charybdotoxin (1) was published, two independent determinations of the structure of this molecule appeared (2) that were similar to each other and in strong disagreement with ours. We have obtained new data and find that some spectral features depend on solvent conditions, which explains some differences between our data and those of the other groups. More important, we conclude that we most probably misassigned an important sequence of amino acids, as suggested by Bontems et al.(3). Therefore, we withdraw our previously reported structure (1) and regret any inconvenience it may have caused. We thank F. Toma for sending us a copy of his paper before publication and for discussions.

Molecular structure of charybdotoxin, a pore-directed inhibitor of potassium ion channels

The three-dimensional structure of charybdotoxin, a high-affinity peptide blocker of several potassium ion channels, was determined by two-dimensional nuclear magnetic resonance (2-D NMR) spectroscopy. Unambiguous NMR assignments of backbone and side chain hydrogens were made for all 37 amino acids. The structure was determined by distance geometry and refined by nuclear Overhauser and exchange spectroscopy back calculation. The peptide is built on a foundation of three antiparallel beta strands to which other parts of the sequence are attached by three disulfide bridges. The overall shape is roughly ellipsoidal, with axes of approximately 2.5 and 1.5 nanometers. Nine of the ten charged groups are located on one side of the ellipsoid, with seven of the eight positive residues lying in a stripe 2.5 nanometers in length. The other side displays three hydrophobic residues projecting prominently into aqueous solution. The structure rationalizes several mechanistic features of charybdotoxin block of the high-conductance Ca2(+)-activated K+ channel.

Assignment of the backbone 1H and 15N NMR resonances of bacteriophage T4 lysozyme

The proton and nitrogen (15NH-H alpha-H beta) resonances of bacteriophage T4 lysozyme were assigned by 15N-aided 1H NMR. The assignments were directed from the backbone amide 1H-15N nuclei, with the heteronuclear single-multiple-quantum coherence (HSMQC) spectrum of uniformly 15N enriched protein serving as the master template for this work. The main-chain amide 1H-15N resonances and H alpha resonances were resolved and classified into 18 amino acid types by using HMQC and 15N-edited COSY measurements, respectively, of T4 lysozymes selectively enriched with one or more of alpha-15N-labeled Ala, Arg, Asn, Asp, Gly, Gln, Glu, Ile, Leu, Lys, Met, Phe, Ser, Thr, Trp, Tyr, or Val. The heteronuclear spectra were complemented by proton DQF-COSY and TOCSY spectra of unlabeled protein in H2O and D2O buffers, from which the H beta resonances of many residues were identified. The NOE cross peaks to almost every amide proton were resolved in 15N-edited NOESY spectra of the selectively 15N enriched protein samples. Residue specific assignments were determined by using NOE connectivities between protons in the 15NH-H alpha-H beta spin systems of known amino acid type. Additional assignments of the aromatic proton resonances were obtained from 1H NMR spectra of unlabeled and selectively deuterated protein samples. The secondary structure of T4 lysozyme indicated from a qualitative analysis of the NOESY data is consistent with the crystallographic model of the protein.

NMR study of the phosphoryl binding loop in purine nucleotide proteins: evidence for strong hydrogen bonding in human N-ras p21

The structure of the phosphoryl binding region of human N-ras p21 was probed by using heteronuclear proton-observed NMR methods. Normal protein and a Gly-12----Asp-12 mutant protein were prepared with two amino acids labeled with 15N at their amide positions: valine and glycine, aspartic acid and glycine, and lysine and glycine. We completed the identification of amide 15NH resonances from Gly-12 and Asp-12 to the end of the phosphoryl binding domain consensus sequence (Lys-16) in protein complexed with GDP and have made tentative amide identifications from Val-9 to Ser-17. The methods used, together with initial identifications of the Gly-12 and -13 amide resonances, were described previously [Campbell-Burk, S. (1989) Biochemistry 28, 9478-9484]. The amide resonances of both Gly-13 and Lys-16 are shifted downfield below 10.4 ppm in both the normal and mutant proteins. These downfield shifts are presumed to be due to strong hydrogen bonds with the beta-phosphate oxygens of GDP.

Structure of an unmodified tRNA molecule

We have used NMR to study the structure of the yeast tRNA(Phe) sequence which was synthesized by using T7 RNA polymerase. Many resonances in the imino 1H- spectrum of the transcript have been assigned, including those of several tertiary interactions. When the Mg2+ concentration is high, the transcript appears to fold normally, and the spectral features of the transcript resemble those of tRNA(Phe). The transcript has been shown to be aminoacylated with kinetics similar to the modified tRNA(Phe) [Sampson, J. R., & Uhlenbeck, O. C. (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 1033-1037], suggesting that the structure of the two molecules must be similar. In the absence of Mg2+ or at [tRNA]:[Mg2+] ratios less than 0.2, the transcript does not adopt the native structure, as shown by both chemical shifts and NOE patterns. In these low Mg2+ conditions, a second GU base pair is found, suggesting a structural rearrangement of the transcript. NMR data indicate that the structure of a mutant having G20 changed to U20 is nearly identical with that of the normal sequence, suggesting that the low aminoacylation activity of this variant is not due to a substantially different conformation.

Use of 13C and 15N isotope labels for proton nuclear magnetic resonance and nuclear Overhauser effect. Structural and dynamic studies of larger proteins and nucleic acids

This article reviews methods based on direct observation of proton NMR in macromolecules containing 13C or 15N labels. The resonances and Overhauser effects of protons attached to the labels can be edited or filtered from the remaining overlapping resonances. This leads to simplification of the spectra when labels are incorporated selectively. In 2D and related methods the label's chemical shift provides a second dimension which is useful for spectral differentiation and identification. The methods are useful for larger proteins and we describe our progress on studies of T4 lysozyme, mass 18.7 kD, in which we have already identified a large number of resonances.

Identification of resonances from an oncogenic activating locus of human N-RAS-encoded p21 protein using isotope-edited NMR

A sample of Escherichia coli-expressed human N-RAS-encoded p21, a 21-kDa protein, was selectively labeled with 15N at each of the 14 glycine amide positions. Two-dimensional proton-observe 15N correlation spectra showed one peak for each glycine residue. Five glycine resonances were identified with residues near the nucleotide binding site and provide useful reporters of several oncogene-activating positions. Three of these resonances were assigned to residues 10, 15, and 115 from the spectrum of a sample that was also labeled with [13C]valine. These resonances showed extra splitting or broadening due to the 13C label, which could be eliminated by 13C decoupling. Two other peaks were unambiguously identified as Gly-12 and Gly-13 using a one-dimensional edited nuclear Overhauser experiment and by spectral comparison with an Asp-12 mutant. These assignments have provided several site-specific probes of critical domains in p21.

Structure of a pre-mRNA branch point/3' splice site region

We have analyzed the solution structure of RNA containing the branch point/3' splice site region of the first intervening sequence (IVS1) of human beta-globin pre-mRNA by nuclease mapping and NMR. Nuclease mapping indicates that there are two distinct structural domains: one contains the branch point region, and the other includes the 3' splice site and second exon sequences. In the branch point domain, the adenosine at which the RNA branch forms appears to be in the loop of a stem/loop structure. The branch point structure does not appear to interact with other parts of the RNA, since its unique nuclease digestion pattern is conserved among transcripts containing the entire intron or only the branch point region. This is confirmed by a comparison of the NMR spectra of two RNA transcripts; a distinct set of resonances appears in the spectra of the RNA containing only branch sequences or including 3' splice site/exon 2 sequences. NMR studies further show that the 3' splice site/exon 2 domain has a lower melting temperature than the branch point domain, suggesting that the two regions are distinct dynamically as well as structurally. Nuclease mapping studies of adenovirus major late IVS1 indicate that this RNA has structural features in common with the human beta-globin transcript.

Proton NMR and NOE structural and dynamic studies of larger proteins and nucleic acids aided by isotope labels: T4 lysozyme

This article reviews methods based on direct observation of proton NMR in macromolecules containing 13C or 15N labels. The resonances and Overhauser effects of protons attached to the labels can be edited or filtered from the remaining overlapping resonances. This leads to simplification of the spectra when labels are incorporated selectively. In 2D and related methods the label's chemical shift provides a second dimension which is useful for spectral differentiation and identification. The methods are useful for larger proteins and we describe our progress on studies of T4 lysozyme, mass 18.7 kD, in which we have already identified a large number of resonances.

Proton NMR measurements of bacteriophage T4 lysozyme aided by 15N isotopic labeling: structural and dynamic studies of larger proteins

A strategy for resolution and assignment of single proton resonances in proteins of molecular mass up to at least 40 kDa is presented. This approach is based on 15N (or 13C) labeling of selected residues in a protein. The resonances from protons directly bonded to labeled atoms are detected in a two-dimensional 1H-15N (or 13C) spectrum. The nuclear Overhauser effects from isotopically tagged protons are selectively observed in one-dimensional isotope-directed measurements. Using this approach, we have observed approximately 160 resonances from 15N-bonded protons in the backbone and sidechains of uniformly 15N-labeled T4 lysozyme (molecular mass = 18.7 kDa). Partial proton-deuterium exchange can be used to simplify the 1H-15N spectrum of this protein. These resonances are identified by amino acid class using selective incorporation of 15N-labeled amino acids and are assigned to specific residues by mutational substitution, multiple 15N and 13C labeling, and isotope-directed nuclear Overhauser effect measurements. For example, using a phenyl[15N]alanine-labeled lysozyme variant containing two consecutive phenylalanine residues in an alpha-helical region, we observe an isotope-directed nuclear Overhauser effect from the amide proton of Phe-66 to that of Phe-67.

Proton-detected heteronuclear edited and correlated nuclear magnetic resonance and nuclear Overhauser effect in solution

The proton has been the nucleus of choice for NMR studies of macromolecules because it is ubiquitous; it provides the highest sensitivity; its resonances can be identified with types of amino and nucleic acids by means of experiments utilizing proton spin-spin interaction and chemical shift; and, most important, proton NMR yields distance information via the nuclear Overhauser effect (NOE). Many of these advantages are lost for larger biopolymers (molecular weight more than 15 kDa) for which the line width is considerably greater than the proton-proton spin-spin interaction. The spin-spin interaction is then useless or difficult to use for assignment; and furthermore the proton line width and the number of proton resonances both increase in proportion to the molecular weight, thereby increasing the problem of resonance overlap to an intolerable degree.

NMR study of isoleucine transfer RNA from Thermus thermophilus

An NMR and nuclear Overhauser effect (NOE) analysis of Thermus thermophilus tRNAIle1a is presented. This species contains modifications including s2T54 and s4U8 [Horie, N., Hara-Yokoyama, M., Yokoyama, S., Watanabe, K., Kuchino, Y., Nishimura, S., & Miyazawa, T. (1985) Biochemistry 24, 5711-5715]. All the expected secondary and reverse Hoogsteen AU pairs were identified, with one possible exception. The general geometry of the T psi C loop is the same as the Escherichia coli species, and there is NOE evidence for an A9-UA12 triple. Preliminary measurements of solvent exchange rates of internally hydrogen-bonded bases suggest that this tRNA is more stable than previously studied E. coli and yeast tRNAs.