Probing the hydrophobic cavity of lipid transfer protein from Nicotiana tabacum through xenon-based NMR spectroscopy

The hydrophobic cavity of Lipid Transfer Protein 1 from Nicotiana tabacum is investigated in detail by NMR using xenon as a spy. The analysis of the (129)Xe chemical shifts and self-relaxation times gives evidence of protein-xenon interaction. Thermodynamics of the binding is characterized through the study of aliphatic (1)H and (13)C chemical shift variation as a function of xenon pressure. The binding constant is evaluated to 75.5 +/- 1.0 M(-1) at 293 K. The location of xenon inside the cavity is deduced from SPINOE experiments. The noble gas appears to occupy four sites, and xenon self-relaxation experiments indicate that it quickly jumps between different sites. The chemical shifts of amide protons and nitrogens also depend on the xenon concentration, either specifically or nonspecifically for atoms at the external surface of the protein. Yet, contrary to aliphatic atoms, they do not correspond to short-range interactions as confirmed by magnetization transfer experiments between laser-polarized xenon and protons in H(2)O. These (15)N chemical shift variations, used in combination with (15)N transverse self-relaxation rates to determine the lower limit of the binding rate, consequently reveal subtle changes in the structure of the protein upon binding.     

NMR-spectroscopic mapping of an engineered cavity in the I14A mutant of HPr from Staphylococcus carnosus using xenon

The interaction between the histidine-containing phosphocarrier protein HPr and xenon atoms in solution is studied in the present paper. Wild-type HPr as well as the exchange mutant I14A have been studied. Specific binding of xenon into an engineered cavity created via the exchange of amino acid residue I14 by alanine could be shown using 1H-15N heteronuclear single-quantum coherence (HSQC) spectroscopy. Xenon binding results in pronounced changes of the 1H and 15N chemical shifts of amide groups close to the cavity. In addition to this observation which allows the NMR-spectroscopic mapping of such cavities, we have shown that the entire molecule is slightly rearranged as a result of xenon binding. In contrast, wild-type HPr only exhibits minor chemical shift changes due to the nonspecific interactions with the xenon atoms in solution.     

Exploring surfaces and cavities in lipoxygenase and other proteins by hyperpolarized xenon-129 NMR

This paper presents an exploratory study of the binding interactions of xenon with the surface of several different proteins in the solution and solid states using both conventional and hyperpolarized (129)Xe NMR. The generation of hyperpolarized (129)Xe by spin exchange optical pumping affords an enhancement by 3-4 orders of magnitude of its NMR signal. As a result, it is possible to observe Xe directly bound to the surface of micromolar quantities of lyophilized protein. The highly sensitive nature of the (129)Xe line shape and chemical shift are used as indicators for the conditions most likely to yield maximal dipolar contact between (129)Xe nuclei and nuclear spins situated on the protein. This is an intermediate step toward achieving the ultimate goal of NMR enhancement of the binding-site nuclei by polarization transfer from hyperpolarized (129)Xe. The hyperpolarized (129)Xe spectra resulting from exposure of four different proteins in the lyophilized, powdered form have been examined for evidence of binding. Each of the proteins, namely, metmyoglobin, methemoglobin, hen egg white lysozyme, and soybean lipoxygenase, yielded a distinctly different NMR line shape. With the exception of lysozyme, the proteins all possess a paramagnetic iron center which can be expected to rapidly relax the (129)Xe and produce a net shift in its resonance position if the noble gas atom occupies specific binding sites near the iron. At temperatures from 223 to 183 K, NMR signals were observed in the 0-40 ppm chemical shift range, relative to Xe in the gas phase. The signals broadened and shifted downfield as the temperature was reduced, indicating that Xe is exchanging between the gas phase and internal or external binding sites of the proteins. Additionally, conventional (129)Xe NMR studies of metmyoglobin and lipoxygenase in the solution state are presented. The temperature dependence of the chemical shift and line shape indicate exchange of Xe between adsorption sites on lipoxygenase and Xe in the solvent on the slow to intermediate exchange time scale. The NMR results are compared with N(2), Xe, and CH(4) gas adsorption isotherms. It is found that lipoxygenase is unique among the proteins studied in possessing a relatively high affinity for gas molecules, and in addition, demonstrating the most clearly resolved adsorbed (129)Xe NMR peak in the lyophilized state.     

129Xe NMR Studies of Pecan Shell-Based Biochar and Structure-Process Correlations

Pecan shell-based biochar is utilized as a filtration medium, sequestrant for metallic ions, soil conditioner, and other applications. One process for creating the biochar involves the use of phosphoric acid at high temperature in a partial oxygen atmosphere to produce a highly porous carbonaceous material. In this work, we found ¹²⁹Xe NMR to be an excellent technique to study micropores in biochar. Thus, the ¹²⁹Xe chemical shift in biochar was found to vary linearly with the xenon pressure; from the data an estimate of about 8–9 Å could be proposed for the average pore diameter in pecan shell-based biochar. Through saturation recovery and 2-D NMR exchange experiments, information on the exchange between free versus bound xenon was obtained. Furthermore, correlations of ¹²⁹Xe NMR data with the carbonization process conditions were made.     

Cryptophane-xenon complexes in organic solvents observed through NMR spectroscopy

The interaction of xenon with cryptophane derivatives is analyzed by NMR by using either thermal or hyperpolarized noble gas. Twelve hosts differing by their stereochemistry, cavity size, and the nature and the number of the substituents on the aromatic rings have been included in the study, in the aim of extracting some clues for the optimization of (129)Xe-NMR based biosensors derived from these cage molecules. Four important properties have been examined: xenon-host binding constant, in-out exchange rate of the noble gas, chemical shift, and relaxation of caged xenon. This work aims at understanding the main characteristics of the host-guest interaction in order to choose the best candidate for the biosensing approach. Moreover, rationalizing xenon chemical shift as a function of structural parameters would also help for setting up multiplexing applications. Xenon exhibits the highest affinity for the smallest cryptophane, namely cryptophane-111, and a long relaxation time inside it, convenient for conservation of its hyperpolarization. However, very slow in-out xenon exchange could represent a limitation for its future applicability for the biosensing approach, because the replenishment of the cage in laser-polarized xenon, enabling a further gain in sensitivity, cannot be fully exploited.     

Development of a functionalized xenon biosensor

NMR-based biosensors that utilize laser-polarized xenon offer potential advantages beyond current sensing technologies. These advantages include the capacity to simultaneously detect multiple analytes, the applicability to in vivo spectroscopy and imaging, and the possibility of "remote" amplified detection. Here, we present a detailed NMR characterization of the binding of a biotin-derivatized caged-xenon sensor to avidin. Binding of "functionalized" xenon to avidin leads to a change in the chemical shift of the encapsulated xenon in addition to a broadening of the resonance, both of which serve as NMR markers of ligand-target interaction. A control experiment in which the biotin-binding site of avidin was blocked with native biotin showed no such spectral changes, confirming that only specific binding, rather than nonspecific contact, between avidin and functionalized xenon leads to the effects on the xenon NMR spectrum. The exchange rate of xenon (between solution and cage) and the xenon spin-lattice relaxation rate were not changed significantly upon binding. We describe two methods for enhancing the signal from functionalized xenon by exploiting the laser-polarized xenon magnetization reservoir. We also show that the xenon chemical shifts are distinct for xenon encapsulated in different diastereomeric cage molecules. This demonstrates the potential for tuning the encapsulated xenon chemical shift, which is a key requirement for being able to multiplex the biosensor.     

NMR spectroscopic study of noble gas binding into the engineered cavity of HPr(I14A) from Staphylococcus carnosus

Xenon binding into preexisting cavities in proteins is a well-known phenomenon. Here we investigate the interaction of helium, neon, and argon with hydrophobic cavities in proteins by NMR spectroscopy. 1H and 15N chemical shifts of the I14A mutant of the histidine-containing phosphocarrier protein (HPr(I14A)) from Staphylococcus carnosus are analyzed by chemical shift mapping. Total noble gas induced chemical shifts, Delta, are calculated and compared with the corresponding values obtained using xenon as a probe atom. This comparison reveals that the same cavity is detected with both argon and xenon. Measurements using the smaller noble gases helium and neon as probe atoms do not result in comparable effects. The dependence of amide proton and nitrogen chemical shifts on the argon concentration is investigated in the range from 10 mM up to 158 mM. The average dissociation constant for argon binding into the engineered cavity is determined to be about 90 mM.     

Diffusion, relaxation, and chemical exchange in casein gels: a nuclear magnetic resonance study

Water in protein/water mixtures can be described in terms of bound water and free water, by exchange between these two states, and by its exchange with appropriate sites on the protein. 1H-NMR diffusion and relaxation measurements provide insights into the mobility of these states. T2 relaxation-time dispersions (i.e., T2 relaxation times at different echo pulse spacings) reveal additional information about exchange. We present a comprehensive set of diffusion and T2 dispersion measurements on casein gels for which the protein/water ratio ranges from 0.25 to 0.5. The combination of these methods, taken in conjunction with concentration dependence, allows a good estimate of the parameters required to fit the data with Luz/Meiboom and Carver/Richards models for relaxation and chemical exchange. We compare the exchange (a) between water and protein and (b) between free water and bound water. Further, we attempt to distinguish chemical site exchange and diffusion/susceptibility exchange.     

Application of Liquid Crystalline NMR Solvents to a Mixture of Ketones

A series of dilute liquid crystalline solvents are used to study the effect of slight anisotropy caused by partial alignment on chemical shift and residual dipolar coupling (RDC) in small molecules. The residual dipolar couplings between protons in solutes are found to be almost independent of the local environment. It is also found that the chemical shift does not change over the concentration range observed. A linear relationship between residual dipolar coupling and liquid crystal concentration is observed at relatively low concentrations, but is severely violated at high concentrations.     

Modulation of lysozyme charge influences interaction with phospholipid vesicles

Lysozyme is a globular protein which is known to bind to negatively charged phospholipid vesicles. In order to study the relationship between charge state of the protein and its interaction with negatively charged phospholipid membranes chemical modifications of the proteins were carried out. Succinylation and carbodiimide modification was used to shift the isoelectric point of lysozyme to lower and higher pH values, respectively. The binding of the modified lysozyme to phospholipid vesicles prepared from phosphatidic acid (PA) was determined using microelectrophoresis and ultracentrifugation. At acidic pH of the solution all lysozyme species reduced the surface charges of PA vesicles. Succinylated lysozyme (succ lysozyme) reduced the electrophoretic mobility (EPM) to nearly zero, whereas native lysozyme and carboxylated lysozyme (carbo lysozyme) changed the surface charge to positive values. At neutral pH, the reduction of surface charges was less for carbo lysozyme and unmodified lysozyme. Succ lysozyme did not change the EPM. Unmodified and carbo lysozyme decreased the magnitude of EPM, but the whole complex was still negatively charged. The bound fraction of all modified lysozyme to PA vesicles at high lysozyme/PA ratios was nearly constant at acidic pH. At low lysozyme/PA ratios the extent of bound lysozyme is changed in the order carbo>unmodified>succ lysozyme. Increasing the pH, the extent of bound lysozyme to PA large unilamellar vesicles (LUV) is reduced, at pH 9.0 only 35% of carbo lysozyme, 23% of unmodified lysozyme is bound, whereas succ lysozyme does not bind at pH 7.4 and 9.0. At low pH, addition of all lysozyme species resulted in a massive aggregation of PA liposomes, at neutral pH aggregation occurs at much higher lysozyme/PA ratios. Lysozyme binding to PA vesicles is accompanied by the penetration of lysozyme into the phospholipid membrane as measured by monolayer techniques. The penetration of lysozyme into the monolayer was modulated by pH and ionic strengths. The interaction of lysozyme with negatively charged vesicles leads to a decrease of the phospholipid vesicle surface hydration as measured by the shift of the maximum of the fluorescence signal of a headgroup labeled phospholipid. The binding of bis-ANS as an additional indicator for the change of surface hydrophobicity is increased at low pH after addition of lysozyme to the vesicles. More hydrophobic patches of the lysozyme-PA complex are exposed at low pH. At low pH the binding process of lysozyme to PA vesicles is followed by an extensive intermixing of phospholipids between the aggregated vesicles, accompanied by a massive leakage of the vesicle aqueous content. The extent of lysozyme interaction with PA LUV at neutral and acidic pH is in the order carbo lysozyme>lysozyme>succ lysozyme.     

Water-protein interactions in microcrystalline crh measured by 1H-13C solid-state NMR spectroscopy

Using solid-state NMR carbon-proton dipolar correlation spectroscopy, we observed hydrogen exchange on the millisecond time scale between water molecules and protein protons in a solid sample. These interactions are shown to be related to important structural features of the protein such as hydrogen-bonding or salt-bridge networks.     

Heteronuclear saturation transfer difference (HSTD) experiment for detection of ligand binding to proteins

This report presents a modified saturation transfer difference experiment for protein–ligand binding studies. A heteronuclear saturation transfer difference (HSTD) is suggested, where in a hetero atom, such as carbon is utilized for monitoring the binding instead of proton. This method is free from some of the problems associated with proton STD experiment, such as lack of sufficient number of protons at the binding site or crowding of spectra due to smaller chemical shift dispersion. The present method has been demonstrated on three systems namely caffeine–HSA, salicylic acid–HSA and glucose–lysozyme, illustrating the utility of the method.     

槲皮素在溶液中的化学交换和自扩散运动

通过对溶于氘代二甲亚砜（DMSO d6）中的槲皮素的自扩散系数和槲皮素羟基质子与溶剂中水质子之间的交换速率常数的NMR测量,研究了交换速率常数与扩散系数随温度和含水量的变化情况.结果表明,化学交换与扩散系数是相互独立的两种运动,活泼质子的化学交换并不需要通过槲皮素分子的扩散而进行.但是活泼质子的表观扩散系数却显著地受化学交换的影响.当以活泼质子为对象时,这种影响需要引起足够的重视.     

Xenon porometry at room temperature

Xenon porometry is a method in which porous material is immersed in a medium and the properties of the material are studied by means of 129Xe nuclear magnetic resonance (NMR) of xenon gas dissolved in the medium. For instance, the chemical shift of a particular signal (referred to as signal D) arising from xenon inside small pockets formed in the pores during the freezing of the confined medium is highly sensitive to the pore size. In the present study, we show that when naphthalene is used as the medium the pore size distribution of the material can be determined by measuring a single one-dimensional spectrum near room temperature and converting the chemical shift scale of signal D to the pore radius scale by using an experimentally determined correlation. A model has been developed that explains the curious behavior of the chemical shift of signal D as a function of pore radius. The other signals of the spectra measured at different temperatures have also been identified, and the influence of xenon pressure on the spectra has been studied. For comparison, 129Xe NMR spectra of pure xenon gas adsorbed to porous materials have been measured and analyzed.     

用多维NMR谱和圆二色CD光谱研究蛋白质亲环素A的结构稳定性

The structural stability of cyclophilin A （CypA） was investigated using H/D exchange and temperature coefficients of chemical shifts of amide protons, monitored by 213 heteronuclear NMR spectroscopy. Amide proton exchange rates were measured by H/D exchange experiments for slow-exchange protons and measured by SEA （Solvent Exposed Amides）-HSQC experiments for fast-exchange protons. Temperature coefficients of chemical shifts and hydrogen exchange rates of amide protons show reasonably good correlation with the protein structure. Totally, 44 out of 153 non-proline assigned residues still exist in 86 d of hydrogen-deuterium exchange at 4 ℃, suggesting that CypA structure should be highly stable. Residues in secondary structures of α2, β1, β2, β5, β6 and β7 might constitute the hydrophobic core of the protein. The change in free energy of unfolding （ △Gu^H2O ） of CypA was estimated to be （21.99± 1.53） kJ·mol^-1 by circular dichroism （CD）. The large free energy change is also an indicator of the high structural stability.     

Reconstructing NMR spectra of "invisible" excited protein states using HSQC and HMQC experiments

Carr-Purcell-Meiboom-Gill (CPMG) relaxation measurements employing trains of 180 degrees pulses with variable pulse spacing provide valuable information about systems undergoing millisecond-time-scale chemical exchange. Fits of the CPMG relaxation dispersion profiles yield rates of interconversion, relative populations, and absolute values of chemical shift differences between the exchanging states, |Deltaomega|. It is shown that the sign of Deltaomega that is lacking from CPMG dispersion experiments can be obtained from a comparison of chemical shifts in the indirect dimensions in either a pair of HSQC (heteronuclear single quantum coherence) spectra recorded at different magnetic fields or HSQC and HMQC (heteronuclear multiple quantum coherence) spectra obtained at a single field. The methodology is illustrated with an application to a cavity mutant of T4 lysozyme in which a leucine at position 99 has been replaced by an alanine, giving rise to exchange between ground state and excited state conformations with a rate on the order of 1450 s(-1) at 25 degrees C.     

129Xe nuclear magnetic resonance study of pitch-based activated carbon modified by air oxidation/pyrolysis cycles: a new approach to probe the micropore size

(129)Xe NMR has been used to study a series of homologous activated carbons obtained from a KOH-activated pitch-based carbon molecular sieve modified by air oxidation/pyrolysis cycles. A clear correlation between the pore size of microporous carbons and the (129)Xe NMR of adsorbed xenon is proposed for the first time. The virial coefficient delta(Xe)(-)(Xe) arising from binary xenon collisions varied linearly with the micropore size and appeared to be a better probe of the microporosity than the chemical shift extrapolated to zero pressure. This correlation was explained by the fact that the xenon collision frequency increases with increasing micropore size. The chemical shift has been shown to vary very little with temperature (less than 9 ppm) for xenon trapped inside narrow and wide micropores. This is indicative of a smooth xenon-surface interaction potential.     

New probes of ligand flexibility in drug design: transferred (13)C CSA-dipolar cross-correlated relaxation at natural abundance

Understanding the impact of molecular flexibility remains an important outstanding problem in rational drug design. Toward this end, we present new NMR relaxation methods that describe ligand flexibility at the atomic level. Specifically, we measure natural abundance (13)C cross-correlated relaxation parameters for ligands in rapid exchange between the free and receptor-bound states. The rapid exchange transfers the bound state relaxation parameters to the free state, such that a comparison of relaxation rates in the absence and presence of protein receptor yields site-specific information concerning the bound ligand flexibility. We perform these measurements for aromatic carbons, which are highly prevalent in drug-like molecules and demonstrate significant cross-correlated relaxation between the (13)C-(1)H dipole-dipole (DD) and (13)C chemical shift anisotropy (CSA) relaxation mechanisms. Our use of natural abundance measurements addresses the practical difficulties of obtaining isotope-labeled ligands in pharmaceutical research settings. We demonstrate our methods on a small ligand of the 42 kDa kinase domain of the p38 MAP kinase. We show that exchange-transferred cross-correlated relaxation measurements are not only sensitive probes of bound ligand flexibility but also offer complementary advantages over standard R(1) = 1/T(1) and R(2) = 1/T(2) measurements. The ligand flexibility profiles obtained from the relaxation data can help assess the influence of dynamics on ligand potency or pharmacokinetic properties or both, and thereby include inherent molecular flexibility in drug design.     

Gas sorption environments in poly(2,6‐dimethyl‐1,4‐phenylene oxide) by xenon‐129 nuclear magnetic resonance: Effects of processing

One‐ and two‐dimensional xenon‐129 nuclear magnetic resonance (¹²⁹Xe NMR) experiments were performed on a series of poly(2,6‐dimethyl‐1,4‐phenylene oxide) (PXE) samples to characterize the sorption environments and the relative mobility of xenon in the samples. Samples of PXE in sealed NMR tubes pressurized with xenon were studied as a function of temperature, pressure, and processing. In a dense cast film of PXE, the shift relative to the free gas resonance is smaller than that observed for typical glassy polymers, indicating a higher free volume environment. Solubility rises rapidly as temperature decreases. The lower shift and rapid increase in solubility with decreasing temperature are consistent with a relatively high free volume environment for gas sorption. If PXE is antiplasticized, the shift is slightly larger, the increase in signal intensity with decreasing temperature is smaller, and the line widths are greater. This sample is a better packed glass with less free volume and slower diffusion. Samples of PXE produced by rapid precipitation have broad lines and even lower shifts corresponding to a wide distribution of higher free volume environments. The appearance of two lines at low temperatures is consistent with the presence of a bimodal distribution of environments similar to what has been observed with positron annihilation lifetime spectroscopy. The resonance closest to the free gas resonance is associated with very large free volume elements relative to those of traditional glassy polymers. In two‐dimensional experiments, there is a rapid exchange of xenon by diffusion between the two environments, indicating the close spatial proximity of the environments. Two‐dimensional experiments and one‐dimensional progressive saturation experiments reflect a rapid exchange of xenon between the sorbed state and the free gas resonance for the precipitated samples. At low temperatures, the high field peak exchanges more rapidly with the free gas. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 1965–1974, 2002     

Measurement of slow (micros-ms) time scale dynamics in protein side chains by (15)N relaxation dispersion NMR spectroscopy: application to Asn and Gln residues in a cavity mutant of T4 lysozyme.

A new NMR experiment is presented for the measurement of micros-ms time scale dynamics of Asn and Gln side chains in proteins. Exchange contributions to the (15)N line widths of side chain residues are determined via a relaxation dispersion experiment in which the effective nitrogen transverse relaxation rate is measured as a function of the number of refocusing pulses in constant-time, variable spacing CPMG intervals. The evolution of magnetization from scalar couplings and dipole-dipole cross-correlations, which has limited studies of exchange in multi-spin systems in the past, does not affect the extraction of accurate exchange parameters from relaxation profiles of NH(2) groups obtained in the present experiment. The utility of the method is demonstrated with an application to a Leu --> Ala cavity mutant of T4 lysozyme, L99A. It is shown that many of the side chain amide groups of Asn and Gln residues in the C-terminal domain of the protein are affected by a chemical exchange process which may be important in facilitating the rapid binding of hydrophobic ligands to the cavity.