High-Resolution NMR Reveals Secondary Structure and Folding of Amino Acid Transporter from Outer Chloroplast Membrane

Solving high-resolution structures for membrane proteins continues to be a daunting challenge in the structural biology community. In this study we report our high-resolution NMR results for a transmembrane protein, outer envelope protein of molar mass 16 kDa (OEP16), an amino acid transporter from the outer membrane of chloroplasts. Three-dimensional, high-resolution NMR experiments on the ¹³C, ¹⁵N, ²H-triply-labeled protein were used to assign protein backbone resonances and to obtain secondary structure information. The results yield over 95% assignment of N, H_N, CO, C_α, and C_β chemical shifts, which is essential for obtaining a high resolution structure from NMR data. Chemical shift analysis from the assignment data reveals experimental evidence for the first time on the location of the secondary structure elements on a per residue basis. In addition T _1Z and T₂ relaxation experiments were performed in order to better understand the protein dynamics. Arginine titration experiments yield an insight into the amino acid residues responsible for protein transporter function. The results provide the necessary basis for high-resolution structural determination of this important plant membrane protein.     

NMR methods for characterizing the state of the surfaces of complex mammalian cells

It is shown that narrow ¹H NMR resonances may be observed in cancer cells, and that these belong to fatty acyl chains of membrane lipids. A variety of NMR techniques such as Gaussian-Lorentzian deconvolution, and T₁ and T₂ measurements, may be used to subdivide these resonances further. The results of these various methods require that in the membrane structures the observed lipids tumble isotropically and sufficiently rapidly to give motionally narrowed ¹H NMR lines.     

On the interpretation of the NMR water-proton relaxivity of photosynthetic membrane samples: Ramifications in the use of EDTA

In thylakoid membrane samples which have had extraneous, nonfunctionally bound manganese ions removed by a low-osmotic wash medium, subsequent treatment with EDTA induces an additional loss in the proton-relaxivity enhancement of the sample. This EDTA-induced loss in proton-relaxivity enhancement occurs at a half-maximal concentration of about 30 μM EDTA for the spin-lattice (T₁) relaxation and about 100 μM EDTA for the spin-spin (T₂) relaxation. It is slowly time dependent, with a half-time of about 5 min, but it can be kinetically separated from the chelation function of EDTA which takes place in less than 3 min. This effect of EDTA can be reversed by thorough washing of the sample in buffer medium. In addition, treatment with EDTA reduces or masks the tetraphenylboron-induced increase in the proton relaxivity, which can also be reversed by thorough washing of the sample of in buffer medium. Temperature-dependence measurements of the proton relaxivity at low-field proton-resonance frequencies indicate that the samples in the presence of EDTA do not reach the diamagnetic limit defined by the removal of functionally bound manganese. These results are interpreted to arise from EDTA-induced microenvironment changes in the membrane which restricts the accessibility of internally bound paramagnetic sites to the solvent phase protons and alters the spin exchange rate within the NMR time frame. It is suggested that this phenomenon may explain the failure to observe a correlation between the proton relaxivity, functionally bound manganese and the O₂-evolving capacity in samples treated with chelating agents (Sharp, R.R. and Yocum, C.F. (1983) Photobiochem. Photobiophys. 5, 193–199). As a consequence of the complex interaction of EDTA with the membrane, the importance and ramifications in the use of chelating agents in photosynthetic manganese measurements is therefore emphasized.     

Isolated epithelial cells of the toad bladder. Their preparation, oxygen consumption, and electrolyte content

Epithelial cells of the toad bladder were disaggregated with EDTA, trypsin, hyaluronidase, or collagenase and were then scraped free of the underlying connective tissue. In most experiments EDTA was complexed with a divalent cation before the tissue was scraped. Q _OO2, sucrose and inulin spaces, and electrolytes of the isolated cells were measured. Cells disaggregated by collagenase or hyaluronidase consumed O₂ at a rate of 4 µl hr^-1 dry wt^-1. Q _OO2 was increased 50% by ADH (100 U/liter) or by cyclic 3'',5''-AMP (10 mM/liter). Na⁺-free Ringer''s depressed the Q _OO2 by 40%. The Q _OO2 of cells prepared by trypsin treatment or by two EDTA methods was depressed by Na⁺-free Ringer''s but was stimulated relatively little by ADH. Two other EDTA protocols produced cells that did not respond to Na⁺ lack or ADH. The intracellular Na⁺ and K⁺ concentrations of collagenase-disaggregated cells were 32 and 117 mEq/kg cell H₂O, respectively. Cation concentrations of hyaluronidase cells were similar, but cells that did not respond to ADH had higher intracellular Na⁺ concentrations. Cells unresponsive to ADH and Na⁺ lack had high sucrose spaces and low transcellular membrane gradients of Na⁺, K⁺, and Cl^-. The results suggest that trypsin and EDTA disaggregation damage the active Na⁺ transport system of the isolated cell. Certain EDTA techniques may also produce a general increase in permeability. Collagenase and hyaluronidase cells appear to function normally.     

Macrophage membrane proteins: Possible role in the regulation of priming for enhanced respiratory burst activity

Brief exposure of macrophages to the proteolytic enzymes papain, elastase, or trypsin primed them for enhanced production of superoxide anion (O₂⁻) in response to stimulation by phorbol myristate acetate (PMA). Priming by trypsin was achieved at 0 °C, at which temperature trypsin functions as a protease but is not internalized, supporting the concept that protease priming depends on modification of the plasma membrane. Analysis of external membrane proteins after radioiodination of intact cells and separation by gel electrophoresis indicated that papain treatment of macrophages resulted in the cleavage of a membrane protein with a molecular weight of approximately 305K. Membranes from macrophages primed by elicitation with Corynebacterium parvum also demonstrated a reduced amount of the membrane protein at approximately 305 kDa, as well as a reduction of a protein at about 270 kDa. Lipopolysaccharideelicited macrophages showed a reduced amount of a protein at about 175 kDa. Continuous spectrophotometric assays of O₂⁻ release from adherent macrophages indicated that after exposure to a stimulus, protease-treated cells produced O₂⁻ more quickly than did control cells (reduced lag time). Inhibitors of protein synthesis augmented the priming effect of papain when added with the protease. These results suggest that protease-induced priming results from inactivation of a membrane protein (or proteins) that exerts a down-regulating effect on the respiratory burst.     

Protein Rotational Dynamics in Aligned Lipid Membranes Probed by Anisotropic T1ρ NMR Relaxation

A membrane-bound form of Pf1 coat protein reconstituted in magnetically aligned DMPC/DHPC bicelles was used as a molecular probe to quantify for the viscosity of the lipid membrane interior by measuring the uniaxial rotational diffusion coefficient of the protein. Orientationally dependent ¹⁵N NMR relaxation times in the rotating frame, or T_1ρ, were determined by fitting individually the decay of the resolved NMR peaks corresponding to the transmembrane helix of Pf1 coat protein as a function of the spin-lock time incorporated into the 2D SAMPI4 pulse sequence. The T_1ρ relaxation mechanism was modeled by uniaxial rotational diffusion on a cone, which yields a linear correlation with respect to the bond factor sin⁴θ_B, where θ_B is the angle that the NH bond forms with respect to the axis of rotation. Importantly, the bond factors can be independently measured from the dipolar couplings in the separated local-field SAMPI4 spectra. From this dependence, the value of the diffusion coefficient D_|| = 8.0 × 10⁵ s^?1 was inferred from linear regression of the experimental T_1ρ data even without any spectroscopic assignment. Alternatively, a close value of D_|| = 7.7 × 10⁵ s^?1 was obtained by fitting the T_1ρ relaxation data for the assigned NMR peaks of the transmembrane domain of Pf1 to a wavelike pattern as a function of residue number. The method illustrates the use of single-helix transmembrane peptides as molecular probes to assess the dynamic parameters of biological membranes by NMR relaxation in oriented lipid bilayers.     

Characterization of heat injury in grapes using h nuclear magnetic resonance methods : changes in transverse relaxation times

Transverse relaxation times (T₂) of tissue water (¹H) in leaves and suspension cultured cells of grape hybrids (Vitis spp. cv `Venus' and `Veeblanc') were measured by nuclear magnetic resonance at various temperatures. The tissue water was characterized by two T₂ time constants. A sharp decrease in T₂ for the major fraction of tissue water was observed in association with heat injury, as measured by electrolyte leakage and triphenyltetrazolium chloride reduction in both leaves and suspension cultured cells. The changes in T₂ as a result of heat injury were irreversible, as indicated by a temperature dependent hysteresis of T₂. Studies using a paramagnetic probe (Mn⁺²) indicated that the plasma membrane was irreversibly damaged at the killing temperature, resulting in a loss of cell compartmentalization. Tissue water in heat-killed samples was characterized by only a single T₂.     

Probing water compartments and membrane permeability in plant cells by 1H NMR relaxation measurements

¹H NMR relaxation times (T₁ and T₂) in parenchyma tissue of apple can identify three populations of water with different relaxation characteristics. By following the uptake of Mn²⁺ ions in the tissue it is shown that the observed relaxation times originate from particular water compartments: the vacuole, the cytoplasm, and the cell wall/extracellular space.

Proton exchange between these compartments is controlled by the plasmalemma and tonoplast membranes. During the Mn²⁺ penetration experiment, conditions occur that cause the relaxation times of protons of cytoplasmic water to be much shorter than their residence time in the cytoplasm. Then the tonoplast permeability coefficient P_d for water can be calculated from the vacuolar T₁ and T₂ values to be 2.44 10^-5 m·s^-1.

     

Long-lived spin state of a tripeptide in stretched hydrogel

The longitudinal (T ₁), transverse (T ₂), and singlet state (T _s) relaxation times of the geminal backbone protons (CH₂) of l-Leu-Gly-Gly were studied by NMR spectroscopy at 9.4 T in a bovine hide gelatin gel composed in D₂O at 25 °C. Gelatin granules were dissolved in a hot solution of the tripeptide and then the solution was allowed to gel inside a flexible silicone tubing. With increases in gelatin content, the T ₂ and T _s of the CH₂ protons correspondingly decreased (T _s/T ₂ ~ constant), while the change in T ₁ was relatively small. The largest observed T _s/T ₁ value was 3.3 at 46 % w/v gelatin that was the lowest gelatin content examined. Stretching the tubing, and hence the gel, brought about anisotropic alignment of the constituents resulting in residual quadrupolar splitting of the resonance from D₂O in ²H NMR spectra, and residual dipolar splitting of the CH₂ resonance in ¹H NMR spectra. WALTZ-16 decoupling during the relaxation intervals extended the singlet state relaxation time, but the efficacy diminished as the gels were stretched. Theoretically predicted T ₁, T ₂, and T _s values, assuming intramolecular dipolar coupling as the only source of relaxation, were within the same order of magnitude as the experimentally observed values. Overall we showed that it is possible to observe a long-lived spin state in an anisotropic medium when T ₂ is shorter than T ₁ in the presence of non-zero residual dipolar couplings.     

Water proton magnetic resonance studies of normal and sickle erythrocytes Temperature and volume dependence

The temperature and cell volume dependence of the NMR water proton linewidth, spin-lattice, and spin-spin relaxation times have been studied for normal and sickle erythrocytes as well as hemoglobin A and hemoglobin S solutions. Upon deoxygenation, the spin-spin relaxation time (T₂) decreases by a factor of 2 for sickle cells and hemoglobin S solutions but remains relatively constant for normal cells and hemoglobin A solutions. The spin-lattice relaxation time (T₁) shows no significant change upon dexygenation for normal or sickle packed red cells. Studies of the change in the NMR linewidth, T₁ and T₂ as the cell hydration is changed indicate that these parameters only slightly by a 10–20% cell dehydration. This result suggests that the reported 10% cell dehydration observed with sickling is not important in the altered NMR properties. Low temperature studies of the linewidth and T₁ for oxy and deoxy hemoglobin A and hemoglobin S solutions suggest that the “bound” water possesses similar properties for all four species. The low temperature linewidth ranges from about 250 Hz at ?15°C to 500 Hz at ?36°C and analysis of the NMR curves yield hydration values near 0.4 g water/g hemoglobin for all four species. The low temperature T₁ data go through a minimum at ?35°C for measurements at 44.4 MHz and ?50°C for measurements at 17.1 MHz and are similar for oxy and deoxy hemoglobin A and hemoglobin S. These similarities in the low temperature NMR data for oxy and deoxy hemoglobin A and hemoglobin S suggest a hydrophobically driven sickling mechanism. The room temperature and low temperature relaxation time data for normal and sickle cells are interpreted in terms of a three-state model for intracellular water. In the context of this model the relaxation time data imply that type III, or irratationally bound water, is altered during the sickling process.     

The state of water in biological systems as studied by proton and deuterium relaxation

Careful experiments on the measurement of the intensity of the deuterium NMR signal for ²H₂O in muscle and in its distillate were performed, and they showed that all ²H₂O in muscles is “NMR visible.”The spin-lattice relaxation time (T₁) of the water protons in the muscle and liver of mice and in egg white has been studied at six frequencies ranging from 4.5 to 6.0 MHz over the temperature range of +37 to −70°C. T₁ values of deuterons in ²H₂O of gastrocnemius muscle and liver of mice have been measured at three frequencies (4.5, 9.21 and 15.35 MHz) over the temperature range of +37 to −20°C. Calculations on T₁ for both proton and deuteron have been made and compared with the experimental data. It is suggested that the reduction of the T₁ values compared to pure water and the frequency dependence of T₁ are due to water molecules in the hydration layer of the macromolecules, and that the bulk of water molecules in the biological tissues and egg white undergoes relaxation like ordinary liquid water.     

A C-detection NMR approach for large glycoproteins

NMR spectroscopy has great potential to provide us with information on structure and dynamics at atomic resolution of glycoproteins in solution. In larger glycoproteins, however, the detrimental fast ¹H transverse relaxation renders the conventional ¹H-detected NMR experiments difficult. ¹³C direct detection potentially offers a valuable alternative to ¹H detection to overcome the fast T₂ relaxation. Here, we applied ¹³C-detected NMR methods to observe the NMR signals of ¹³C-labeled glycans attached to the Fc fragment of immunoglobulin G with a molecular mass of 56 kDa. Spectral analysis revealed that a ¹³C-detected ¹³C-¹³C NOESY experiment is highly useful for spectral assignments of the glycans of large glycoproteins. This approach would be, in part, complementary to ¹³C-¹³C TOCSY and ¹H-detection experiments.     

Sensitivity of ACL volume and T21 relaxation time to magnetic resonance imaging scan conditions

Anterior cruciate ligament (ACL) volume and T₂¹ relaxation times from magnetic resonance (MR) images have been previously shown to predict the structural properties of healing ligaments. We investigated whether MR imaging scan resolution and condition (in vivo, in situ, or ex vivo) affected ACL volume and T₂¹ relaxation times in intact ligaments. ACLs of 14 pigs were imaged using a 3 T scanner and a six-channel flexcoil using at least two of four possible scan conditions: (1) in vivo moderate resolution (n = 14); (2) in vivo high resolution (n = 7); (3) in situ high resolution acquired within 60 minutes of euthanasia (n = 6); and (4) ex vivo high resolution following hind limb disarticulation and one freeze-thaw cycle (n = 7). T₂¹ relaxation times were mapped to the ACL voxels. The total ACL volume was then divided into four sub-volumes (Vol_1–4) based on predetermined increasing ranges of T₂¹ times. ACL T₂¹ statistics (first quartile, median, and standard deviation (SD)) were computed. Scan resolution had no effect on the total ACL volume, but Vol₁ and first quartile T₂¹ times decreased with high resolution and in situ/ex vivo scan conditions. The most dramatic differences in T₂¹ summary statistics were between in vivo moderate and ex vivo high resolution scan conditions that included a freeze-thaw cycle: ACL T₂¹ SD increased by over 50% in 9 animals, and more than 90% in 4 animals. Our results indicated that T₂¹-based prediction models to quantify in vivo structural properties of healing ligaments should be based on high resolution in vivo MR scan conditions.     

Membrane interactions in small fast-tumbling bicelles as studied by 31P NMR

Small fast-tumbling bicelles are ideal for studies of membrane interactions at molecular level; they allow analysis of lipid properties using solution-state NMR. In the present study we used ³¹P NMR relaxation to obtain detailed information on lipid head-group dynamics. We explored the effect of two topologically different membrane-interacting peptides on bicelles containing either dimyristoylphosphocholine (DMPC), or a mixture of DMPC and dimyristoylphosphoglycerol (DMPG), and dihexanoylphosphocholine (DHPC). KALP21 is a model transmembrane peptide, designed to span a DMPC bilayer and dynorphin B is a membrane surface active neuropeptide. KALP21 causes significant increase in bicelle size, as evidenced by both dynamic light scattering and ³¹P T₂ relaxation measurements. The effect of dynorphin B on bicelle size is more modest, although significant effects on T₂ relaxation are observed at higher temperatures. A comparison of ³¹P T₁ values for the lipids with and without the peptides showed that dynorphin B has a greater effect on lipid head-group dynamics than KALP21, especially at elevated temperatures. From the field-dependence of T₁ relaxation data, a correlation time describing the overall lipid motion was derived. Results indicate that the positively charged dynorphin B decreases the mobility of the lipid molecules  – in particular for the negatively charged DMPG – while KALP21 has a more modest influence. Our results demonstrate that while a transmembrane peptide has severe effects on overall bilayer properties, the surface bound peptide has a more dramatic effect in reducing lipid head-group mobility. These observations may be of general importance for understanding peptide–membrane interactions.     

Evidence that neutral spingomyelinase of cultured murine neuroblastoma cells is oriented externally on the plasma membrane

The activity of the neutral, Mg²⁺-stimulated sphingomyelinase of cultured neuroblastoma cells (N1E-115) is enriched in the plasma membrane fraction and is reduced following treatment of intact or broken cells with trypsin, α-chymotrypsin, papain, and protease. Two protease-sensitive enzymes of the cell interior (lactate dehydrogenase and NADPH-cytochrome c reductase) are not affected by protease treatment of intact cells. These results indicate that the neutral, Mg²⁺-stimulated sphingomyelinase is oriented externally on the plasma membrane of the cultured neuroblastoma cell.     

Active trans-plasma membrane water cycling in yeast is revealed by NMR

Plasma membrane water transport is a crucial cellular phenomenon. Net water movement in response to an osmotic gradient changes cell volume. Steady-state exchange of water molecules, with no net flux or volume change, occurs by passive diffusion through the phospholipid bilayer and passage through membrane proteins. The hypothesis is tested that plasma membrane water exchange also correlates with ATP-driven membrane transport activity in yeast (Saccharomyces cerevisiae). Longitudinal ¹H₂O NMR relaxation time constant (T₁) values were measured in yeast suspensions containing extracellular relaxation reagent. Two-site-exchange analysis quantified the reversible exchange kinetics as the mean intracellular water lifetime (τ_i), where τ_i⁻¹ is the pseudo-first-order rate constant for water efflux. To modulate cellular ATP, yeast suspensions were bubbled with 95%O₂/5%CO₂ (O₂) or 95%N₂/5%CO₂ (N₂). ATP was high during O₂, and τ_i⁻¹ was 3.1 s⁻¹ at 25°C. After changing to N₂, ATP decreased and τ_i⁻¹ was 1.8 s⁻¹. The principal active yeast ion transport protein is the plasma membrane H⁺-ATPase. Studies using the H⁺-ATPase inhibitor ebselen or a yeast genetic strain with reduced H⁺-ATPase found reduced τ_i⁻¹, notwithstanding high ATP. Steady-state water exchange correlates with H⁺-ATPase activity. At volume steady state, water is cycling across the plasma membrane in response to metabolic transport activity.     

31P nuclear magnetic resonance studies on relaxation parameters and line broadening of intracellular metabolites of HeLa cells.

The 40-MHz ³¹P nuclear magnetic resonance (nmr) spectrum of intact HeLa cells contains seven broad peaks with some detectable splittings. The linewidths were significantly broader than for those of cell-free systems such as cell extracts, indicating that the cellular environment is responsible for the unusual line broadening. Resolution of these peaks at 40 MHz is sufficient to make certain assignments and the relaxation parameters of some of the intracellular metabolites have been measured. The spin-lattice relaxation times (T₁) ranged from 0.3 s for adenosine triphosphate (ATP) to about 3 s for inorganic phosphate (P_i) and monophosphate compounds. Nuclear Overhauser enhancements (NOE) were induced by proton irradiation with the possible exception of ATP. The relaxation parameters were compared to those of cell-free compounds and in all cases T₁ and NOE were smaller for the intracellular metabolites. The relaxation parameters for ATP were affected the most. This behavior was mimicked with mixtures of cell-free metabolites containing paramagnetic ions. The larger change in both T₁ and NOE of intracellular ATP could be accounted for by selective binding of paramagnetic ions. This phenomenon also explains some of the line broadening in the cell spectrum especially that of ATP. The spin-spin relaxation times (T₂) of P₁ and monophosphate compounds as measured by a pulse technique did not account for the observed linewidths. This is due to the presence of chemical shift envelopes arising from pH heterogeneity. All resonances were broader at 146 MHz because of the line broadening by paramagnetic ions and the presence of chemical shift envelopes. Other mechanisms of line broadening may also be significant. There was little difference in resolution of spectra at 40 and 146 MHz. Water proton linewidths and T₂ values were measured for HeLa cells and for some minced tissue preparations. The water linewidth in tissue samples was broader than that in the cell suspension. The large linewidths in tissues arise mainly from chemical shift envelopes caused by magnetic field nonuniformity in the tissue samples. There appears to be a small chemical shift envelope from magnetic nonuniformity in HeLa cells as well. The ¹H results on envelopes were extrapolated to ³¹P studies on cells and tissues. Possible methods for reducing linewidths arising from the various proposed broadening mechanisms were discussed.     

Photo-induced electron transport and water state in Rhodospirillum rubrum chromatophores

It is shown that in bacterial chromatophores the pronounced changes in the free water content with a proton spin-spin relaxation time (T₂) of 10^?3—10^?2 s does not influence the efficiency of electron transfer from the photosynthetic reaction centre to the membrane pool of secondary acceptors. An abrupt inhibition of this process occurs only after the loss of the water with faster proton spin-spin relaxation time (T₂ of 10^?4 s). The process is reversible. The water fraction in question is obviously bound to the chromatophore proteins and forms the primary hydration layer.     

Effects of temperature and field strength on the NMR relaxation times of 23Na in frog striated muscle

Pulsed NMR techniques have been applied to the study of the relaxation parameters characterizing ²³Na within frog striated muscle. Experiments were performed at 3°C, 22–24°C and 39°C at a Larmor frequency of 15.7 MHz; at 22–24°C, measurements were obtained both at 15.7 MHz and at 7.85 MHz.As previously reported, only a single spine-lattice relaxation time (T₁) was observed, but both slow (T₂)_I and fast (T₂)_II components of the spin-spin relaxation time were measured. The effect of temperature (θ) upon (1/T₁) was qualitatively similar to that reported for ²³Na in free solution; (θ) did not significantly affect (1/T₂) over the range of temperatures studied. (1/T₂)_I, and to a lesser degreee, (1/T₁) exhibited a modest inverse dependence of doubtful significance on the Larmor frequency.The data are examined within the framework of a simple specific model; a conservative values in assumed for the quadrupolar coupling constant characterizing immobilized intracellular Na⁺. Within this framework, the results suggest that the fraction of bound ions whose molecular tumbling is severely restricted does not exceed some few percent of the total sodium population.     

The effect of changing extracellular osmolality on water transport in the human red blood cell as measured by the cell water residence time and the activation energy of water transport

A pulse NMR technique employing low extracellular Mn²⁺ concentrations has been used in following the effect of variations in extracellular osmolality on water transport through the human red blood cell membrane. We report results including the effect of osmolality on the cell water lifetime (τ_a) and, for the first time, the effect on the proton spin-spin relaxation of the intracellular water (T_2a) and the activation energy for the water transport process. Current results are encouraging in correlating the effects seen in this study with suspected membrane functional changes occurring in both in vivo and in vitro aging and during in vitro preservation attempts.