Molecular mobilities in chromaffin granules magnetic field dependence of proton T1 relaxation times

The magnetic field dependence of the NMR spin-lattice relaxation time of water protons in intact bovine chromaffin vesicles has been studied over the range 1.00–23.49 kG. The T₁ relaxation time shows a dispersion a t field values near 20 kG. The observed proton resonance arises mainly from solvent protons (¹H₂O), but the relaxation rate, which is a weighted average over all sites with which the solvent protons rapidly exchange (i.e., NH and OH protons), is dominated by exchangeable protons in the most slowly moving soluble component. The field dependence of the T₁ dispersion demonstrates the existence of a site of exchangeable protons for which τ_r = 1.9±0.5 ns at 3°C. This site is assigned to ATP and cationic groups to which its phosphate esters are complexed, since previously measured correlation times of epinephrine and the chromogranin backbone are nearly an order of magnitude too short to explain the T₁ dispersion. Quantitative estimates of the relative numbers of exchangeable protons on the different soluble components support this interpretation. The temperature dependence of T₁ of the peak due to exchangeable protons has also been measured over a temperature range ?3 to 25°C. T₁ lengthens by about 30% over this range and exhibits no discontinuous behavior, as would be expected if a gel transition or structural alterations in the storage complex occurred. T₁ lengthens by less than 10% in chromaffin granule pastes that have been maintained at 25°C for 24 h, indicating considerable thermal stability in the storage complex. Possible effects on the solvent T₁ due to paramagnetic ions have been considered with the conclusion that they are probably negligible or of minor significance.     

The interaction between water and the polar head in inverted phosphatidylcholine micelles A 2H and 31P relaxation study

²H and ³¹P spin-lattice relaxation times (T₁) were studied for invented egg phosphatidylcholine micelles in CCl₄ as functions of ²H₂O concentration. When the ²H₂O/phosphatidylcholine mole ratio changed from 1.0 to 18.0, T₁ of ³¹P increased by about 2.6 fold, whereas T₁ of ²H increased by about 50 fold. A quantitative analysis of the deuterium T₁ data showed that there is only one water molecule tightly bound to the polar head, and it is in rapid exchange with the rest of the water molecules. The activation energy for the deuterium T₁ was 7.1 ± 0.8 kcal/mol (30 ± 3 kJ/mol), and was independent of the ²H₂O concentration.     

Nuclear Magnetic Resonance Evidence using D2O for Structured Water in Muscle and Brain

The electric quadrupole moment of the deuterium nucleus provides a nuclear magnetic resonance (NMR) probe of electric field gradients, and thereby of organization of tissue water. 8-17% of H₂O in rat muscle and brain was replaced by D₂O from 50% deuterated drinking water. The peak height of the steady-state NMR spectrum of D in muscle water was 74% lower than that of an equal concentration of D₂O in liquid water. Longitudinal NMR relaxation times (T₁) of D in water of muscle and brain averaged 0.092 and 0.131 sec, respectively, compared with 0.47 sec in D₂O in liquid water. Transverse NMR relaxation times (T₂) averaged 0.009 and 0.022 sec in D₂O of muscle and brain, respectively, compared with 0.45 sec in D₂O in liquid water. These differences cannot be explained by paramagnetic ions or by magnetic inhomogeneities, which leaves increased organization of tissue water as the only tenable hypothesis. Evidence was also obtained that 27% of muscle water and 13% of brain water exist as a separate fraction with T₂ of D₂O less than 2 × 10^-3 sec, which implies an even higher degree of structure. Each of the two fractions may consist of multiple subfractions of differing structure.     

Comparison of experimental and theoretical data on hydrogen-deuterium exchange for ten globular proteins

The number of protons available for hydrogen-deuterium exchange was predicted for ten globular proteins using a method described elsewhere by the authors. The average number of protons replaced by deuterium was also determined by mass spectrometry of the intact proteins in their native conformations. Based on these data, we find that two models proposed earlier agree with each other in estimation of the number of protons replaced by deuterium. Using a model with a probability scale for hydrogen bond formation, we estimated a number of protons replaced by deuterium that is close to the experimental data for long-term incubation in D₂O (24 h). Using a model based on estimations with a scale of the expected number of contacts in globular proteins there is better agreement with the experimental data obtained for a short period of incubation in D₂O (15 min). Therefore, the former model determines weakly fluctuating parts of a protein that are in contact with solvent only for a small fraction of the time. The latter model (based on the scale of expected number of contacts) predicts either flexible parts of a protein chain exposed to interactions with solvent or disordered parts of the protein.     

A proton magnetic relaxation study of human ferrihaemoglobin in aqueous salt solutions

The proton magnetic relaxation time, T₁, has been measured at 29 MH_z in 0.1M KH₂PO₄ and 0.1M NaCI (both pH 6) aqueous solutions of human ferrihaemoglobin, the protein concentrations ranging from 0.5 to 5 mM per haem. The linear dependence on protein concentration of the enhancement in relaxation rates, Δ(1/T₁), due to the presence of the paramagnetic iron in haemoglobin was confirmed at 34°C and at ～10°C. In the middle temperature range there is a thermally activated process, whose energy of activation depends on protein concentration. This dependence is different for the two salt solutions; E_a increases with c_Hb for 0.1M KH₂PO₄ and decreases for 0.1M NaCI. The model of water-proton exchange between the bulk solvent and the sixth coordination site of the haem iron was used to calculate the distance from the “liganded” water protons to the haem iron. This yields distances much larger than those determined by X-ray crystal structure analysis. A model is proposed which reconciliates both types of data. The low-temperature relaxation rates cannot be used in deriving quantitative stereochemical data for the haem pocket because of its special shape. Irrespective of the molecular model adopted, the experimental results show clearly that, both at low (～10°C) and higher (>34°C) temperatures, the interaction of paramagnetic haem iron with water protons is practically the same for the two aqueous solutions. The dynamic state of the haemoglobin molecule, as indicated by the middle-temperature range, is completely different in 0.1M KH₂PO₄ and 0.1M NaCl, pH 6.     

Kinetic Studies on the Initial Crystallization Process of Lysozyme in the Presence of D2O and H2O

In the initial stages of the crystallization of egg-white lysozyme, monomeric lysozyme aggregates rapidly and forms a nucleus in the presence of high salt concentrations. The formation process of the aggregates was examined to make clear the difference between the situations in heavy water and in water at the same sodium ion concentration. The aggregation in both cases was observed at unsaturated and/or saturated lysozyme concentrations. The turbidity at 350 nm of lysozyme increased remarkably within 60 min under each experimental condition and showed no appreciable changes over 60 min. The increase of turbidity in H₂O was much slower than in D₂O at the same salt concentration (3%). Lysozyme showed a critical concentration for nucleus formation whose value in H₂O was lower than in D₂O at 3% salt concentration. There are two different aggregation models, depending on the concentration of lysozyme. However, similar results were not obtained at 3% sodium ions in H₂O. The initial aggregation rate was also dependent on the concentrations of both lysozyme and NaCI. Therefore, the effect of lysozyme concentration on the aggregation process in H₂O may be smaller than in D₂O.     

Oxygen diffusion in phospholipid artificial membranes studied by Fourier transform nuclear magnetic resonance

Spin-lattice (T_i) relaxation mesurements can provide information about the presence of oxygen in the environment of a nucleus, since oxygen, by virtue of its paramagnetic properties, increases T_i relaxation rates. Spin-lattice relaxation times were measured for the choline, fatty acid methylene, and fatty acid methyl protons of sonicated dimyristoyl phosphatidyl choline vesicles in D₂O at several oxygen pressures. The increase in relaxation rate due to oxygen was found to be greater for the fatty acid resonances than for the choline resonance. This was interpreted to indicate the presence of oxygen in the hydrocarbon core of the bilayer. In addition, the T_i relaxation data permitted calculation of the oxygen diffusion coefficient in the water and lipid phases.     

Proton relaxation studies of diphosphopyridine coenzymes

The proton relaxation times of DPNH and 1-(2,6-dichlorobenzyl)-dihydronicotinamide (DCB-DHN) and their respective C4 deuterium-labeled dihydronicotinamide compounds were studied by Fourier transform NMR spectroscopy. The geminal C4 protons were found to exhibit unusually short relaxation times in comparison to the other dihydronicotinamide protons. Deuterium substitution at C4 increases the relaxation time of the remaining C4 proton. The deuterium relaxation time of the C4 deuterium labels has been measured. The small value of the deuterium T₁ precludes any significant contribution of the deuterium-proton scalar coupling. The advantages of C4 deuterium labeling in binding studies of DPNH with enzymes using NMR spectroscopy are also presented.     

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.     

NMR study of 17O from H217O in human erythrocytes

Human erythrocytes were incubated in a Ringer's solution enriched with 10–18% H₂¹⁷O. The longitudinal relaxation time (T₁) of the ¹⁷O was determined separately in samples of red cell suspesions, packed cells, and supernatant. The longitudinal relaxation of ¹⁷O in erythrocyte suspensions was non-exponential, reflecting water exchange across the cell membranes as well as relaxation processes inside and outside the cell.The T₁ of intracellular ¹⁷O is 4–5 times shorter than in the supernatant, similar to the enhancement of proton relaxation by hemoglobin in erythrocytes and free solution at the frequency applied (8.13 MHz). This datum is consistent with the thesis that hemoglobin modifies the NMR relaxation behavior of water inside cells and in free solution in the same way.The rate constant

for water exchange was calculated to be 60 and 107 s⁻¹ at 25 and at 37° C, respectively. The apparent activation energy for

over the temperature range 23–37° C was 8.7±1.0 kcal/mole.     

31P-NMR spectrum of phosphocreatine: Deuterium-induced splitting of the signal

It has been found in experiments with high resolution ³¹P-NMR spectroscopy (200 MHz) that the phosphocreatine peak is splitted into two different peaks in the mixtures of H₂O and D₂O and is single but with different chemical shifts in pure H₂O and D₂O. This phenomenon is explained by substitution of protons of guanidino group in phosphocreatine by deuterium. The effect of splitting disappeared at extreme pH values (>8.5 or <4.0) and at temperatures higher than 45°C due to accelerated proton-deuterium exchange. Creatine kinase added to phosphocreatine solution also lowered its temperature of peaks' collapse by 5°–10°C. A saturation (spin) transfer method was used to show that the phosphoryl group transfer to ADP in creatine kinase active center is slower with deuterium-substituted phosphocreatine than with H-phosphocreatine. The data are taken to show the importance of the proton transfer step in the creatine kinase reaction mechanism and acceleration of phosphocreatine proton-deuterium exchange by creatine kinase.     

Quantification of protein backbone hydrogen-deuterium exchange rates by solid state NMR spectroscopy

We present the quantification of backbone amide hydrogen-deuterium exchange rates (HDX) for immobilized proteins. The experiments make use of the deuterium isotope effect on the amide nitrogen chemical shift, as well as on proton dilution by deuteration. We find that backbone amides in the microcrystalline α-spectrin SH3 domain exchange rather slowly with the solvent (with exchange rates negligible within the individual ¹⁵N–T ₁ timescales). We observed chemical exchange for 6 residues with HDX exchange rates in the range from 0.2 to 5 s⁻¹. Backbone amide ¹⁵N longitudinal relaxation times that we determined previously are not significantly affected for most residues, yielding no systematic artifacts upon quantification of backbone dynamics (Chevelkov et al. 2008b). Significant exchange was observed for the backbone amides of R21, S36 and K60, as well as for the sidechain amides of N38, N35 and for W41ε. These residues could not be fit in our previous motional analysis, demonstrating that amide proton chemical exchange needs to be considered in the analysis of protein dynamics in the solid-state, in case D₂O is employed as a solvent for sample preparation. Due to the intrinsically long ¹⁵N relaxation times in the solid-state, the approach proposed here can expand the range of accessible HDX rates in the intermediate regime that is not accessible so far with exchange quench and MEXICO type experiments.     

施肥对板栗林地土壤N2O通量动态变化的影响

2011年6月—2012年6月期间,在浙江省临安市典型板栗林地进行施肥对土壤N2O通量变化影响的试验研究。目的在于探明不同施肥处理下板栗林地土壤N2O通量的动态变化规律,并探讨土壤N2O通量和土壤环境因子之间的关系。试验设置4个处理:对照(不施肥)、无机肥、有机肥、有机无机混合肥。采用静态箱-气相色谱法测定了板栗林地土壤N2O通量,并测定了土壤温度、水分、水溶性有机碳(WSOC)和微生物量碳(MBC)含量。结果表明:板栗林土壤N2O通量呈显著季节性变化,最大值出现在夏季,最小值出现在冬季;而且,施肥处理显著提高土壤N2O年均通量和年累积量;在整个试验期间,无机肥、有机肥和有机无机混合肥处理下土壤N2O的排放系数分别达到0.96%、1.45%和1.29%。此外,施肥也显著增加了土壤WSOC和MBC的含量(P<0.05)。不同施肥处理条件下,土壤N2O通量与土壤5 cm处温度、WSOC含量间均呈极显著正相关(P<0.01),但与MBC含量之间的相关性不显著。土壤N2O排放与土壤含水量间除对照处理外均没有显著相关性。综上所述,施肥引起土壤WSOC含量的增加可能是施肥增加板栗林地土壤N2O排放速率的主要原因之一。     

Intracellular water in Artemia cysts (brine shrimp): Investigations by deuterium and oxygen-17 nuclear magnetic resonance

The dormant cysts of Artemia undergo cycles of hydration-dehydration without losing viability. Therefore, Artemia cysts serve as an excellent intact cellular system for studying the dynamics of water-protein interactions as a function of hydration. Deuterium spin-lattice (T₁) and spin-spin (T₂) relaxation times of water in cysts hydrated with D₂O have been measured for hydrations between 1.5 and 0.1 g of D₂O per gram of dry solids. When the relaxation rates (I/T₁, I/T₂) of ²H and ¹⁷O are plotted as a function of the reciprocal of hydration (1/H), an abrupt change in slope is observed near 0.6 g of D₂O (or H₂ ¹⁷O)/gram of dry solids, the hydration at which conventional metabolism is activated in this system. The results have been discussed in terms of the two-site and multisite exchange models for the water-protein interaction as well as protein dynamics models. The ²H and ¹⁷O relaxation rates as a function of hydration show striking similarities to those observed for anisotropic motion of water molecules in protein crystals.

It is suggested here that although the simple two-site exchange model or n-site exchange model could be used to explain our data at high hydration levels, such models are not adequate at low hydration levels (<0.6 g H₂O/g) where several complex interactions between water and proteins play a predominant role in the relaxation of water nuclei. We further suggest that the abrupt change in the slope of I/T₁ as a function of hydration in the vicinity of 0.6 g H₂O/g is due to a change in water-protein interactions resulting from a variation in the dynamics of protein motion.

     

Water–Protein Hydrogen Exchange in the Micro-Crystalline Protein Crh as Observed by Solid State NMR Spectroscopy

We report site-resolved observation of hydrogen exchange in the micro-crystalline protein Crh. Our approach is based on the use of proton T₂^′ -selective ¹H–¹³C–¹³C correlation spectra for site-specific assignments of carbons nearby labile protein protons. We compare the proton T₂^′ selective scheme to frequency selective water observation in deuterated proteins, and discuss the impacts of deuteration on ¹³C linewidths in Crh. We observe that in micro-crystalline proteins, solvent accessible hydroxyl and amino protons show comparable exchange rates with water protons as for proteins in solution, and that structural constraints, such as hydrogen bonding or solvent accessibility, more significantly reduce exchange rates.     

Magnetic cross-relaxation among protons in protein solutions.

The magnetic spin-lattice relaxation rates of solvent water nuclei are known to increase upon addition of diamagnetic solute protein. This enhancement of the relaxation rate is a function of magnetic field, and the orientational relaxation time of the protein molecules can be deduced from analysis of the field-dependent relaxation rates. Although the nature of the interactions that convey information about the dynamics of protein motion to the solvent molecules is not established, it is known that there is a contribution to the relaxation rates of solvent protons that plays no role in the relaxation of solvent deuterons and 17O nuclei. We show here that the additional interaction arises from a cross-relaxation process between solvent and solute protons. We introduce a heuristic three-parameter model in which protein protons and solvent protons are considered as two separate thermodynamic systems that interact across the protein-solvent interface. The three parameters are the intrinsic relaxation rates of each system and a cross-relaxation term. The sign of the latter term must always be positive, for all values of magnetic field, in order for magnetization energy to flow from the hotter to the cooler system. We find that the magnetic field-dependence of the cross-relaxation contribution is much like that of the remaining solvent proton relaxation, i.e., about the same as the deuteron relaxation field dependence. This finding is not compatible with the predictions of expressions for the cross-relaxation that have been used by other authors, but not applied to data over a wide range of magnetic field strength. The model predicts that the relaxation behavior of both the protein protons and the solvent protons is the sum of two exponentials, the relative contributions of which would vary with protein concentration and solvent isotopic composition in a fashion suggestive of the presence of two classes of protein protons, when there is in reality only one. This finding has immediate implications for the interpretation of published proton relaxation rates in complex systems such as tissues; these data should be reexamined with cross-relaxation taken into account.     

Water Mobility and Distribution in Green Coffee Probed by Time-Domain Nuclear Magnetic Resonance

Water distribution in green coffee was studied by means of pulsed nuclear magnetic resonance (NMR). Hydration experiments for relaxometry measurements were performed by adding either H₂O or D₂O to dried green coffee beans up to 35% (dry basis) or, alternatively, by moisture absorption in a controlled humidity environment. The CPMG experimental relaxation decay curves were acquired using a benchtop time-domain NMR analyzer at each hydration level and as a function of time. All NMR data were fitted according to the Laplace inversion approach to obtain the proton mobility distributions of water in the hydrated beans. By comparing the T ₂ relaxograms of the hydrated beans with the ones observed in the untreated raw beans, it was found that up to ??10% water exhibits a rather restricted proton mobility. Hydration experiments carried out with D₂O highlighted the contribution of the chemical exchange between the water protons and those of the solid matrix to the overall NMR signal. A possible interpretation of the data in terms of the antiplasticizer and plasticizer effect of water is offered.     

High-level 2H/13C/15N labeling of proteins for NMR studies

Summary The protein human carbonic anhydrase II (HCA II) has been isotopically labeled with ²H, ¹³C and ¹⁵N for high-resolution NMR assignment studies and pulse sequence development. To increase the sensitivity of several key ¹H/¹³C/¹⁵N triple-resonance correlation experiments, ²H has been incorporated into HCA II in order to decrease the rates of ¹³C and ¹H_N T₂ relaxation. NMR quantities of protein with essentially complete aliphatic ²H incorporation have been obtained by growth of E. coli in defined media containing D₂O, [1,2-¹³C₂, 99%] sodium acetate, and [¹⁵N, 99%] ammonium chloride. Complete aliphatic deuterium enrichment is optimal for ¹³C and ¹⁵N backbone NMR assignment studies, since the ¹³C and ¹H_N T₂ relaxation times and, therefore, sensitivity are maximized. In addition, complete aliphatic deuteration increases both resolution and sensitivity by eliminating the differential ²H isotopic shift observed for partially deuterated CH_nD_m moieties.     

Mechanistic Insight into the H<Subscript>2</Subscript>O/D<Subscript>2</Subscript>O Isotope Effect in the Proton Transport of the Influenza Virus M2 Protein

The M2 proton channel is essential for the replication of the flu virus and is a known drug target. The functional mechanism of channel activation and conductance is key to both the basic biology of viral replication and the design of drugs that can withstand mutations. A quantitative model was previously developed for calculating the rate of proton transport through the M2 channel. The permeant proton was assumed to diffuse to the pore, obligatorily bind to the His37 tetrad, and then dissociate and be released to either side of the tetrad. Here the model is used to calculate the effect of a change in solvent from H₂O to D₂O on the rate of proton transport. The solvent substitution affects two parameters in the model: the proton diffusion constant and the pK _a for proton binding to the His37 tetrad. When the known effects on these two parameters are included, the deuterium isotope effect calculated from the model is in quantitatively agreement with experimental results. This strict test of the theoretical model provides strong support for the hypothesis that the permeant proton obligatorily binds to and then unbinds from the His37 tetrad. This putatively essential role of the His37 tetrad in the functional mechanism of the M2 channel makes it a promising target for designing mutation-tolerant drugs.     

Effect of Na+ and K+ Ions on the Initial Crystallization Process of Lysozyme in the Presence of D2O and H2O

In the initial stage of the crystallization of egg-white lysozyme, monomeric lysozyme aggregated rapidly to form a nucleus in the presence of high salt concentrations. In the present studies, we examined the initial aggregation process of lysozyme (initial crystallization process of lysozyme) in D₂O/H₂O with sodium ions or potassium ions, and investigated the relationship between the surface hydrophobicity and the aggregation rate of lysozyme. The effect of sodium ions or potassium ions on the initial aggregation process of lysozyme in D₂O was clearly different from H₂O. The initial aggregation rate of lysozyme in H₂O was slower than in D₂O. In the case of H₂O, the initial aggregation rate was about the same in both ions. But in the case of D₂O, the initial aggregation rate was affected by the ion species and the value was lower in potassium ions than in sodium ions. These results suggest that the interaction between lysozyme molecules is stronger in D₂O than in H₂O. Furthermore, sodium ions have a stronger effect on the interaction than potassium ions in the case of D₂O. There was a good correlation among the initial aggregation rate, surface hydrophobicity, and -potential of lysozyme. The hydrophobic interaction may be an important active force in the initial aggregation process of lysozyme.