Proton Exchange Time Research Articles

Ion influence on surface water dynamics and proton exchange at protein surfaces – A unified model for transverse and longitudinal NMR relaxation dispersion

In all biologically relevant media, proteins interact in the presence of surrounding ions, and such interactions are water-mediated. Water molecules play a crucial role in the restructuring of proteins in solution and indeed in their biological activity. Surface water dynamics and proton exchange at protein surfaces is investigated here using NMR relaxometry, for two well-known globular proteins, lysozyme and bovine serum albumin, with particular attention to the role of surface ions. We present a unified model of surface water dynamics and proton exchange, accounting simultaneously for the observed longitudinal and transverse relaxation rates. The most notable effect of salt (0.1 M) concerns the slow surface water dynamics, related to rare water molecules embedded in energy wells on the protein surface. This response is protein-specific. On the other hand, the proton exchange time between labile protein-protons and water-protons at the protein surface seems to be very similar for the two proteins and is insensitive to the addition of salts at the concentration studied.

Ion and water transport reasonably involves rotation and pseudorotation: measurement and modeling the temperature dependence of small-angle neutron scattering from aqueous SrI2.

X-ray and neutron scattering have provided insight into the short range (<8 Å) structures of ionic solutions for over a century. For longer distances, single scattering bands have, however, been seen. For the non-hydrolyzing salt SrI2 in aqueous (D2O) solution, a structure sufficient to scatter slow neutrons has been seen to persist down to a concentration of 0.1 mol L-1 where the measured average spacing between scatterers is over 20 Å. Theoretical studies of such long distance solution structures are difficult, and these difficulties are discussed. The width of the distribution in distances between the scatterers (ions, ion pairs, etc.) remains less than 10 Å, which approximates the average size of the ions and their first hydration shell. Here, we measure the temperature dependence from 10 °C to 90 °C of the small angle neutron scattering (SANS) by a 0.5 molar SrI2 solution in D2O and find that this surprisingly narrow distribution of the distances remains constant within experimental uncertainty. This structure of the ions in the solution appears to endure because changes in interion distances along any single spatial dimension require displacements near the size of a water molecule. Together, the experimental measurements support a rotatory mechanism for simultaneous ion transport and water countertransport. Since rotation minimizes displacement of the solution framework, it is suggested that water transport alone also involves rotation of multimolecular structures, and that the interpretation of single-molecule water rotation is confounded by pseudorotation that results from paired picosecond proton exchanges. It is pointed out that NMR-determined millisecond to microsecond proton exchange times of chelated-metal-ion bound waters and the much faster chelate rotational correlation times around 10 picoseconds, both of which require making and breaking of hydrogen bonds, are difficult to impossible to reconcile.

Low-loss waveguides in a single-crystal lithium niobate thin film.

We report low-loss channel waveguides in a single-crystal LiNbO(3) thin film achieved using the annealed proton exchange process. The simulation indicated that the mode size of the α phase channel waveguide could be as small as 1.2 μm(2). Waveguides with several different widths were fabricated, and the 4 μm-wide channel waveguide exhibited a mode size of 4.6 μm(2). Its propagation loss was accurately evaluated to be as low as 0.6 dB/cm at 1.55 μm. The single-crystal lattice structure in the LiNbO(3) thin film was preserved by a moderate annealed proton exchange process (5 min of proton exchange at 200°C, followed by 3 h annealing at 350°C), as revealed by measuring the extraordinary refractive index change and x ray rocking curve. A longer proton exchange time followed by stronger annealing would destroy the crystal structure and induce a high loss in the channel waveguides.

Fabrication and characterization of single mode annealed proton exchanged waveguides in -x-cut lithium niobate

Lithium niobate is a key, well-known material in optical communication that maintains its importance due to its high speed in electro-optical modulators and other optical devices. Using a benzoic acid proton exchange method and annealing in wet O2, we have fabricated waveguides along the y-axis of -x-cut lithium niobate substrate. We have optimized proton exchange and annealing time to make waveguides with the highest transmission we observed to date. The optical transmission was measured in waveguides between 3μm and 7μm in width, and 10mm in length. The near-field mode properties of the waveguides were also examined. In addition, we discovered that the transmission through waveguides is reduced by the surface residues which are underestimated in most fabrication processes. This paper outlines the full fabrication process as well as characterization methods in detail, including a supercontinuum laser source.

Quantification of H2O2 concentrations in aqueous solutions by means of combined NMR and pH measurements

The NMR transverse relaxation time T(2), determined by a CPMG multipulse sequence, of aqueous hydrogen peroxide (H(2)O(2)) solutions strongly depends on the rate of exchange of the spin-bearing protons between the H(2)O(2) and H(2)O molecules. For pulse separations exceeding the inverse exchange rate, this value becomes a constant only depending on proton exchange time and magnetic field strength. Since this exchange time depends in a non-analytical way on the concentration of H(2)O(2) and on the pH value, a measurement of T(2) and pH allows the inversion of the data for the non-invasive determination of the H(2)O(2) concentration. The generation of calibration data for a range of concentrations and pH values is presented and is applied to a heterogeneously catalyzed H(2)O(2) decomposition involving commercial catalyst pellets. The evolution of the concentration during the course of reactions is monitored and the long-time deactivation of the pellet is demonstrated using this technique. The method is suggested as a means for contact-free and non-invasive on-line monitoring of H(2)O(2) concentrations.

Influence of the Geometrical Configuration on Optical Damage of LiNbO3 Planar Waveguides

Geometrical effects on the optical damage in proton exchanged LiNbO 3 waveguides are analyzed. Light intensity thresholds and beam profiles at different intensities have been measured for guides prepared on z- and x-cuts. z-cut α-phase proton exchanged guides show a threshold intensity of the same order of magnitude but slightly greater than x-cut. The more important differences between both guides cuts are a clear asymmetry of beam-profile in x-cut guides as opposite to z-cut and the existence of a chaotic evolution at high intensities only found in x-cut guides. The influence of the proton-exchange time on optical damage threshold has been also investigated in z-cut waveguides to compare them with recent reported data on x-cut guides.

Light intensity dependence of holographic response and dark decays in α-phase PE:LiNbO3waveguides

The influence of the light intensity on the recording/erasing of photorefractive gratings has been studied in α-phase proton exchanged LiNbO3 waveguides. The saturating refractive index modulation increases in a non-linear way as a function of the recording intensity and reaches a region of erratic values above a certain intensity threshold, which increases with the exchange time used for preparing the guides. Erratic values are attributed to photorefractive self-defocusing of the recording beams, while the thresholding effect is attributed to the sharp index modulation increase with the intensity associated to the intrinsic defect NbLi. It has also been confirmed that the proton exchange time affects the photorefractive response and that the dark conductivity can be disregarded with regard to the photoconductivity in the high intensity range near the intensity threshold.

Integrated-optic wavelength demultiplexer on lithium niobate by double proton exchange

An integrated-optic wavelength demultiplexer produced by double proton exchange on z-cut lithium niobate is demonstrated. The mode sorting effect and waveguide dispersion characteristics are utilized to demultiplex the optical fields at the wavelengths 980 nm and 1550 nm. The opposite waveguide dispersion in the two output waveguides can be obtained by designing the aspect ratio of the waveguide structure and the refractive index profile of the waveguide. The design parameters include the waveguide width, the proton-exchange time, the annealing time, and the depth of the second proton-exchanged layer. The semivectorial finite difference method is utilized to calculate the effective index of the guided mode in the output waveguide in order to obtain the required waveguide dispersion for wavelength demultiplexing. In the experiment, the effects of waveguide width, branching angle, and depth of the second proton-exchanged layer on the device performance are discussed.

Wavelength-tunable polarization converter utilizing the strain induced by proton exchange in lithium niobate

A new wavelength-tunable polarization converter utilizing the strain induced by proton exchange is demonstrated in x-cut LiNbO3. The light polarization is converted by the strain-optic effect through the phase-matched coupling of two orthogonal polarizations. The stress-applying structure is designed to be composed of several proton-exchanged strip regions for maximization of the stress distribution. The principle of birefringent chain filters is utilized to design the device structure in order to avoid the requirement of large stress, which results in serious cracks on the substrate surface. The overlap integral between the optical field distribution and the stress distribution can be enhanced simply by prolonging the proton-exchange time. Besides, the stress distribution and its strength in the stress-applying structure can be fine tuned without affecting the waveguide characteristics such that the principle of the birefringent chain filters is completely satisfied. Therefore, the polarization-conversion efficiency can be optimized when utilizing this exclusive stress-tuning ability. By the thermal-optic effect, the wavelength of maximum conversion can be tuned at a rate of -0.115 nm/°C with a maximum conversion efficiency of 92.41%. The proposed polarization converter has the advantages of adequate stress distribution and strength, high parameter-tuning feasibility, low propagation loss, easy fabrication, and low fabrication cost.

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A new electrooptically wavelength-tunable polarization converter by strain-optic effect on LiNbO/sub 3/ is presented. The polarization conversion is achieved by the tilt of waveguide principal axis caused by the stress induced by the proton-exchanged region on the single side of the waveguide. Simply increasing the proton-exchange time can enlarge the stress-distributed region and its interaction with the input light, thus, the conversion efficiency can be enhanced. By electrooptic effect, the wavelength of maximum conversion can be tuned at a rate of 0.081 nm/V with a maximum conversion efficiency of 92.4%.

Alteration of A.T base-pair opening kinetics by the ammonium cation in DNA A-tracts.

We have investigated by NMR the effects of NH(4)(+) on the chemical shifts, on the structure, and on the imino proton exchange kinetics of two duplexes containing an A-tract, [d(CGCGAATTCGCG)](2) and [d(GCA(4)T(4)GC)](2), and of a B-DNA duplex,[d(CGCGATCGCG)](2). Upon NH(4)(+) addition to [d(CGCGAATTCGCG)](2), the adenosine H2 protons, the thymidine imino protons, and the guanosine imino proton of the adjacent G.C pair show unambiguous chemical shifts. Similar shifts are observed in the A-tract of [d(GCA(4)T(4)GC)](2) and for the A5(H2) proton of the B DNA duplex [d(CGCGATCGCG)](2). The localization of the shifted protons suggests an effect related to NH(4)(+) binding in the minor groove. The cross-peak intensities of the NOESY spectra collected at low and high NH(4)(+) concentrations are comparable, and the COSY spectra do not show any change of the sugar pucker. This indicates a modest effect of ammonium binding on the duplex structures. Nevertheless, the imino proton exchange catalysis by ammonia provides evidence for a substantial effect of NH(4)(+) binding on the A.T base-pair kinetics in the A-tracts. Proton exchange experiments performed at high and low NH(4)(+) concentrations show the occurrence of two native conformations in proportions depending on the NH(4)(+) concentration. The base-pair lifetimes and the open-state lifetimes of each conformation are distinct. Exchange from each conformation proceeds via a single open state. But if, and only if, the NH(4)(+) concentration is kept larger than 1 M, the A.T imino proton exchange times of A-tract sequences exhibit a linear dependence versus the inverse of the NH(3) proton acceptor concentration. This had been interpreted as an indication for two distinct base-pair opening modes (Wärmländer, S., Sen, A., and Leijon, M. (2000) Biochemistry 39, 607-615).

Nuclear magnetic relaxation dispersion of ferritin and ferritin-like magnetic particle solutions: a pH-effect study.

The relaxation mechanism of water protons in the presence of ferritin is still being debated. In this work, the pH dependence of the relaxation induced by ferritin and Fercayl, a ferritin-like akaganeite particle, is studied through T1 and T2 nuclear magnetic relaxation dispersion (NMRD) profiles. To differing extents, the relaxation brought about by both systems is significantly affected by pH. A proton exchange time of 33 ns (at pH 6 and 37 degrees C) is deduced from the fittings of Fercayl T1 NMRD profiles. The linearity of the relationship between 1/T2 and the magnetic field B0 for ferritin and Fercayl solutions is not altered by changes in pH. The parameters of this linearity strongly depend on pH for the latter, while remaining unchanged for the former. These results are interpreted in terms of an exchange between protons belonging to hydroxyl groups at the surface of the particle and bulk water protons.

Adenine protonation in domain B of the hairpin ribozyme.

Protein enzymes often use ionizable side chains, such as histidine, for general acid-base catalysis because the imidazole pK(a) is near neutral pH. RNA enzymes, on the other hand, are comprised of nucleotides which do not have apparent pK(a) values near neutral pH. Nevertheless, it has been recently shown that cytidine and adenine protonation can play an important role in both nucleic acid structure and catalysis. We have employed heteronuclear NMR methods to determine the pK(a) values and time scales of chemical exchanges associated with adenine protonation within the catalytically essential B domain of the hairpin ribozyme. The large, adenine-rich internal loop of the B domain allows us to determine adenine pK(a) values for a variety of non-Watson-Crick base pairs. We find that adenines within the internal loop have pK(a) values ranging from 4.8 to 5.8, significantly higher than the free mononucleotide pK(a) of 3. 5. Adenine protonation results in potential charge stabilization, hydrogen bond formation, and stacking interactions that are expected to stabilize the internal loop structure at low pH. Fast proton exchange times of 10-50 micros were determined for the well-resolved adenines. These results suggest that shifted pK(a) values may be a common feature of adenines in non-Watson-Crick base pairs, and identify two adenines which may participate in hairpin ribozyme active site chemistry.

Exchange rates of ethanol with water in water-saturated cement pastes probed by NMR

Diffusion of ethanol into water-saturated white cement pastes has been investigated by carbon and proton nuclear magnetic resonance (NMR). The diffusion of ethanol was shown to be Fickian, assuming one-dimensional diffusion under perfect sink boundary conditions. Derived diffusion coefficients were found to increase with increasing water/cement (w/c) ratio from (2.7 ± 0.5) 10 −8 cm 2 /s at w/c = 0.30 to (59 ± 5) 10 −8 cm 2 /s at w/c = 1.0. At the end of the exchange process, only a fraction of the total volume of water is exchanged with ethanol, varying from 60% for samples containing mainly micro- and mesopores to about 80% for samples where additional capillary pores are present. Time needed to reach 90% and 95% exchange of the total intrudable amount of ethanol in cylindrical samples with diameter of 5.5 mm varied from 1 day to nearly 3 weeks. This has importance for exchange in larger samples with typical diameters of 10 mm or more (as used in mercury intrusion porosimetry), which may require on the order of months for 90% exchange to take place. The mole fraction of ethanol and water in the pore system was determined from sampled carbon and proton NMR spectra vs. exchange time by comparing H 2 O-saturated and D 2 O-saturated samples. At the end of the exchange process, water was found to occupy the remaining volume not accessible to ethanol. In the tested w/c ratio range, the water content in all samples is below the value where damage to the pore structure normally occurs due to internal tension when exposed to drying. An empirical relationship between chemical shift of the CH 3 CH 2 OH/H 2 O peak and mole fraction of ethanol is derived, enabling the mole fraction of ethanol from the NMR peak to be estimated.

Determination of ordinary refractive index profile for a planar waveguide by transmission spectrum analysis

We introduce a new method to determine the ordinary refractive index profile of a planar waveguide on a crystal plate. The index profile of the planar waveguide can be numerically divided into multilayers; the transmission spectrum of the multilayer waveguide can be calculated and numerically analyzed to fit the measured transmission spectrum. We demonstrated this method on a proton exchanged planar waveguide in z-cut LiTaO3. We found that the ordinary refractive index profile of this waveguide can very well be described by a Fermi–Dirac function. The index profile evolution with proton exchange time and anneal time were obtained together with the diffusion coefficients for the proton exchange and anneal processes. We discovered that, for the proton exchange process in LiTaO3, there exists a surface diffusion phenomenon which has a much smaller diffusion coefficient than that of the bulk diffusion.

Raman spectroscopic study of proton-exchanged LiTaO3 crystals

Raman spectra of LiTaO3 crystals with different proton-exchange times are examined. The oblique phonon at 190 cm−1 and A1(TO) phonons at 356 and 596 cm−1 appear in the transverse A1- and E-symmetry spectra, respectively. Their intensities change with proton-exchange time and reach a maximum in the spectrum of the sample with about 8 h treatment. In the E-symmetry spectra, the intensities of E(TO) modes also show a dependence on proton-exchange time and reach a maximum in the spectrum of the sample with 12 h treatment. These results are attributed to both the internal strain resulting from the order–disorder distribution of protons inside the sample and the enhanced photorefractive effect. In addition, the existence of energy transfer between A1(TO) and E(TO) modes is ascribed to the coexistence of paraelectric and ferroelectric phases in the protonated samples.

NMR relaxation rates and blood oxygenation level.

A linear relationship between the proton relaxation rates and the fraction of deoxyhemoglobin of circulating whole blood (fHb) has been established in vitro at 4.7 T. These results have been interpreted on the basis of the additivity of relaxation rates. The slope of the lines of transverse relaxation rates (R2) versus fHb was found to increase with interpulse delay in Carr-Purcell Meiboom-Gill (CPMG) experiments. The Luz-Meiboom relation applied to this interpulse delay dependence of R2 suggests a two-site chemical exchange rather than a diffusion mechanism. The 1-ms water proton exchange time derived from these observations has been interpreted in terms of exchange between exchangeable protons close to the paramagnetic center of hemoglobin and protons of bulk water.

Swelling characteristics of proton-exchanged LiNbO 3 waveguides

The swelling of proton-exchanged waveguides in LiNbO3 due to the LiNbO3-HNbO3 transformation is reported. The induced surface stresses could make a significant contribution to the index change and birefringence. The dependence of the swelling on the proton-exchange time and temperature has been characterised and agrees well with diffusion theory.

Segmental differences in the stability of thetrp-repressor peptide backbone

Exchange lifetimes of amide protons in trp-repressor with and without the corepressor, L-tryptophan, were studied by heteronuclear 2D NMR spectroscopy. The amide proton exchange times revealed pronounced differences in the stability of different regions of the trp-repressor. The dimeric core of the molecule is relatively compact and homogeneous in terms of the measured parameters in both apo- and holorepressors. On the other hand the DNA-binding region appears less stable and more susceptible to the exchange of its backbone protons with the solvent. The NMR findings reported here are consistent with and amplify information on the stability of the trp-repressor obtained by other methods.

Processes of base-pair opening and proton exchange in Z-DNA

Using proton magnetic resonance, we have investigated imino and amino proton exchange in the Z form of the four oligomers d(Cbr8GCGCbr8G), d(CGm5CGCG), d(CG)6, and d(CG)12. In the latter two oligomers, all five exchangeable protons have been assigned. We find that proton acceptors such as NH3 or the basic form of Tris enhance imino proton exchange. The base-pair lifetime can then be obtained by extrapolation of the exchange time to infinite concentration of proton acceptor. For d(CG)6 and d(CG)12, the values are ca. 3.5 ms at 80 degrees C and ca. 130 ms at 35 degrees C. The latter value is about 65 times longer than in the same oligomers in the B form. The activation energy of base-pair opening, 80 kJ/mol, is the same in the Z and the B forms of d(CG)12. At 5 degrees C, the base-pair lifetime is about 3 s, much smaller than the time constant of the Z to B transition, to which it is therefore unrelated. The base-pair dissociation constant at 35 degrees C, 0.5 X 10(-6), is 5 times smaller than for the same oligomers in the B form. In the absence of added catalyst, at pH 7, the exchange time of the imino proton is 30 min at 5 degrees C. That of both cytidine amino protons, assigned by NOE, is about 50 min. The longest proton exchange time, ca. 330 min, is assigned unambiguously to the guanosine amino protons. Thus assigned and interpreted in terms of exchange chemistry rather than structural kinetics, the exchange times do not support earlier models of Z-DNA internal motions.