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PubMed1987

Proton and sodium 23 magnetic resonance imaging of human ocular tissues. A model study.

Clinical evaluation of uveal melanomas by magnetic resonance imaging (MRI) techniques depends on developing an understanding of the appearance of these tumors in magnetic resonance (MR) images. We have determined MR characteristics of uveal melanomas by proton (1H) and sodium 23 MRI of freshly enucleated human eyes at 1.5 tesla. The MR images were obtained using two-turn proton and 23Na surface coils, designed to both transmit and receive the radiofrequency signal. Proton MRI techniques included saturation recovery and spin echo; the gradient-recalled echo technique was used for 23Na MRI. Proton and 23Na MR images provide complementary information; contrast between intraocular tumors and vitreous, lens, or subretinal hemorrhage may be varied by using MR pulse sequences that emphasize tissues based on T1, T2, proton, or sodium density values. A combination of proton and 23Na MRI provides differentiation between normal ocular structures and intraocular tumors, as well as associated complications, such as retinal detachments and subretinal hemorrhages.

Eye↗
PubMed1999

Sodium and proton MR properties of cartilage during compression.

Proton and sodium MR relaxation times of bovine articular cartilage specimens were measured as a function of proteoglycan (PG) depletion and as a function of mechanical compression. Proton and sodium relaxation times of normal cartilage were compared with relaxation times of PG-depleted cartilage to evaluate the significance of PG depletion-induced changes in MR relaxation parameters. These comparisons were conducted for both uncompressed and mechanically compressed states. The mechanical compressions were performed with an MR-compatible pressure cell and evaluated dynamically via interleaved one-dimensional proton and sodium MR projection imaging. The comparisons indicate that sodium relaxation parameters are sensitive to PG depletion when cartilage is in a mechanically compressed state or an uncompressed state. In contrast, proton relaxation parameters do not change significantly with PG depletion when cartilage is in an uncompressed state. However, during mechanical compression, proton T2 becomes sensitive to PG depletion. These results support the potential of sodium magnetic resonance imaging (MRI) as a possible modality for obtaining imaging contrast related to PG depletion. The results also indicate the potential of proton MRI to provide such contrast if the image acquisition is conducted in conjunction with a mechanical compression via physical exercise.J. Magn. Reson Imaging 10:961-967, 1999.

Animals↗
PubMed2002

Accurate prediction of proton chemical shifts. II. Peptide analogues.

Proton chemical shifts of eight cyclic amide molecules were measured in DMSO and D2O solutions. The magnetic shieldings of the corresponding aliphatic, aromatic, and amide protons were calculated by Hartree-Fock and DFT, using the 6-311G**, 6-311++G**, and TZVP basis sets. For aliphatic protons, all of these methods reproduce the experimental values in DMSO solutions excellently after linear regression. The Hartree-Fock method tends to give slightly better agreement than DFT. The best performance is given by the HF/6-311G** method, with an rms deviation of 0.068 ppm. The deviations from experimental chemical shifts in D2O solutions are only slightly larger than those in DMSO solutions. This suggests that we can use the calculated gas phase proton chemical shifts directly to predict experimental data in various solvents, including water. For amide protons, which exchange with water and form hydrogen bonds with DMSO, only modest agreement is obtained, as expected. The present studies confirm that the GIAO approach can reach high accuracy for the relative chemical shifts of aliphatic and aromatic protons at a low cost. Such calculations may provide constraints for the conformational analysis of proteins and other macromolecules.

Amides↗
PubMed1990

Quantitative studies of hydrodynamic effects and cross-relaxation in protein solutions and tissues with proton and deuteron longitudinal relaxation times.

Longitudinal relaxation times T1 of water protons were measured in 5% protein solutions at different static magnetic fields (0.47, 2, and 7 T), for proteins with molecular weight ranging between 1.4 and 480 kDa and in solvents of varying degrees of deuteration. T1 values were also obtained for rat liver soaked with Krebs-Ringer solutions of varying degrees of deuteration at the above fields. For the samples containing D2O, T1 for deuterium was also measured at fields 2 and 7 T. The deuterium measurements were used to estimate water rotational correlation times which were in turn used to estimate the contribution of so-called "hydrodynamic effects" of macromolecules to proton relaxation. The proton relaxation rates at full deuteration were compared with those in protonated solvent (water) to obtain a second, direct measurement of this effect. Both measurements provide quantitation of the hydrodynamic effects, free from the contributions of other effects that are transparent to deuteration, and results from both measurements agree with each other reasonably well. The cross-relaxation rate between solute and solvent protons, and the contribution of paramagnetic impurities in the samples were also obtained from the proton T1 studies. The experimental results show that the hydrodynamic effects (intramolecular and intermolecular water-water interactions) are about the same magnitude in all the proteins studied as well as in rat liver. However, the cross-relaxation rate generally increases with increasing protein molecular weight. Measurements in soaked rat liver indicate that the cross-relaxation rate per unit mass of solute is much higher in tissues than in simple solutions of proteins of similar mean molecular weight. The results challenge the prevailing concept that the relaxation properties of biological tissues may be treated as a simple superposition of the properties of their constituents.

Animals↗
PubMed1992

Proton relaxation studies of water compartmentalization in a model neurological system.

Proton relaxation measurements from 18 crayfish abdominal nerve cords (a model of human CNS) are used to demonstrate that the transverse (though not the longitudinal) relaxation can be decomposed into four reproducible components that, in conjunction with optical and electron microscopy of the morphology, can be assigned to three water compartments within the cord and possibly to the mobile lipid protons. The assignments are extraaxonal water protons (32 +/- 9% and mean T2 = 600 +/- 200 ms), axonal water protons (59 +/- 12% and mean T2 = 200 +/- 30 ms), intramyelinic water protons (7 +/- 4% and mean T2 = 50 +/- 20 ms), and finally an unsubstantiated assignment of lipid protons (2.0 +/- 2.0% and mean T2 = 7 +/- 4 ms).

Algorithms↗
PubMed2004

Quantitative description of proton exchange processes between water and endogenous and exogenous agents for WEX, CEST, and APT experiments.

The proton exchange processes between water and solutes containing exchangeable protons have recently become of interest for monitoring pH effects, detecting cellular mobile proteins and peptides, and enhancing the detection sensitivity of various low-concentration endogenous and exogenous species. In this work, the analytic expressions for water exchange (WEX) filter spectroscopy, chemical exchange-dependent saturation transfer (CEST), and amide proton transfer (APT) experiments are derived by the use of Bloch equations with exchange terms. The effects of the initial states for the system, the difference between a steady state and a saturation state, and the relative contributions of the forward and backward exchange processes are discussed. The theory, in combination with numerical calculations, provides a useful tool for designing experimental schemes and assessing magnetization transfer (MT) processes between water protons and solvent-exchangeable protons. As an example, the case of endogenous amide proton exchange in the rat brain at 4.7 T is analyzed in detail.

Animals↗
PubMed2005

Effect of strong homonuclear proton coupling on localized (13)C detection using PRESS.

The effect of strong homonuclear proton coupling on (13)C incorporation measurements by either indirect or direct means was investigated (and illustrated with glutamate) both numerically and experimentally at 3.0 T. In particular, two sequences were considered, each using a proton PRESS sequence for localization. The indirect (13)C detection method incorporated the POCE (proton observe carbon edited) technique onto PRESS, and for direct (13)C detection a DEPT (distortionless enhancement by polarization transfer) sequence was appended to the PRESS localization. Both analysis and experiment demonstrate that when strong homonuclear coupling of protons is additional to heteronuclear coupling with (13)C spins, the (13)C measures derived from either the indirect PRESS-POCE sequence or the direct-but-enhanced PRESS-DEPT sequence are significantly modified. Specifically, the MR lineshapes of both (13)C-bonded and nonbonded protons are changed during (13)C incorporation, giving rise, for example, to a potential cross-contamination of < or =30% between glutamate (13)C(3) and (13)C(4) measures from the PRESS-POCE indirect method. During direct-but-enhanced detection, the DEPT enhancement is reduced for glutamate (13)C(2), (13)C(3), and (13)C(4) but not equally, and the reduction is further exacerbated by proton PRESS localization, which gives rise to enhancements that are strong functions of PRESS TE(1) and TE(2).

Algorithms↗
PubMed2001

Magnetic coupling between water and creatine protons in human brain and skeletal muscle, as measured using inversion transfer (1)H-MRS.

Using the inversion transfer technique, the possible magnetic coupling between water protons and the protons of low-molecular weight metabolites was investigated in human brain and skeletal muscle at 1.5 T. The localized (1)H-MR spectra were recorded at different times after selective inversion of the water resonance. Water inversion led to a significant transient reduction in the signal intensity of the methyl protons of creatine/phosphocreatine, in both tissues. This is indicative of magnetic coupling between the protons of water and those of creatine/phosphocreatine. Neither the choline and N-acetylaspartate protons in brain nor the protons of the trimethylammonium pool in skeletal muscle showed a significant magnetic coupling to mobile water.

Brain Chemistry↗
PubMed2004

New technologies in radiation therapy for pediatric brain tumors: the rationale for proton radiation therapy.

BACKGROUND: Pediatric brain tumors are frequently treated with radiation therapy and often cured. The long-term side effects of treatment with high-energy X-rays (photons) can be substantial. Proton radiation therapy may limit these late effects. PROCEDURE: The physical difference between photon and proton irradiation is compared. The clinical benefits of the superior physical properties of proton beam radiation therapy are explained for children with brain tumors. RESULTS: At biologically equivalent doses, proton radiation therapy offers tumor control similar to photon radiation therapy. The superior physical properties of proton beams make this mode of radiation therapy less likely to cause late effects. CONCLUSIONS: For many children with brain tumors, proton beam radiation therapy may limit the late effects of radiation therapy and therefore offer an advantage over techniques using photons.

Brain Neoplasms↗
PubMed2004

Calculating proton uptake/release and binding free energy taking into account ionization and conformation changes induced by protein-inhibitor association: application to plasmepsin, cathepsin D and endothiapepsin-pepstatin complexes.

The protein-inhibitor binding energies of enzymes are often pH dependent, and binding induces either proton uptake or proton release. The proton uptake/release and the binding energy for three complexes with available experimental data were numerically studied: pepstatin-cathepsin D, pepstatin-plasmepsin II and pepstatin-endothiapepsin. Very good agreement with the experimental data was achieved when conformational changes were taken into account. The role of the desolvation energy and the conformational changes was revealed by modeling the complex, the separated molecules in the complex conformation and the free molecules. It was shown that the conformational changes induced by the complex formation are as important for the proton transfer as the loss of solvation energy caused by the burial of interface residues. The residues responsible for the proton transfer were identified and their contribution to the proton uptake/release calculated. These residues were found to be scattered along the whole protein rather than being localized only at the active site. In the case of cathepsin D, these residues were found to be highly conserved among the cathepsin D sequences of other species. It was shown that conformation and ionization changes induced by the complex formation are critical for the correct calculation of the binding energy. Taking into account the electrostatics and the van der Waals (vdW) energies within the Boltzmann distribution of energies and allowing ionization and conformation changes to occur makes the calculated binding energy more realistic and closer to the experimental value. The interplay between electrostatic and vdW forces makes the pH dependence of the binding energy smoother, because the vdW force acts in reaction to the changes of the electrostatic energy. It was found that a small fraction of the ionizable groups remain uncharged in both the free and complexed molecules. The sequence and structural position of these groups aligns well within the three proteases, suggesting that these may have specific role.

Amino Acid Sequence↗
PubMed1988

Vibrational spectroscopy of bacteriorhodopsin mutants: I. Tyrosine-185 protonates and deprotonates during the photocycle.

The techniques of FTIR difference spectroscopy and site-directed mutagenesis have been combined to investigate the role of individual tyrosine side chains in the proton-pumping mechanism of bacteriorhodopsin (bR). For each of the 11 possible bR mutants containing a single Tyr----Phe substitution, difference spectra have been obtained for the bR----K and bR----M photoreactions. Only the Tyr-185----Phe mutation results in the disappearance of a set of bands that were previously shown to be due to the protonation of a tyrosinate during the bR----K photoreaction [Rothschild et al.: Proceedings of the National Academy of Sciences of the United States of America 83:347, (1986]). The Tyr-185----Phe mutation also eliminates a set of bands in the bR----M difference spectrum associated with deprotonation of a Tyr; most of these bands (e.g., positive 1272-cm-1 peak) are completely unaffected by the other ten Tyr----Phe mutations. Thus, tyrosinate-185 gains a proton during the bR----K reaction and loses it again when M is formed. Our FTIR spectra also provide evidence that Tyr-185 interacts with the protonated Schiff base linkage of the retinal chromophore, since the negative C = NH+ stretch band shifts from 1640 cm-1 in the wild type to 1636 cm-1 in the Tyr-185----Phe mutant. A model that is consistent with these results is that Tyr-185 is normally ionized and serves as a counter-ion to the protonated Schiff base. The primary photoisomerization of the chromophore translocates the Schiff base away from Tyr-185, which raises the pKa of the latter group and results in its protonation.

Amino Acid Sequence↗
PubMed2006

Collision-induced dissociation of protonated tetrapeptides containing beta-alanine, gamma-aminobutyric acid, epsilon-aminocaproic acid or 4-aminomethylbenzoic acid residues.

The influence of the presence and position of a single beta-alanine, gamma-aminobutyric acid, epsilon-aminocaproic acid or 4-aminomethylbenzoic acid residue on the tendency to form b(n)+ -and y(n)+ -type product ions was determined using a group of protonated tetrapeptides with general sequence XAAG, AXAG and AAXG (where X refers to the position of amino acid substitution). The hypothesis tested was that the 'alternative' amino acids would influence product ion signal intensities by inhibiting or suppressing either the nucleophilic attack or key proton transfer steps by forcing the adoption of large cyclic intermediates or blocking cyclization altogether. We found that specific b ions are diminished or eliminated completely when betaA, gammaAbu, Cap or 4AMBz residues are positioned such that they should interfere with the intramolecular nucleophilic attack step. In addition, differences in the relative proton affinities of the alternative amino acids influence the competition between complementary b(n) and y(n) ions. For both the AXAG and the XAAG series of peptides, collision-induced dissociation (CID) generated prominent b ions despite potential inhibition or suppression of intramolecular proton migration by the betaA, gammaAbu, Cap or 4AMBz residues. The prominent appearance of b ions from the AXAG and XAAG peptide is noteworthy, and suggests either that proton migration occurs through larger, 'whole' peptide cyclic intermediates or that fragmentation proceeds through a population of [M+H]+ isomers that are initially protonated at amide O atoms.

4-Aminobenzoic Acid↗
PubMed1993

A sensitive new fluorescence assay for measuring proton transport across liposomal membranes.

6-Methoxy-N-(3-sulfopropyl)-quinolinium (SPQ) is a fluorophore that is collisionally quenched by halide anions and is widely used to measure chloride ion transport across cellular and liposomal membranes. We report a new finding that SPQ fluorescence is also quenched by the zwitterionic hydrogen ion buffers introduced by Good et al. [(1966) Biochemistry 5, 467-477]. Although buffer quenching interferes with chloride ion measurements using SPQ, it can be turned to good advantage for measurements of proton flux. The basis for this application is that, for most buffers, the anion quenches and the zwitterion does not. Accordingly, buffer quenching of SPQ can be used to assay proton transport across liposomal membranes. We describe application of the technique to liposomes in which proton transport was mediated by ionophores and by the purified, reconstituted uncoupling protein of brown adipose tissue mitochondria. Because SPQ detects changes in buffer anion concentration, it can be used to measure changes in total acidity, which is the parameter desired when measuring net proton transport. Furthermore, this technique can be used to measure proton transport under conditions in which pH changes are minimized with buffers, and, consequently, effects of pH on proton transport can be dissociated from the transport itself.

Anions↗
PubMed1993

An efficient procedure for assignment of the proton, carbon and nitrogen resonances in 13C/15N labeled nucleic acids.

An efficient method is presented for the assignment of the proton, carbon, and nitrogen resonances in the NMR spectra of isotopically labeled nucleic acids. The assignment strategy starts by identifying all protons and carbons belonging to the same sugar ring through application of a set of 2D or 3D heteronuclear HCCH NMR experiments. Next the individual sugar rings are connected to their corresponding bases through intra-residue 1H-1H nuclear Overhauser effects (NOEs) observed in a 3D (1H, 13C, 1H) NOESY-HMQC experiment. Sequential NOE connectivities observed in this experiment are then used to assign each residue in the nucleotide sequence. The imino protons and nitrogens, and the cytidine amino protons and nitrogens, are assigned by 2D (15N, 1H) HMQC and 3D (1H, 15N, 1H) NOESY-HMQC experiments in H2O. This assignment procedure is illustrated on the 99% 13C/15N labeled RNA duplex r(GGCGCUUGCGUC)2. The application of these multi-dimensional heteronuclear magnetic resonance experiments enormously simplifies the resonance assignment of nucleic acids and allows assignment of many more protons, carbons and nitrogens than was possible using standard techniques on unlabeled molecules. Since a larger percentage of the protons can now be assigned by these experiments, much more NMR structural information can be obtained which will significantly extend the size limit for solution structure determinations of RNAs.

Base Sequence↗
PubMed2001

pK(a) Calculations suggest storage of an excess proton in a hydrogen-bonded water network in bacteriorhodopsin.

Calculations of protonation states and pK(a) values for the ionizable groups in the resting state of bacteriorhodopsin have been carried out using the recently available 1.55 A resolution X-ray crystallographic structure. The calculations are in reasonable agreement with the available experimental data for groups on or near the ion transport chain (the retinal Schiff base; Asp85, 96, 115, 212, and Arg82). In contrast to earlier studies using lower-resolution structural data, this agreement is achieved without manipulations of the crystallographically determined heavy-atom positions or ad hoc adjustments of the intrinsic pK(a) of the Schiff base. Thus, the theoretical methods used provide increased reliability as the input structural data are improved. Only minor effects on the agreement with experiment are found with respect to methodological variations, such as single versus multi-conformational treatment of hydrogen atom placements, or retaining the crystallographically determined internal water molecules versus treating them as high-dielectric cavities. The long-standing question of the identity of the group that releases a proton to the extracellular side of the membrane during the L-to-M transition of the photocycle is addressed by including as pH-titratable sites not only Glu204 and Glu194, residues near the extracellular side that have been proposed as the release group, but also an H(5)O(2)(+) molecule in a nearby cavity. The latter represents the recently proposed storage of the release proton in an hydrogen-bonded water network. In all calculations where this possibility is included, the proton is stored in the H(5)O(2)(+) rather than on either of the glutamic acids, thus establishing the plausibility on theoretical grounds of the storage of the release proton in bacteriorhodopsin in a hydrogen-bonded water network. The methods used here may also be applicable to other proteins that may store a proton in this way, such as the photosynthetic reaction center and cytochrome c oxidase.

Bacteriorhodopsins↗
PubMed1996

Synergetic mechanisms in energy and signal transduction: photo oscillating proton transport in bacteriorhodopsin.

Receptor proteins, linked with G-proteins and effector proteins, which act in signal information and energy transduction are key elements in biochemical systems that dissipate energy and rely on maintenance of order. Until now they have not yet been considered as elements for synergetic mechanisms. This paper describes the synergetic mechanisms of the archaebacterial signal and energy receptor bacteriorhodopsin (bR), for which, recently, light induced oscillations have been experimentally demonstrated. A synergetic mechanisms for proton pumping by this protein is presented. An important precondition is the ability of the molecule to significantly reduce its entropy (i.e. to increase its order through export of entropy) during the photo cycle. This should be paralleled by a systematic and organized change of pK values along the proton transducting "channel". The interaction of occupied and vacant protonation sites at such energized amino acid chains gives rise to feedback loops leading to an autocatalytic mechanism of proton transfer which, in combination with nonlinearities at the membrane interfaces and a time delay during the proton back flux, provides a simplified mechanism for oscillative light induced proton pumping. The expected relevance of autocatalytic and synergetic processes as inbuilt mechanisms for energy conversion and signal processing and the maintenance of order is discussed.

Amino Acids↗
PubMed1983

On the relation between rapid light-induced Ca2+ release and proton uptake in rod outer segment disk membranes.

In this paper we review our experiments on the light-induced Ca2+ release and proton uptake at the rod outer segment (ROS) disk membrane using flash-spectrophotometry and the indicating dyes arsenazo III and bromcresol purple. We used three different ROS preparations in order to locate the intracellular site of Ca2+ release. The ionophore A23187 was required to communicate the Ca2+ release to the indicator located in the external medium in both ROS with an intact and with a leaky plasma membrane. A23187 was also required to observe the Ca2+ released in the interior of vesicles prepared by sonication of ROS. From this we conclude that the site of Ca2+ release is located at the luminal side of the disk membrane, whereas this Ca2+ was not transported across the disk membrane under our experimental conditions and on the time scale of our experiments (20 s). Light-induced Ca2+ release was inhibited by electrolysis in the suspension medium provided that the electrolytes gained access to the compartment where Ca2+ was released. The effectivity to inhibit Ca2+ release markedly increased from monovalent to divalent to trivalent cations. The results strongly suggest that electrolytes (cations) act by screening the electrostatic potential at the disk membrane surface due to the presence of a net fixed negative surface charge. The surface potential controls the free Ca2+ concentration at the membrane surface and, therefore, controls the amount of Ca2+ bound to the disk membrane. The kinetics of light-induced Ca2+ release and proton uptake showed a similar dependence on the structural status of the ROS. In sonicated ROS almost linear Arrhenius plots were observed for metarhodopsin II formation, Ca2+ release and proton uptake (energy of activation 150 kJ/mol). In intact ROS both Ca2+ release and proton uptake showed a nonlinear Arrhenius plot with rate constants up to 30-fold slower than metarhodopsin II formation. At temperatures above 10 degrees C a process other than metarhodopsin II formation rate limited both ligh-induced proton uptake and Ca2+ release (energy of activation 42 kJ/mol). A model is discussed in which metarhodopsin II formation triggers the uptake of proton(s) into the disk membrane lowering the surface potential. A reduction potential of the surface in turn decreases the free Ca2+ concentration at the surface thereby causing the release of part of the bound Ca2+.

Acetates↗
PubMed1989

Vacuolar proton pumps.

Recently a new class of proton-translocating ATPases has been localized to endomembrane compartments in plant, fungal, and mammalian cells. These proton pumps are large hetero-oligomers which have an ATP hydrolytic sector that is functionally and structurally distinct from a transmembranous proton pore. Enzymatic characteristics of these proton pumps are discussed as well as the current state of knowledge regarding subunit composition and function. In addition, recent primary sequence data are discussed which indicate that these proton pumps share a common ancestor with F1F0-type proton pumps of mitochondria.

Animals↗