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At least 271 records · Page 15Linked to original sources
PubMed1987

Conformational analysis of the deoxyribofuranose ring in DNA by means of sums of proton-proton coupling constants: a graphical method.

A graphical method is presented for the conformational analysis of the sugar ring in DNA fragments by means of proton-proton couplings. The coupling data required for this analysis consist of sums of couplings, which are referred to as sigma 1' (= J1'2' + J1'2''), sigma 2' (= J1'2' + J2'3' + J2'2''), sigma 2'' (= J1'2'' + J2''3' + J2'2'') and sigma 3' (= J2'3' + J2''3' + J3'4'). These sums of couplings correspond to the distance between the outer peaks of the H1', H2', H2'' and H3' [31P] resonances, respectively, (except for sigma 2' and sigma 2'' in the case of a small chemical shift difference between the H2' and H2'' resonances) and can often be obtained from 1H-NMR spectra via first-order measurement, obviating the necessity of a computer-assisted simulation of the fine structure of these resonances. Two different types of graphs for the interpretation of the coupling data are discussed: the first type of graph serves to probe as to whether or not the sugar ring occurs as a single conformer, and if so to analyze the coupling data in terms of the geometry of this sugar ring. In cases where the sugar ring does not occur as a single conformer, but as a blend of N- and S-type sugar puckers, the second type of graph is used to analyze the coupling data in terms of the geometry and population of the most abundant form. It is shown that the latter type of analysis can be carried out on the basis of experimental values for merely sigma 1',sigma 2' and sigma 2'', without any assumptions or restrictions concerning a relation between the geometry of the N- and S-type conformer. In addition, the question is discussed as to how insight can be gained into the conformational purity of the sugar ring from the observed fine structure of the H1' resonance. Finally, a comparison is made between experimental coupling data reported for single-stranded and duplex DNA fragments and covalent RNA-DNA hybrids on the one hand and the predicted couplings and sums of couplings presented in this paper on the other hand.

Computer Graphics↗
PubMed1997

Proton NMR study of triantennary complex type N-linked glycan chains: assignment of proton chemical shifts of the beta-Man residue in a basic unit of the triantennary glycan chain having a GlcNAc beta 1-->6 Man alpha 1-->6 Man beta-->sequence.

The chemical shifts of ring protons of the beta-Man residue in a triantennary complex type N-linked glycan chain having a GlcNAc beta 1-->6(GlcNAc beta 1-->2)Man alpha 1-->6 Man beta sequence were unambiguously determined by two-dimensional proton nuclear magnetic resonance (1H-NMR) spectroscopic methods. The chemical shift of H4 (3.84 ppm) of the beta-Man residue was for the first time revealed to be different from those (approximately 3.77 ppm) of biantennary and alternative type of triantennary glycans having a GlcNAc beta 1-->2 Man alpha 1-->6 Man beta sequence, but quite close to that (3.86 ppm) of a pentaantennary glycan containing a GlcNAc beta 1-->6 residue on the Man alpha 1-->6 Man beta sequence. Thus, the addition of GlcNAc beta 1-->6 residue on the Man-4' residue, whose formation is catalyzed by GlcNAc transferase V, is considered to cause a down-field shift of beta-Man H4 in the complex-type N-glycan chains. One possible explanation of this phenomenon is that the conformation of Man alpha 1-->6 arm is folded back toward the proximal core region, as is the case with the complex-type N-glycan chains with the bisecting GlcNAc residue.

Acetylglucosamine↗
PubMed1995

Proton NMR study of the trimannosyl unit in a pentaantennary N-linked decasaccharide structure. Complete assignment of the proton resonances and conformational characterization.

The chemical shifts of all the ring protons of the three Man residues in a pentaantennary glycan chain have been unambiguously assigned by two-dimensional proton nuclear magnetic resonance (1H-NMR) spectroscopic methods. The study, using chemical shift and J values on the conformation of the trimannosyl unit, revealed that the rotamer about the C5-C6 bond of the alpha 1-->6 linkage in the sequence of Man alpha 1-->6Man beta 1--> is predominantly confined to a gauche-gauche rotamer (omega = 180 degrees, omega = O6-C6-C5-H5) and not to a gauche-trans rotamer (omega = -60 degrees). We do not know of any previous demonstration that the dihedral angle omega (O6-C6-C5-H5) in Man alpha 1-->6Man beta 1--> is preferentially 180 degrees in complex-type N-linked glycans having no bisecting GlcNAc residue.

Amino Acid Sequence↗
PubMedDate not supplied

Time resolved properties of acoustic pulses generated in water and in soft tissue by pulsed proton beam irradiation--a possibility of doses distribution monitoring in proton radiation therapy.

Time-resolved acoustic pulses generated in water and in soft tissue by pulsed proton beam irradiation were observed. The spatial resolution of depth dose distribution in the clinically applied beam intensity is estimated about 3 mm by means of TOF measurement. The dependence of the acoustic signal intensity on the temperature of medium was examined. Proportionality of acoustic pulse intensity to absorbed dose per pulse was confirmed as well. These results suggest the possibility of clinical application to monitor dose distribution in the patient's body during irradiation of pulsed proton beam.

Humans↗
PubMed1989

Active proton secretion and potassium absorption in the rabbit outer medullary collecting duct. Functional evidence for proton-potassium-activated adenosine triphosphatase.

We examined the hypothesis that proton-potassium-activated adenosine triphosphatase (H-K-ATPase) mediates K absorption and acidification in the inner stripe of the outer medullary collecting duct (OMCDi). Rabbits were fed a low-K diet (0.55% K) for 7-14 d because we have demonstrated previously that this low-K diet stimulates K-absorptive flux by the OMCDi. Proton secretion was measured as net total CO2 flux (JTCO2) by microcalorimetry. After basal collections, either vehicle or an inhibitor of gastric H-K-ATPase, omeprazole (0.1 mM), was added to the perfusate during the second period. Addition of vehicle to the perfusate changed neither the transepithelial voltage (VT, in millivolts) nor the JTCO2. In contrast, the addition of omeprazole (0.1 mM) to the perfusate abolished JTCO2 (from 14.5 +/- 5.6 to -0.1 +/- 3.1 pmol.mm-1.min-1) without significantly affecting VT. In additional experiments, in 16 tubules there was significant net K absorption (JK) of 5.0 +/- 1.0 pmol.mm-1.min-1 during the basal period, which exceeded the rate of K absorption that could be attributed to a paracellular voltage-mediated pathway (JKP = 1.0 +/- 0.4 pmol.mm-1.min-1, P less than 0.01). Administration of vehicle did not significantly affect either VT or JK. However, omeprazole abolished JK (from 5.1 +/- 1.0 to 0.1 +/- 2.5 pmol.mm-1.min-1) without affecting VT or JNa. The present results demonstrate that the OMCDi possesses an active, omeprazole-sensitive acidification and K-absorptive mechanism. These findings are consistent with the presence of H-K-ATPase activity in this nephron segment.

Absorption↗
PubMed2006

Charge delocalization in proton channels, II: the synthetic LS2 channel and proton selectivity.

In this study, the minimalist synthetic LS2 channel is used as a prototype to examine the selectivity of protons over other cations. The free-energy profiles along the transport pathway of LS2 are calculated for three cation species: a realistic delocalized proton (including Grotthuss shuttling)--H(+), a classical (nonshuttling) hydronium--H(3)O(+), and a potassium cation--K(+). The overall barrier for K(+) is approximately twice as large as that for H(+), explaining the >100 times larger maximal ion conductance for the latter, in qualitative agreement with the experimental result. The profile for the classical hydronium is quantitatively intermediate between those of H(+) and K(+) and qualitatively more similar to that of H(+), for which the locations of the peaks are well correlated with the troughs of the pore radius profile. There is a strong correlation between the free-energy profiles and the very different characteristic hydration structures of the three cation species. This work suggests that the passage of various cations through ion channels cannot always be explained by simple electrostatic desolvation considerations.

Biophysics↗
PubMed1982

1H-NMR studies on nucleotide binding to the sarcoplasmic reticulum Ca2+ ATPase. Determination of the conformations of bound nucleotides by the measurement of proton-proton transferred nuclear Overhauser enhancements.

The glycosidic bond torsion angles and the conformations of the ribose of Mg2+ATP, Mg2+ADP and Mg2+AdoPP[NH]P (magnesium adenosine 5'-[beta, gamma-imido]triphosphate) bound to Ca2+ATPase, both native and modified with fluorescein isothiocyanate (FITC), in intact sarcoplasmic reticulum have been determined by the measurement of proton-proton transferred nuclear Overhauser enhancements by 1H-NMR spectroscopy. This method shows clearly the existence of a low-affinity ATP binding site after modification of the high-affinity site with FITC. For all three nucleotides bound to both the high-affinity (catalytic) site and the low-affinity site, we find that the conformation about the glycosidic bond is anti, the conformation of the ribose 3'-endo of the N type and the conformation about the ribose C4'-C5' bond either gauche-trans or trans-gauche. The values for the glycosidic bond torsion angles chi (O4'-C1'-N9-C4) for Mg2+ATP, Mg2+ADP and Mg2+AdoPP[NH]P bound to the low-affinity site of FITC-modified Ca2+ATPase are approximately equal to 270 degrees, approximately equal to 260 degrees and approximately equal to 240 degrees respectively. In the case of the nucleotides bound to the high-affinity (catalytic) site of native Ca2+ATPase, chi lies in the range 240-280 degrees.

Adenosine Diphosphate↗
PubMed2005

Protonation, deprotonation, and protonation: conjugated photochemical reactions of ferrocenylazophenol.

4-Ferrocenylazophenol (FAP) and 8-(4-ferrocenylazophenoxy)octanyl-1-bromide (FAOB) have been synthesized and their protonation and photochemical behavior have been investigated. FAP showed reversible protonation and deprotonation behavior in the presence of trifluoroacetic acid and potassium tert-butylate, respectively. FAP and FAOB exhibit high photoreactivity, which was induced through excitation of not only the pi-pi* band by UV light but also the d-pi* band by green light. The photoreaction of FAP and FAOB in ethanol or acetonitrile with a trace amount of water afforded phenylhydrazonocyclopentadiene (PHP) derivatives, indicating that hydrolysis of the photoexcited species occurs.

Journal Article↗
PubMed1994

An evaluation of least-squares fits to COSY spectra as a means of estimating proton-proton coupling constants. II. Applications to polypeptides.

A new computational method for simultaneously estimating all the proton-proton coupling constants in a molecule from COSY spectra [Yang, J.-X. and Havel, T.F. (1994) J. Biomol. NMR, 4, 807-826] is applied to experimental data from two polypeptides. The first of these is a cyclic hexapeptide denoted as VDA (-D-Ala1-Phe2-Trp3-Lys(Z)4-Val5-Phe6-), in deuterated DMSO, while the second is a 39-residue protein, called decorsin, in aqueous solution. The effect of different data processing strategies and different initial parameter values on the accuracy of the coupling constants was explored. In the case of VDA, most of the coupling constants did not depend strongly on the initial values chosen for the optimization or on how the data were processed. This, together with our previous experience using simulated data, implies strongly that these values are accurate estimates of the coupling constants. They also differ by an average of only 0.36 Hz from the values of the 14 coupling constants that could be measured independently by established methods. In the case of decorsin, many of the coupling constants exhibited a moderate dependence on their initial values and a strong dependence on how the data were processed. With the most successful data processing strategy, the amide-alpha coupling constants differed by an average of 1.11 Hz from the 21 values that could be measured by established methods, while two thirds of the three-bond coupling constants fell within 1.0 Hz of the ranges obtained by applying the Karplus relation to an independently computed ensemble of distance geometry structures. The averages of the coupling constants over multiple optimizations using random initial values were computed in order to obtain the best possible estimates of the coupling constants. Most clearly incorrect averages can be identified by large standard deviations in the coupling constants or the associated line widths and chemical shifts, and can be explained by strong coupling and/or overlap with the water signal, the diagonal peaks or other cross peaks.

Amino Acid Sequence↗
PubMed1980

Conformational analysis of ribonucleosides from proton-proton coupling constants.

A graphical method is described which permits the determination in solution of conformational equilibria and parameters of ribonucleosides from proton-proton coupling constants. The method is based on the pseudorotational concept and the use of the Karplus equation. Using a large number of 1H-NMR data on ribonucleosides from the literature, on optimal set of Karplus constants, A = 10.0, B = -1.2, was obtained. It is shown that this set of Karplus constants, in connection with the pseudorotational treatment, describes satisfactorily the nucleoside conformations, especially the pucker amplitude. The solution results are compared with X-ray data and the differences are discussed. The method can be used either graphically or by direct computer treatment of the data.

Magnetic Resonance Spectroscopy↗
PubMed1984

Internal mobility in a double-stranded B DNA hexamer and undecamer. A time-dependent proton-proton nuclear Overhauser enhancement study.

The internal mobility of the deoxyribose H2'-H2" and base C(H5)-C(H6) and T(CH3)-T(H6) vectors has been investigated by means of time-dependent nuclear Overhauser enhancement (NOE) measurements in a B DNA hexamer and undecamer. Cross-relaxation rates between these proton pairs are determined from the initial slopes of the time development of the NOEs, and, as the interproton distances between these proton pairs are fixed, apparent correlation times for the 3 interproton vectors are calculated from the cross-relaxation rate data. It is shown that there is little residue to residue variation in the cross-relaxation rates of the interproton vectors within each oligonucleotide, that the mean apparent correlation times of the C(H5)-C(H6) and T(CH3)-T(H6) vectors are approximately equal and significantly greater than that of the H2'-H2" vectors, and that the data for the H2'-H2" vectors of both oligonucleotides and the C(H5)-C(H6) and T(CH3)-T(H6) vectors of the undecamer cannot be accounted for by isotropic tumbling alone. The data are analysed in terms of a two motion model with isotropic tumbling and a single internal motion. The relaxation time of the internal motion at 23 degrees C is less than or equal to 1 ns for the H2'-H2" vectors of both oligonucleotides and less than or equal to 3 ns for the C(H5)-C(H6) and T(CH3)-T(H6) vectors of the undecamer. In the case of the H2'-H2" vectors, however, the amplitude of the internal motion is found to be too large to be compatible with the known stereochemistry of DNA. This finding can only be explained by invoking additional degrees of internal freedom with a larger number of internal motions of small amplitude of the type deduced from the analysis of crystallographic thermal factors [(1984) J. Mol. Biol. 173, 361-388].

Chemical Phenomena↗
PubMed2004

Monocyclopentadienylhydride derivatives of ruthenium: stereoselective proton transfer and proton-hydride exchange in an extremely short dihydrogen bond.

Diastereomerically pure complexes of formula CpRuCl(PP) and CpRuH(PP) with chiral ferrocenyl diphosphines were prepared and the selectivity of proton-transfer processes over the monohydride compounds with different acids was studied. With 1 equiv of HBF(4) the cis-dihydrogen and trans-dihydride complexes were formed while with 3 equiv of CF(3)CO(2)H the trans-dihydride derivative was the only product. However, the use of 1 equiv of CF(3)CO(2)H led to a dihydrogen bonded complex with an extremely short RuH...HO(2)CF(3) interaction that exhibits proton-hydride exchange. Using the labeled acid CF(3)CO(2)D, a stereoselective transference of the deuteron was demonstrated that implies the previous epimerization of the monohydride and the subsequent attack of the acid in the position previously occupied by the hydride.

Journal Article↗
PubMed2005

NMR relaxation study of the protonated form of 1,8-Bis(dimethylamino)naphthalene in isotropic solution: anisotropic motion outside of extreme narrowing and ultrafast proton transfer.

The protonated form of 1,8-bis(dimethylamino)naphthalene (DMANH(+)) consists of a rigid, aromatic framework, substituted by two amino groups that are connected by a strong, symmetric (on the NMR time-scale) hydrogen bond bridge. The reorientational motion of the molecule in dimethylformamide-d7 solution was characterized by T(1) and NOE measurements for aromatic (13)C nuclei. Treating the reorientation of DMANH(+) as anisotropic rotational diffusion of a rigid body, the diffusion tensor was determined with good accuracy. Measurements and interpretation of (15)N T(1) and NOE indicate that the proton transfer between potential minima in the hydrogen bond bridge is faster than the molecular reorientation.

Journal Article↗
PubMed2006

Hydrogen transfer between sulfuric acid and hydroxyl radical in the gas phase: competition among hydrogen atom transfer, proton-coupled electron-transfer, and double proton transfer.

In an attempt to assess the potential role of the hydroxyl radical in the atmospheric degradation of sulfuric acid, the hydrogen transfer between H2SO4 and HO* in the gas phase has been investigated by means of DFT and quantum-mechanical electronic-structure calculations, as well as classical transition state theory computations. The first step of the H2SO4 + HO* reaction is the barrierless formation of a prereactive hydrogen-bonded complex (Cr1) lying 8.1 kcal mol(-1) below the sum of the (298 K) enthalpies of the reactants. After forming Cr1, a single hydrogen transfer from H2SO4 to HO* and a degenerate double hydrogen-exchange between H2SO4 and HO* may occur. The single hydrogen transfer, yielding HSO4* and H2O, can take place through three different transition structures, the two lowest energy ones (TS1 and TS2) corresponding to a proton-coupled electron-transfer mechanism, whereas the higher energy one (TS3) is associated with a hydrogen atom transfer mechanism. The double hydrogen-exchange, affording products identical to reactants, takes place through a transition structure (TS4) involving a double proton-transfer mechanism and is predicted to be the dominant pathway. A rate constant of 1.50 x 10(-14) cm(3) molecule(-1) s(-1) at 298 K is obtained for the overall reaction H2SO4 + HO*. The single hydrogen transfer through TS1, TS2, and TS3 contributes to the overall rate constant at 298 K with a 43.4%. It is concluded that the single hydrogen transfer from H2SO4 to HO* yielding HSO4* and H2O might well be a significant sink for gaseous sulfuric acid in the atmosphere.

Journal Article↗
PubMed1992

Taxol: quantitative internuclear proton-proton distances in CDCl3 solution from nOe data: 2D nmr ROESY buildup rates at 500 MHz.

Quantitative nmr internuclear proton-proton distance measurements obtained by observation of the initial buildup rates of nOe's in 2D ROESY spectra of taxol [1] in CDCl3 are reported. A comparison to the X-ray crystal structure of taxotere [2] is made, and the results are discussed in terms of previous studies of structure-activity relationships.

Antineoplastic Agents, Phytogenic↗
PubMed2001

Sugar conformation of a stereospecific 2'-R or 2'-S deuterium-labeled DNA decamer studied with proton-proton J coupling constants.

The sugar conformation of a DNA decamer was studied with proton-proton 3J coupling constants. Two samples, one comprising stereospecifically labeled 2'-R-2H for all residues and the other 2'-S-2H, were prepared by the method of Kawashima et al. [J. Org. Chem. (1995) 60, 6980-6986; Nucleosides Nucleotides (1995) 14, 333-336], the deuterium labeling being highly stereospecific (> or = 99% for all 2''-2H, > or = 98% for 2'-2H of A, C, and T, and > or = 93% for 2'-2H of G). The 3J values of all H1'-H2' and H1'-H2'' pairs, and several H2'-H3' and H2''-H3' pairs were determined by line fitting of 1D spectra with 0.1-0.2 Hz precision. The observed J coupling constants were explained by the rigid sugar conformation model, and the sugar conformations were found to be between C3'-exo and C2'-endo with phi(m) values of 26 degrees to 44 degrees, except for the second and 3' terminal residues C2 and C10. For the C2 and C10 residues, the lower fraction of S-type conformation was estimated from JH1'H2' and JH1'H2'' values. For C10, the N-S two-site jump model or Gaussian distribution of the torsion angle model could explain the observed J values, and 68% S-type conformation or C1'-exo conformation with 27 degrees distribution was obtained, respectively. The differences between these two motional models are discussed based on a simple simulation of J-coupling constants.

Carbohydrate Conformation↗
PubMed2006

Correlated proton motion in hydrogen bonded systems: tuning proton affinities.

The theorem of matching proton affinities (PA) has been widely used in the analysis of hydrogen bonds. However, most experimental and theoretical investigations have to cope with the problem that the variation of the PA of one partner in the hydrogen bond severely affects the properties of the interface between both molecules. The B3LYP/d95+(d,p) analysis of two hydrogen bonds coupled by a 5-methyl-1H-imidazole molecule showed that it is possible to change the PA of one partner of the hydrogen bond while maintaining the properties of the interface. This technique allowed us to correlate various properties of the hydrogen bond directly with the difference in the PAs between both partners: it is possible to tune the potential energy surface of the bonding hydrogen atom from that of an ordinary hydrogen bond (localized hydrogen atom) to that of a low barrier hydrogen bond (LBHB, delocalized hydrogen atom) just by varying the proton affinity of one partner. This correlation shows clearly that matching PAs are of lesser importance for the formation of a LBHB than the relative energy difference between the two tautomers of the hydrogen bond.

Journal Article↗