Hydrogen-deuterium Exchange Kinetics Research Articles

"Asymmetric" opening reaction mechanism of Z-DNA base pairs: a hydrogen exchange study.

With the tritium-Sephadex method, the hydrogen-exchange kinetics of the five NH protons of guanine and cytosine residues in Z-form poly(dG-dC) X poly (dG-dC) were measured as a function of temperature and catalyst concentration. Over the measured temperature range from 0 to 34 degrees C, two classes of protons with constant amplitudes are found. The three protons of the fast class, which were assigned to the guanine amino and imino protons, have an exchange half-time in the minute time range (at 20 degrees C the half-time is 2.5 min) and an activation energy of 18 kcal mol-1. Since these two types of protons exchange at the same rate in spite of their grossly different pK values, the exchange of these protons must be limited by the same nucleic acid conformational change. The two cytosine amino protons of the slow class are especially slow with exchange half-times in the hour time range (at 20 degrees C the exchange half-time is 1 h) and the activation energy is 20 kcal mol-1. The exchange of these two protons is not limited by some nucleic acid conformational change as shown by the marked exchange acceleration of these protons upon addition of 0.2 M imidazole. In addition, we have also reexamined the hydrogen-deuterium exchange kinetics of the amino protons of guanosine cyclic 2',3'-monophosphate by a spectral difference method using a stopped-flow spectrophotometer. The measured kinetic process is monophasic with a rate constant of 3 s-1 at 20 degrees C, which is in the same range as the predicted rate constant of the guanine amino protons.(ABSTRACT TRUNCATED AT 250 WORDS)

Effect of B-Z transition and nucleic acid structure on the conformational dynamics of bound ethidium dimer measured by hydrogen deuterium exchange kinetics.

Ethidium dimer is shown to bind by intercalation, almost equally well, to the B and Z form of poly[(dG-m5dC)].poly[(dG-m5dC)], whereas the ethidium monomer shows a strong preference for the B form. The hydrogen-deuterium (H-D) exchange kinetics of the ethidium dimer bound to the B and Z form of poly [(dG-m5dC)].poly[(dG-m5dC)] could then be compared. The kinetics of the H-D exchange were strikingly slower when the dye was bound to Z DNA as compared to B DNA. The exchange kinetics were also modified when ethidium dimer was bound to tRNA and to a triple stranded structure. It is proposed that a dynamic fluctuation at the level of the nucleic acid could modulate the dynamic fluctuation at the level of the bound ligand.

Dynamic structure of DNA complexes. Fluorometric measurement of hydrogen-deuterium exchange kinetics of dna-bound ethidium dimer and acridine-ethidium dimer.

The hydrogen-deuterium (H-D) exchange kinetics of free and DNA-bound ethidium dimer and acridine-ethidium heterodimer were measured by stopped flow using fluorescence detection. This technique allowed a very accurate measurement of the exchange process. The H-D exchange kinetics were measured in various environments. In some cases, it was observed that the H-D exchange was much faster than the dissociation rate of dimer-DNA complexes. This showed that the exchange was taking place directly from the bound state. Furthermore, the action of a catalyst (imidazolium ion) on the rate of H-D exchange showed that a dynamic structural fluctuation of the ligand in its DNA complex was a necessary step on the exchange process.

Effects of ADP and AMPPNP on the hydrogen-deuterium exchange kinetics in Ca2+, Mg2+-ATpase of sarcoplasmic reticulum.

The kinetics of the hydrogen-deuterium exchange reaction in sarcoplasmic reticulum (SR) membranes isolated from rabbit skeletal muscle was followed by infrared absorption measurements. The exchange rate in SR was much lower than that in the soluble proteins reported so far. When adenylyl-imidophosphate (AMPPNP, an TP analog) was present, the exchange rate was lower than that in free SR and it was the lowest when ADP was present. The effect of the nucleotides on the exchange rate reflects the conformational change of the Ca2+, Mg2+-ATpase of SR membranes on binding the nucleotides. The structure of e Ca2+, Mg2+-ATPase is more restricted in the following order: SR + ADP greater than SR + AMPPNP greater than free SR.

Temperature-induced change in the Ca2+-dependent ATPase activity and in the state of the ATPase protein of sarcoplasmic reticulum membrane.

The temperature dependence of the Ca2+-dependent ATPase activity and of the conformational fluctuation of the ATPase molecule has been measured for four kinds of preparations: fragmented sarcoplasmic reticulum, MacLennan's enzyme (purified ATPase preparation), and DOL and egg PC-ATPase (purified ATPase preparations in which lipids are replaced with dioleoyllecithin and egg yolk lecithin, respectively). It has been found that Arrhenius plots of the Ca2+-dependent ATPase activity show a break at about 18 degrees C for all the preparations. Hydrogen--deuterium exchange kinetics of the peptide NH protons were used to measure the conformational fluctuation of the protein molecules. Van't Hoff plots of the conformational fluctuation amplitude of a region near the surface of the ATPase molecule also show a break at about 18 degrees C for all the preparations. It is concluded that the break at around 18 degrees C is not related to a gel-liquid crystalline transition of lipids but to a change in the conformation of the ATPase molecule existing in fluid lipids.

Quantitative 250 MHz proton magnetic resonance study of hydrogen-deuterium exchange Angiotensin II hormone in trifluoroethanol

Hydrogen-deuterium exchange kinetics of (Asn 1-Val 5) angiotensin II has been investigated by proton magnetic resonance at 250 MHz in deuterated trifluoroethanol, as an approach to the “in situ” hormone conformation. An interactive program was specially developed to perform the data analysis on a computer similar to those used for spectroscopic data acquisition. Nine exchange sites are evidenced and characterized by their individual kinetic parameters. Three of them are assigned to peptide NH hydrogens. and the six remaining to slowly exchanging side chain protons. At 11 °C, more than three peptide hydrogens, sterically hindered or involved in hydrogen bonds, do not exchange. These results corroborate previous circular dichroism and infrared investigations performed in the same solvent, and suggest a family of well-folded conformations, stabilized in trifluoroethanol by internal hydrogen bonds, involving both the backbone and the side chain hydrogens.

Hydrogen-deuterium exchange kinetics of the C-2 protons of imidazole and histidine compounds.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydrogen-deuterium exchange kinetics of the C-2 protons of imidazole and histidine compoundsJ. H. Bradbury, B. E. Chapman, and F. A. PellegrinoCite this: J. Am. Chem. Soc. 1973, 95, 18, 6139–6140Publication Date (Print):September 1, 1973Publication History Published online1 May 2002Published inissue 1 September 1973https://doi.org/10.1021/ja00799a063RIGHTS & PERMISSIONSArticle Views297Altmetric-Citations51LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (255 KB) Get e-Alerts Get e-Alerts

Solution conformation of the ferrichromes: III. A comparative proton magnetic resonance study of glycineand serine-containing ferrichromes

Ferrichrome, ferricrocin, ferrichrysin and ferrichrome A are ferric cyclohexapeptides whose general primary composition is represented by ▪ where the Res 2,3 sites are occupied by glycyl or l-seryl residues and Orn 1,2,3 stands for δ- N-acyl-δ- N-hydroxy- l-ornithyl. The latter provide the hydroxamate ligands which co-ordinate the metal ion. The 220 MHz proton magnetic resonance spectra of Al 3+ and Ga 3+ chelates of the four homologous peptides in aqueous and in deutero-dimethylsulfoxide solutions are reported and analyzed in terms of the molecular conformations. In both solvents the chemical shifts of the amide proton resonances and their temperature dependences are consistent with a structure containing two transannular hydrogen bonds, as in the Schwyzer model for cyclohexapeptides. The metal ion enforces the structure of the peptide backbone; thus, the reported conformational differences resulting from residue substitutions at sites 2 and 3, as well as from solvation effects, are virtually eliminated upon its binding. The chelates exhibit pronounced chemical shift differences among the amide N H's with markedly reduced temperature dependences for four of them. Gross amide hydrogendeuterium exchange kinetics in 2H 2O indicates that these four amides have a highly diminished interaction with the solvent. The comparative spectra of the analogous chelates permits unequivocal assignments of all proton resonances to residues in the absolute sequence. The magnitude of the amide N HC a H spin-spin couplings yields estimates of the conformational φ dihedral angles. Aside from slight seryl side-chain solvation pressures, the proton magnetic resonance data for the chelates in solution are in good agreement with the static X-ray crystallographic model for ferrichrome A.