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Berlin Brandenburg

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  • 1
    Language: English
    In: The journal of physical chemistry. B, 01 October 2015, Vol.119(39), pp.12644-52
    Description: The paramagnetic relaxation times of the aromatic and β protons of Tyr59 and His68 residues of the native ubiquitin and of Tyr59 residue of the non-native ubiquitin were determined from an analysis of chemically induced dynamic nuclear polarization (CIDNP) kinetics obtained during the photoreaction of the protein and 2,2'-dipyridyl excited in the triplet state. Using the paramagnetic relaxation times determined earlier for the radicals of free amino acids as an internal standard and assuming that the hyperfine interaction (HFI) anisotropy is very similar for the radicals of free amino acids and the corresponding radicals of amino acid residues in the proteins, we determined parameters that characterize the intramolecular mobility of different protons in native and two non-native states of ubiquitin. The latter are denatured at pH 2 and 57 °C, and the A-state at pH 2 in a 60%/40% methanol/water mixture. The determination of the two parameters of intramolecular mobility (i.e., the correlation time of internal motion, τ(e), and the order parameter, S(2)) was only possible by analyzing paramagnetic relaxation data obtained at two magnetic fields (4.7 and 9.4 T) using nuclear magnetic resonance (NMR) spectrometry. Intramolecular correlation times fall into the submicrosecond-microsecond time scale. Longer correlation times and higher order parameters were found for the less accessible Tyr59 residue than for the His68 residue, as well as for the more buried β protons than for the aromatic protons for both of the protein residues in the native state. For Tyr59, intramolecular mobility increases following the loss of the tertiary structure of ubiquitin. These findings strongly support the reliability of the obtained data.
    Keywords: Ubiquitin -- Chemistry
    ISSN: 15206106
    E-ISSN: 1520-5207
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  • 2
    Language: English
    In: The journal of physical chemistry. B, 11 October 2012, Vol.116(40), pp.12221-6
    Description: Intramolecular electron transfer (IET) in the oxidized dipeptide Tyr-Trp was investigated in the pH range from 1.0 to 3.1 by the method of time-resolved chemically induced dynamic nuclear polarization. The results were compared with data obtained earlier for Trp-Tyr. Surprisingly, it was found that the direction of IET changes with the order of the amino acid residues in the peptide. For Tyr-Trp, the rate constant of electron transfer from tyrosine residue to tryptophanyl cation radical is below 1.2 × 10(4) s(-1), whereas for Trp-Tyr, the value of this rate constant is 5.5 × 10(5) s(-1). Conversely, for oxidized Tyr-Trp at pH range 2.1 and lower, electron transfer from tryptophan residue to tyrosyl radical is observed. The rate constant of this reaction is proportional to the concentration of protons in aqueous solution, and at pH 1.0 is equal to 6.5 × 10(5) s(-1). The change in direction of IET observed for oxidized Tyr-Trp dipeptide is presumably due to the positive charge at the N-terminal amino group of the peptide, which promotes electron transfer in the direction of the N-terminus.
    Keywords: Dipeptides -- Chemistry ; Tryptophan -- Chemistry ; Tyrosine -- Chemistry
    ISSN: 15206106
    E-ISSN: 1520-5207
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  • 3
    Language: English
    In: The journal of physical chemistry. B, 19 July 2012, Vol.116(28), pp.8058-63
    Description: As a model for chemical DNA repair, reduction of guanosyl radicals in the reaction with cysteine or the dipeptide cysteine-glycine has been studied by time-resolved chemically induced dynamic nuclear polarization (CIDNP). Radicals were generated photochemically by pulsed laser irradiation of a solution containing the photosensitizer 2,2'-dipyridyl, guanosine-5'-monophosphate, and the amino acid or peptide. In neutral and basic aqueous solution, the neutral guanosyl radical is formed via electron or hydrogen atom transfer to the triplet excited dye. The rate constants for reduction of guanosyl radical were determined by quantitative analysis of the CIDNP kinetics, which are sensitive to the rates of fast radical reactions. The rate constants vary from (1.0 ± 0.3) × 10(7) M(-1) s(-1) for the thiol form of cysteine to (1.6 ± 0.2) × 10(8) M(-1) s(-1) for the thiolate anion. These values are comparable with corresponding rate constants for reduction of neutral guanosyl radical by tyrosine.
    Keywords: Cysteine -- Chemistry ; Glycine -- Chemistry ; Guanosine Monophosphate -- Chemistry
    ISSN: 15206106
    E-ISSN: 1520-5207
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  • 4
    Language: English
    In: The journal of physical chemistry. B, 08 January 2015, Vol.119(1), pp.140-9
    Description: Time-resolved chemically induced dynamic nuclear polarization (CIDNP) was used to investigate reversible intramolecular electron transfer (IET) in short-lived oxidized peptides, which had different structures and contained tryptophan and tyrosine residues, in an acidic aqueous solution with a pH below the pKa of the tryptophanyl cation radical. The CIDNP kinetic data were obtained at the microsecond scale and were analyzed in detail to calculate the rate constants for electron transfer in both directions: from the tyrosine residue to the tryptophanyl cation radical, kf, and from the tryptophan residue to the neutral tyrosyl radical, kr. The charge of the terminal amino group and the presence of glycine and proline spacers were shown to strongly affect the rate constants of the reaction under study. Among these functional groups, the presence and the location of the positive charge on the amino group in close proximity to the cationic indolyl radical had the strongest effect on the rate constant of the forward IET from the tyrosine residue to the tryptophanyl radical cation, kf. This effect was manifested as an increase of 2 orders of magnitude in kf for a change in the linkage order between residues in the dipeptide: kf = 4 × 10(3) s(-1) for the oxidized Tyr-Trp increased to kf = 5.5 × 10(5) s(-1) in oxidized Trp-Tyr. The reverse rate constant for IET was less sensitive to the amino group charge. Moreover, the presence of glycine or proline spacers in the peptides with a tryptophan residue at the N-terminus not only reduced the IET rate constant but also shifted the equilibrium of the IET in the reaction under study toward the formation of tyrosyl radicals with respect to the peptide Trp-Tyr. That is, the glycine or proline spacers affected the difference in the reduction potential of the tryptophanyl and tyrosyl radicals.
    Keywords: Peptides -- Chemistry ; Tryptophan -- Chemistry ; Tyrosine -- Chemistry
    ISSN: 15206106
    E-ISSN: 1520-5207
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  • 5
    Language: English
    In: The journal of physical chemistry. A, 10 July 2014, Vol.118(27), pp.4966-74
    Description: The photo-oxidation of purine nucleotides adenosine-5'-monophosphate (AMP) and guanosine-5'-monophosphate (GMP) by 3,3',4,4'-benzophenone tetracarboxylic acid (TCBP) has been investigated in aqueous solutions using nanosecond laser flash photolysis (LFP) and time-resolved chemically induced dynamic nuclear polarization (CIDNP). The pH dependences of quenching rate constants and of geminate polarization are measured within a wide range of pH values. As a result, the chemical reactivity of reacting species in different protonation states is determined. In acidic solution (pH 9.4), kq = 1.0 × 10(8) M(-1) s(-1) (AMP, pH 〉 6.5). Surprisingly, the strong influence of the protonation state of the phosphoric group on the oxidation of adenosine-5'-monophosphate is revealed: the deprotonation of the AMP phosphoric group (6.5) decreases the quenching rate constant from 5.0 × 10(8) M(-1) s(-1) (4.9 6.5).
    Keywords: Hydrogen-Ion Concentration ; Benzophenones -- Chemistry ; Carboxylic Acids -- Chemistry ; Purine Nucleotides -- Chemistry
    ISSN: 10895639
    E-ISSN: 1520-5215
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  • 6
    Language: English
    In: The journal of physical chemistry. B, 29 October 2015, Vol.119(43), pp.13619-29
    Description: A new technique is developed that allows one to carry out the signal amplification by reversible exchange (SABRE) experiments at high magnetic field. SABRE is a hyperpolarization method, which utilizes transfer of spin order from para-hydrogen to the spins of a substrate in transient iridium complexes. Previously, it has been thought that such a transfer of spin order is only efficient at low magnetic fields, notably, at level anti-crossing (LAC) regions. Here it is demonstrated that LAC conditions can also be fulfilled at high fields under the action of a RF field. The high-field RF-SABRE experiment can be implemented using commercially available nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) machines and does not require technically demanding field-cycling. The achievable NMR enhancements are around 100 for several substrates as compared to their NMR signals at thermal equilibrium conditions at 4.7 T. The frequency dependence of RF-SABRE is comprised of well pronounced peaks and dips, whose position and amplitude are conditioned solely by the magnetic resonance parameters such as chemical shifts and scalar coupling of the spin system involved in the polarization transfer and by the amplitude of the RF field. Thus, the proposed method can serve as a new sensitive tool for probing transient complexes. Simulations of the dependence of magnetization transfer (i.e., NMR signal amplifications) on the frequency and amplitude of the RF field are in good agreement with the developed theoretical approach. Furthermore, the method enables continuous re-hyperpolarization of the SABRE substrate over a long period of time, giving a straightforward way to repetitive NMR experiments.
    Keywords: Amplitude ; Magnetic-Field ; Exchange ; Chemical-Shift ; Thermal-Equilibrium ; Iridium-Complex ; Spinning-System ; Hydrogen ; Magnetisation-Transfer ; Amplitude ; Magnetisches Feld ; Austausch ; Chemische Verschiebung ; Thermisches Gleichgewicht ; Iridiumkomplex ; Spinnsystem ; Wasserstoff ; Magnetisierungstransfer ; Chemistry;
    ISSN: 15206106
    E-ISSN: 1520-5207
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  • 7
    Language: English
    In: The journal of physical chemistry. A, 16 January 2014, Vol.118(2), pp.339-49
    Description: The kinetics of the photooxidation of aromatic amino acids histidine (His), tyrosine (Tyr), and tryptophan (Trp) by 3,3',4,4'-benzophenonetetracarboxylic acid (TCBP) has been investigated in aqueous solutions using time-resolved laser flash photolysis and time-resolved chemically induced dynamic nuclear polarization. The pH dependence of quenching rate constants is measured within a large pH range. The chemical reactivities of free His, Trp, and Tyr and of their acetylated derivatives, N-AcHis, N-AcTyr, and N-AcTrp, toward TCBP triplets are compared to reveal the influence of amino group charge on the oxidation of aromatic amino acids. The bimolecular rate constants of quenching reactions between the triplet-excited TCBP in the fully deprotonated state and tryptophan, histidine, and tyrosine with a positively charged amino group are kq = 2.2 × 10(9) M(-1) s(-1) (4.9 9.4), kq = 3.0 × 10(8) M(-1) s(-1) (pH 〉 9.2), and kq = (4.0-10.0) × 10(8) M(-1) s(-1) (9.0 〈 pH 〈 10.1) that are close to those for the N-acetylated derivatives. Thus, it has been established that the presence of charged amino group changes oxidation rates by a significant factor; i.e., His with a positively charged amino group quenches the TCBP triplets 5 times more effectively than N-AcHis and His with a neutral amino group. The efficiency of quenching reaction between the TCBP triplets and Tyr and Trp with a positively charged amino group is about 3 times as high as that of both Tyr and Trp with a neutral amino group, N-AcTyr and N-AcTrp.
    Keywords: Amino Acids, Aromatic -- Chemistry
    ISSN: 10895639
    E-ISSN: 1520-5215
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  • 8
    In: Physical Chemistry Chemical Physics, 2014, Vol.16(16), pp.7584-7594
    Description: Magnetic field dependence of long-lived spin states (LLSs) of the -CH 2 protons of aromatic amino acids was studied. LLSs are spin states, which are immune to dipolar relaxation, thus having lifetimes far exceeding the longitudinal relaxation times; the simplest example of an LLS is given by the singlet state of two coupled spins. LLSs were created by means of the photo-chemically induced dynamic nuclear polarization technique. The systems studied were amino acids, histidine and tyrosine, with different isotopomers. For labeled amino acids with the -CH and aromatic protons substituted by deuterium at low fields the LLS lifetime, T LLS , for the -CH 2 protons was more than 40 times longer than the T 1 -relaxation time. Upon increasing the number of protons the ratio T LLS / T 1 was reduced; however, even in the fully protonated amino acids it was about 10; that is, the long-lived mode was still preserved in the system. In addition, the effect of paramagnetic impurities on spin relaxation was studied; field dependencies of T 1 and T LLS were measured. LLSs were also formed in tyrosine-containing dyads; a T LLS / T 1 ratio of 7 was found, usable for extending the spin polarization lifetime in such systems.
    Keywords: Chemistry;
    ISSN: 1463-9076
    E-ISSN: 1463-9084
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  • 9
    Language: English
    In: The journal of physical chemistry. A, 08 November 2012, Vol.116(44), pp.10668-75
    Description: The kinetics of triplet state quenching of 3,3',4,4'-benzophenone tetracarboxylic acid (BPTC) by DNA bases adenine, adenosine, thymine, and thymidine has been investigated in aqueous solution using time-resolved laser flash photolysis. The observation of the BPTC ketyl radical anion at λ(max) = 630 nm indicates that one electron transfer is involved in the quenching reactions. The pH-dependence of the quenching rate constants is measured in detail. As a result, the chemical reactivity of the reactants is assigned. The bimolecular rate constants of the quenching reactions between triplet BPTC and adenine, adenosine, thymine, and thymidine are k(q) = 2.3 × 10(9) (4.7 〈 pH 〈 9.9), k(q) = 4.0 × 10(9) (3.5 〈 pH 〈 4.7), k(q) = 1.0 × 10(9) (4.7 〈 pH 〈 9.9), and k(q) = 4.0 × 10(8) M(-1) s(-1) (4.7 〈 pH 〈 9.8), respectively. Moreover, it reveals that in strong basic medium (pH = 12.0) a keto-enol tautomerism of thymine inhibits its reaction with triplet BPTC. Such a behavior is not possible for thymidine because of its deoxyribose group. In addition, the pH-dependence of the apparent electrochemical standard potential of thymine in aqueous solution was investigated by cyclic voltammetry. The ΔE/ΔpH ≈ -59 mV/pH result is characteristic of proton-coupled electron transfer. This behavior, together with the kinetic analysis, leads to the conclusion that the quenching reactions between triplet BPTC and thymine involve one proton-coupled electron transfer.
    Keywords: Photochemical Processes ; Protons ; Benzophenones -- Chemistry ; Carboxylic Acids -- Chemistry ; DNA -- Chemistry
    ISSN: 10895639
    E-ISSN: 1520-5215
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  • 10
    Language: English
    In: The Journal of Chemical Physics, 28 December 2013, Vol.139(24)
    Description: Coherent polarization transfer effects in a coupled spin network have been studied over a wide field range. The transfer mechanism is based on exciting zero-quantum coherences between the nuclear spin states by means of non-adiabatic field jump from high to low magnetic field. Subsequent evolution of these coherences enables conversion of spin order in the system, which is monitored after field jump back to high field. Such processes are most efficient when the spin system passes through an avoided level crossing during the field variation. The polarization transfer effects have been demonstrated for N-acetyl histidine, which has five scalar coupled protons; the initial spin order has been prepared by applying RF-pulses at high magnetic field. The observed oscillatory transfer kinetics is taken as a clear indication of a coherent mechanism; level crossing effects have also been demonstrated. The experimental data are in very good agreement with the theoretical model of coherent polarization transfer. The method suggested is also valid for other types of initial polarization in the spin system, most notably, for spin hyperpolarization.
    Keywords: Articles
    ISSN: 0021-9606
    E-ISSN: 1089-7690
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