Activated Ion Electron Capture Dissociation (AI ECD) of proteins: synchronization of infrared and electron irradiation with ion magnetron motion.

Here, we show that to perform activated ion electron capture dissociation (AI-ECD) in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer equipped with a CO(2) laser, it is necessary to synchronize both infrared irradiation and electron capture dissociation with ion magnetron motion. This requirement is essential for instruments in which the infrared laser is angled off-axis, such as the Thermo Finnigan LTQ FT. Generally, the electron irradiation time required for proteins is much shorter (ms) than that required for peptides (tens of ms), and the modulation of ECD, AI ECD, and infrared multiphoton dissociation (IRMPD) with ion magnetron motion is more pronounced. We have optimized AI ECD for ubiquitin, cytochrome c, and myoglobin; however the results can be extended to other proteins. We demonstrate that pre-ECD and post-ECD activation are physically different and display different kinetics. We also demonstrate how, by use of appropriate AI ECD time sequences and normalization, the kinetics of protein gas-phase refolding can be deconvoluted from the diffusion of the ion cloud and measured on the time scale longer than the period of ion magnetron motion

The Role of the D13 (1520) Resonance in eta Electroproduction

We investigate the electroproduction of eta mesons below a center of momentum energy of 1.6 GeV, with particular emphasis on the roles of the N*(1535) and N*(1520) resonances. Using the effective Lagrangian approach, we show that the transverse helicity amplitude of the N*(1535) can be extracted with good accuracy from the new eta electroproduction data, under reasonable assumptions for the strength of the longitudinal helicity amplitude. In addition, although the differential cross section is found to to have a small sensitivity to the N*(1520) resonance, it is shown that a recently completed double polarization experiment is very sensitive to this resonance.Comment: 7 pages, Revtex, 3 figure

The relativistic impulse approximation for the exclusive electrodisintegration of the deuteron

The electrodisintegration of the deuteron in the frame of the Bethe-Salpeter approach with a separable kernel of the nucleon-nucleon interaction is considered. This conception keeps the covariance of a description of the process. A comparison of relativistic and nonrelativistic calculations is presented. The factorization of the cross section of the reaction in the impulse approximation is obtained by analytical calculations. It is shown that the photon-neutron interaction plays an important role.Comment: 31 pages, 14 figures, 1 tabl

A hydrogen beam to characterize the ASACUSA antihydrogen hyperfine spectrometer

The antihydrogen programme of the ASACUSA collaboration at the antiproton decelerator of CERN focuses on Rabi-type measurements of the ground-state hyperfine splitting of antihydrogen for a test of the combined Charge-Parity-Time symmetry. The spectroscopy apparatus consists of a microwave cavity to drive hyperfine transitions and a superconducting sextupole magnet for quantum state analysis via Stern-Gerlach separation. However, the small production rates of antihydrogen forestall comprehensive performance studies on the spectroscopy apparatus. For this purpose a hydrogen source and detector have been developed which in conjunction with ASACUSA's hyperfine spectroscopy equipment form a complete Rabi experiment. We report on the formation of a cooled, polarized, and time modulated beam of atomic hydrogen and its detection using a quadrupole mass spectrometer and a lock-in amplification scheme. In addition key features of ASACUSA's hyperfine spectroscopy apparatus are discussed.

Threshold eta and eta' electroproduction off nucleons

The electroproduction of eta and eta' mesons on the proton and the neutron is investigated at tree level within the framework of U(3) chiral perturbation theory. In addition to the Born terms low-lying resonances such as the vector mesons and J^P= 1/2^+, 1/2^- baryon resonances are included explicitly and their contributions are calculated. Results for the separated differential cross sections are presented.Comment: 24 pages, 7 figure

Quasifree Pion Electroproduction from Nuclei in the Δ\Delta Region

We present calculations of the reaction $A(e,e^\prime \pi N)B$ in the distorted wave impulse approximation. The reaction allows for the study of the production process in the nuclear medium without being obscured by the details of nuclear transition densities. First, a pion electroproduction operator suitable for nuclear calculations is obtained by extending the Blomqvist-Laget photoproduction operator to the virtual photon case. The operator is gauge invariant, unitary, reference frame independent, and describes the existing data reasonably well. Then it is applied in nuclei to predict nuclear cross sections under a variety of kinematic arrangements. Issues such as the effects of gauge-fixing, the interference of the $\Delta$ resonance with the background, sensitivities to the quadrupole component of the $\Delta$ excitation and to the electromagnetic form factors, the role of final-state interactions, are studied in detail. Methods on how to experimentally separate the various pieces in the coincidence cross section are suggested. Finally, the model is compared to a recent SLAC experiment.Comment: 27 pages in REVTEX, plus 22 PS figures embedded using psfig.sty (included), uuencode

A mini-twister variant and impact of residues/cations on the phosphodiester cleavage of this ribozyme class.

Nucleolytic ribozymes catalyze site-specific cleavage of their phosphodiester backbones. A minimal version of the twister ribozyme is reported that lacks the phylogenetically conserved stem P1 while retaining wild-type activity. Atomic mutagenesis revealed that nitrogen atoms N1 and N3 of the adenine-6 at the cleavage site are indispensable for cleavage. By NMR spectroscopy, a pKa value of 5.1 was determined for a 13C2-labeled adenine at this position in the twister ribozyme, which is significantly shifted compared to the pKa of the same adenine in the substrate alone. This finding pinpoints at a potential role for adenine-6 in the catalytic mechanism besides the previously identified invariant guanine-48 and a Mg2+ ion, both of which are directly coordinated to the non-bridging oxygen atoms of the scissile phosphate; for the latter, additional evidence stems from the observation that Mn2+ or Cd2+ accelerated cleavage of phosphorothioate substrates. The relevance of this metal ion binding site is further emphasized by a new 2.6 Å X-ray structure of a 2′-OCH3-U5 modified twister ribozyme

Photo- and Electron-Production of Mesons on Nucleons and Nuclei

In these lectures I will show some results obtained with the chiral unitary approach applied to the photo and electroproduction of mesons. The results for photoproduction of $\eta \pi^0 p$ and $K^0 \pi^0 \Sigma^+$, together with related reactions will be shown, having with common denominator the excitation of the $\Delta(1700)$ resonance which is one of those dynamically generated in the chiral unitary approach. Then I will show results obtained for the $e^+ e^- \to \phi f_0(980)$ reaction which reproduce the bulk of the data except for a pronounced peak, giving support to a new mesonic resonance, X(2175). Results will also be shown for the electromagnetic form factors of the $N^*(1535)$ resonance, also dynamically generated in this approach. Finally, I will show some results on the photoproduction of the $\omega$ in nuclei, showing that present experimental results claiming a shift of the $\omega$ mass in the medium are tied to a particular choice of background and are not conclusive. One the other hand, the same experimental results show unambiguously a huge increase of the $\omega$ width in the nuclear medium.Comment: Lecture at the "International School of Nuclear Physics", 29th Course Quarks in Hadrons and Nuclei, Erice, Italy, September 2007. Note added in Proofs concerning the mixed events technique and other comments on omega productio

Electron Capture Dissociation Mass Spectrometry of Tyrosine Nitrated Peptides

In vivo protein nitration is associated with many disease conditions that involve oxidative stress and inflammatory response. The modification involves addition of a nitro group at the position ortho to the phenol group of tyrosine to give 3-nitrotyrosine. To understand the mechanisms and consequences of protein nitration, it is necessary to develop methods for identification of nitrotyrosine-containing proteins and localization of the sites of modification.Here, we have investigated the electron capture dissociation (ECD) and collision-induced association (CID) behavior of 3-nitrotyrosine-containing peptides. The presence of nitration did not affect the CID behavior of the peptides. For the doubly-charged peptides, addition of nitration severely inhibited the production of ECD sequence fragments. However, ECD of the triply-charged nitrated peptides resulted in some singly-charged sequence fragments. ECD of the nitrated peptides is characterized by multiple losses of small neutral species including hydroxyl radicals, water and ammonia. The origin of the neutral losses has been investigated by use of activated ion (AI) ECD. Loss of ammonia appears to be the result of non-covalent interactions between the nitro group and protonated lysine side-chains