EnCOUNTer: a parsing tool to uncover the mature N-terminus of organelle-targeted proteins in complex samples

Mascot Distiller processing method for protein N-terminal acetylation quantitation. (PDF 24 kb

Vibrational spectroscopy and DFT calculations of 1,​3-​dibromo-​2,​4,​6-​trimethylbenzene: Anharmonicity, coupling and methyl group tunneling

International audienceThe Raman, IR and INS spectra of 1,3-dibromo-2,4,6-trimethylbenzene (DBMH) were recorded in the 80-3200 cm-1 range. The molecular conformation and vibrational spectra of DBMH were computed at the MPW1PW91/LANL2DZ level. Except for the methyl 2 environment, the agreement between the DFT calculations and the neutron diffraction structure is almost perfect (deviations < 0.01 Å for bond lengths, < 0.2° for angles). The frequencies of the internal modes of vibration were calculated with the harmonic and anharmonic approximations; the later method yields results that are in remarkable agreement with the spectroscopic data, resulting in a confident assignment of the vibrational bands. Thus, no scaling is necessary. The coupling, in phase or anti-phase, of the motions of symmetrical C-Br and C-Me bonds is highlighted. Our DFT calculations suggest that the torsion of methyl groups 4 and 6 is hindered in deep wells, whereas methyl group 2 is a quasi-free rotor. The failure of the calculations to determine the frequencies of the methyl torsional modes is explained as follows: DFT does not consider the methyl spins and assumes localization of the protons, whereas the methyl groups must be treated as quantum rotors

New antibiotic molecules: bypassing the membrane barrier of gram negative bacteria increases the activity of peptide deformylase inhibitors

International audienceBACKGROUND : Multi-drug resistant (MDR) bacteria have become a major concern in hospitals worldwide and urgently require the development of new antibacterial molecules. Peptide deformylase is an intracellular target now well-recognized for the design of new antibiotics. The bacterial susceptibility to such a cytoplasmic target primarily depends on the capacity of the compound to reach and accumulate in the cytosol. METHODOLOGY/PRINCIPAL FINDINGS : To determine the respective involvement of penetration (influx) and pumping out (efflux) mechanisms to peptide deformylase inhibitors (PDF-I) activity, the potency of various series was determined using various genetic contexts (efflux overproducers or efflux-deleted strains) and membrane permeabilizers. Depending on the structure of the tested molecules, two behaviors could be observed: (i) for actinonin the first PDF-I characterized, the AcrAB efflux system was the main parameter involved in the bacterial susceptibility, and (ii), for the latest PDF-Is such as the derivatives of 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide, the penetration through the membrane was a important limiting step CONCLUSIONS/SIGNIFICANCE : Our results clearly show that the bacterial membrane plays a key role in modulating the antibacterial activity of PDF-Is. The bacterial susceptibility for these new antibacterial molecules can be improved by two unrelated ways in MDR strains: by collapsing the Acr efflux activity or by increasing the uptake rate through the bacterial membrane. The efficiency of the second method is associated with the nature of the compound

Bis(4-acetyl­phen­yl) selenide

In the title compound, C16H14O2Se, the dihedral angle between the benzene rings is 87.08 (11)°. In the crystal, mol­ecules are linked into layers parallel to the bc plane by inter­molecular C—H⋯O hydrogen bonds

Nt-acetylation-independent turnover of SQUALENE EPOXIDASE 1 by Arabidopsis DOA10-like E3 ligases

The acetylation-dependent (Ac/)N-degron pathway degrades proteins through recognition of their acetylated N-termini (Nt) by E3 ligases called Ac/N-recognins. To date, specific Ac/N-recognins have not been defined in plants. Here we used molecular, genetic, and multiomics approaches to characterize potential roles for Arabidopsis (Arabidopsis thaliana) DEGRADATION OF ALPHA2 10 (DOA10)-like E3 ligases in the Nt-acetylation-(NTA)-dependent turnover of proteins at global- and protein-specific scales. Arabidopsis has two endoplasmic reticulum (ER)-localized DOA10-like proteins. AtDOA10A, but not the Brassicaceae-specific AtDOA10B, can compensate for loss of yeast (Saccharomyces cerevisiae) ScDOA10 function. Transcriptome and Nt-acetylome profiling of an Atdoa10a/b RNAi mutant revealed no obvious differences in the global NTA profile compared to wild type, suggesting that AtDOA10s do not regulate the bulk turnover of NTA substrates. Using protein steady-state and cycloheximide-chase degradation assays in yeast and Arabidopsis, we showed that turnover of ER-localized SQUALENE EPOXIDASE 1 (AtSQE1), a critical sterol biosynthesis enzyme, is mediated by AtDOA10s. Degradation of AtSQE1 in planta did not depend on NTA, but Nt-acetyltransferases indirectly impacted its turnover in yeast, indicating kingdom-specific differences in NTA and cellular proteostasis. Our work suggests that, in contrast to yeast and mammals, targeting of Nt-acetylated proteins is not a major function of DOA10-like E3 ligases in Arabidopsis and provides further insight into plant ERAD and the conservation of regulatory mechanisms controlling sterol biosynthesis in eukaryotes

Dual lysine and N-terminal acetyltransferases reveal the complexity underpinning protein acetylation

Protein acetylation is a highly frequent protein modification. However, comparatively little is known about its enzymatic machinery. N-alpha-acetylation (NTA) and epsilon-lysine acetylation (KA) are known to be catalyzed by distinct families of enzymes (NATs andKATs, respectively), although the possibility that the sameGCN5-relatedN-acetyltransferase (GNAT) can perform both functions has been debated. Here, we discovered a new family of plastid-localizedGNATs, which possess a dual specificity. All characterizedGNATfamily members display a number of unique features. Quantitative mass spectrometry analyses revealed that these enzymes exhibit both distinctKAand relaxedNTAspecificities. Furthermore, inactivation ofGNAT2 leads to significantNTAorKAdecreases of several plastid proteins, while proteins of other compartments were unaffected. The data indicate that these enzymes have specific protein targets and likely display partly redundant selectivity, increasing the robustness of the acetylation processin vivo. In summary, this study revealed a new layer of complexity in the machinery controlling this prevalent modification and suggests that other eukaryoticGNATs may also possess these previously underappreciated broader enzymatic activities

Remarque sur les relations entre transitions de phase, défauts de réseau et phénomènes Debye dans les solides

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Étude par résonance magnétique protonique de la dynamique des molécules engagées dans quelques clathrates monocristallins d’hydroquinone deutériée

Dans le but d’approfondir nos résultats en ce qui concerne le mouvement des molécules encagées dans quelques clathrates d’hydroquinone monocristallins, l’étude RMP a été poursuivie sur des échantillons où le réseau d’hydroquinone est fortement deutérié. Le pourcentage de deutériation est déterminé par spectrographie de masse. Les calculs du second moment et de la largeur du spectre ont pu être effectués pour diverses hypothèses de réorientation des molécules encagées. Les résultats expérimentaux précisent les conclusions antérieures

Étude comparée des mouvements de réorientation moléculaire de benzènes penta et hexasubstitués à l’état solide :

Dans le but de détecter le phénomène de réorientation moléculaire en phase solide, nous avons examiné les propriétés diélectriques de composés substitués du tétraméthyl-1.2.4,5-benzène (durène) et du pentaméthylbenzène. Ces produits étaient en général fondus dans le condensateur de mesure, et ensuite étudiés à l'état compact de 80 °K à la fusion, dans la gamme de fréquences 100 Hz à 3 MHz.Aux températures inférieures à 300 °K. les dérivés hexasubstitués polaires (chlore-, brome- et iodopentaméthvlhenzènet présentent une variation de ε* caractéristique d’un phénomène d'absorption dipolaire lié à la réorientation. Le dérivé iodé semble posséder un changement de phase à 240 °K.Dans le même domaine de températures, les composés penlasubstituès polaires à molécules suffisamment symétriques présentent au moins une phase douée d’absorption dipolaire.Dans le cas du bromodurène. cette phase n'est stable qu'au dessus de 310 °K, Elle ne peut être étudiée aux basses fréquences qu'à l'état métastable après une trempe. Il en est de même de la phase = haute température = du chloropentaméthylbenzène, stable au-dessus de 395 °K. Aux températures proches de leurs températures de fusion, tous les composés examinés présentent une évolution très lente de leur permittivité qui. à température constante, se stabilise à une valeur supérieure à celle du liquide correspondant