Lysine-specific acetylated proteome from the archaeon Thermococcus gammatolerans reveals the presence of acetylated histones.

Thermococcus gammatolerans EJ3 is an extremophile archaeon which was revealed as one of the most radioresistant organisms known on Earth, withstanding up to 30 kGy gamma-ray radiations. While its theoretical proteome is rather small, T. gammatolerans may enhance its toolbox by post-translational modification of its proteins.

Prioritizing targets for structural biology through the lens of proteomics: the archaeal protein TGAM_1934 from Thermococcus gammatolerans.

ORFans are hypothetical proteins lacking any significant sequence similarity with other proteins. Here, we highlighted by quantitative proteomics the TGAM_1934 ORFan from the hyperradioresistant Thermococcus gammatolerans archaeon as one of the most abundant hypothetical proteins. This protein has been selected as a priority target for structure determination on the basis of its abundance in three cellular conditions.

N- and O-acetylation of threonine residues in the context of proteomics.

The detection of post-translational modifications (PTMs) of proteins is a matter of intensive research. Among all possible pitfalls that may lead to misidentifications, the chemical stability of modified peptides is scarcely questioned. Global proteomic studies devoted to protein acetylation are becoming popular.

Major soluble proteome changes in Deinococcus deserti over the earliest stages following gamma-ray irradiation.

Background: Deinococcus deserti VCD115 has been isolated from Sahara surface sand. This radiotolerant bacterium represents an experimental model of choice to understand adaptation to harsh conditions encountered in hot arid deserts. We analysed the soluble proteome dynamics in this environmentally relevant model after exposure to 3 kGy gamma radiation, a non-lethal dose that generates massive DNA damages.

Revisiting iodination sites in thyroglobulin with an organ-oriented shotgun strategy.

Thyroglobulin (Tg) is secreted by thyroid epithelial cells. It is essential for thyroid hormonogenesis and iodine storage. Although studied for many years, only indirect and partial surveys of its post-translational modifications were reported.

Palladium motion in cyclomeric compounds: a theoretical study.

Density functional theory (DFT)/B3LYP calculations have been carried out to study successive intramolecular 1,n palladium shifts (n = 3-5) in palladium complexes of organic cyclomers. Such shifts of the PdBr(phosphine) moiety, which is bound to the cyclomer and which exchanges concomitantly with a hydrogen atom distant by n carbon atoms from palladium, might lead to an endless motion around the cyclomer. The cyclomers that have been analyzed are either the [1,1,1,1]paracyclophane 1, a THF-based 16-crown-4 structure 2, or the THF-ethylene cyclic dimer 3 (THF = tetrahydrofuran).

Proteomics-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons.

Deinococcaceae are a family of extremely radiation-tolerant bacteria that are currently subjected to numerous studies aimed at understanding the molecular mechanisms for such radiotolerance. To achieve a comprehensive and accurate annotation of the Deinococcus deserti genome, we performed an N terminus-oriented characterization of its proteome. For this, we used a labeling reagent, N-tris(2,4,6-trimethoxyphenyl)phosphonium acetyl succinimide, to selectively derivatize protein N termini.

Identification of uranyl binding proteins from human kidney-2 cell extracts by immobilized uranyl affinity chromatography and mass spectrometry.

To improve our knowledge on protein targets of uranyl ion (UO(2)(2+)), we set up a proteomic strategy based on immobilized metal-affinity chromatography (IMAC). The successful enrichment of UO(2)(2+)-interacting proteins from human kidney-2 (HK-2) soluble cell extracts was obtained using an ion-exchange chromatography followed by a dedicated IMAC process previously described and designed for the uranyl ion. By mass spectrometry analysis we identified 64 proteins displaying varied functions.

Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti.

To better understand adaptation to harsh conditions encountered in hot arid deserts, we report the first complete genome sequence and proteome analysis of a bacterium, Deinococcus deserti VCD115, isolated from Sahara surface sand. Its genome consists of a 2.8-Mb chromosome and three large plasmids of 324 kb, 314 kb, and 396 kb.

Autophosphorylated residues involved in the regulation of human chk2 in vitro.

Human checkpoint kinase 2 is a major actor in checkpoint activation through phosphorylation by ataxia telangiectasia mutated in response to DNA double-strand breaks. In the absence of de novo DNA damage, its autoactivation, reported in the event of increased Cds1/checkpoint kinase 2 (Chk2) expression, has been attributed to oligomerization. Here we report a study performed on autoactivated recombinant Chk2 proteins that aims to correlate kinase activity and phosphorylation status.

Specific capture of uranyl protein targets by metal affinity chromatography.

To improve general understanding of biochemical mechanisms in the field of uranium toxicology, the identification of protein targets needs to be intensified. Immobilized metal affinity chromatography (IMAC) has been widely developed as a powerful tool for capturing metal binding proteins from biological extracts. However uranyl cations (UO2(2+)) have particular physico-chemical characteristics which prevent them from being immobilized on classical metal chelating supports.

Through-space intramolecular palladium rearrangement in substituted aryl complexes: theoretical study of the aryl to alkylpalladium migration process.

DFT/B3LYP calculations have been carried out to study intramolecular 1,n palladium shifts (n = 3-5) between sp2 and sp3 carbon atoms in alkylarylpalladium systems. Such shifts, which also involve a concomitant exchange with a hydrogen atom of the alkylaryl ligand, are quite often a pivotal step of several organic transformations mediated by palladium complexes. We show that the intimate mechanism for the 1,3 shift corresponds to a Pd(IV) pathway, whereas a Pd(II) pathway is favored in the case of 1,5 migrations.

THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain.

The tRNA:m2(2)G10 methyltransferase of Pyrococus abyssi (PAB1283, a member of COG1041) catalyzes the N2,N2-dimethylation of guanosine at position 10 in tRNA. Boundaries of its THUMP (THioUridine synthases, RNA Methyltransferases and Pseudo-uridine synthases)--containing N-terminal domain [1-152] and C-terminal catalytic domain [157-329] were assessed by trypsin limited proteolysis. An inter-domain flexible region of at least six residues was revealed.

Can weak interactions modify the binding properties of a strong nitrogen donor? Unusual N-coordination of a phosphoranylidene-substituted pyrazolone unit towards palladium(II) centres: an experimental and theoretical study.

Selective N(2)-binding of 3-methyl-1-phenyl-4-(triphenylphosphoranylidene)-2-pyrazolin-5-one (L) has been found in two palladium(II) complexes, [PdCl(2)L(2)](2) and [Pd(o-C(6)H(4)CH(2)NMe(2))Cl](3). X-Ray diffraction studies show that the pyrazole rings lie almost perpendicular to the coordination plane. In both complexes the metal atom is located out of the plane defined by the pyrazole ring(s)(dihedral angle between the plane and the Pd-N vector approximately 30 degrees).

Screening of human serum proteins for uranium binding.

About 20% of uranyl ions in serum are associated with the protein pool. A few of them such as transferrin have been characterized, but most still have to be identified to obtain a better explanation of the biochemical toxicology and kinetics of uranium. We designed an in vitro sensitive procedure involving a combination of bidimensional chromatography with time-resolved fluorescence, coupled with proteomic analysis, to identify uranium-binding proteins in human serum fractions.

Industrial process proteomics: alfalfa protein patterns during wet fractionation processing.

A proteome reference map of major soluble proteins from Medicago sativa (alfalfa) leaves and stems has been established for the first time. Among 195 spots analyzed by mass spectrometry and N-terminal Edman sequencing, 117 spots were unambiguously identified, representing 87 different proteins. Of these 87 proteins, 13 proteins were directly identified from the partial genome of Medicago sativa, 30 from expressed sequenced tags (ESTs) of the model legume Medicago truncatula and 44 from closely relative species by a cross-species protein identification method.

Cyclocarbopalladation involving an unusual 1,5-palladium vinyl to aryl shift as termination step: theoretical study of the mechanism.

A DFT/B3LYP model study has been carried out on the cyclocarbopalladation and on an unusual 1,5 vinyl to aryl palladium shift which are the two first steps of a cyclocarbopalladation-Stille coupling tandem reaction of various gamma-bromopropargylic-1,2 diols with alkenyls or alkynyl stannanes catalyzed by Pd(PPh(3))(4). From the calculations, the active intermediates in the catalytic process appear to bear a single phosphine ligand, the palladium(II) center keeping in all cases a square-planar coordination pattern either through intramolecular binding of the triple bond or via an intramolecular Pd..

Deciphering structure and topology of conserved COG2042 orphan proteins.

Background: The cluster of orthologous group COG2042 has members in all sequenced Eukaryota as well as in many Archaea. The cellular function of these proteins of ancient origin remains unknown. PSI-BLAST analysis does not indicate a possible link with even remotely-related proteins that have been functionally or structurally characterized.

sigma-Bond Metathesis Reactions Involving Palladium(II) Hydride and Methyl Complexes: A Theoretical Assessment.

sigma-Bond metathesis reactions of water and methanol with palladium hydride and methyl complexes to yield hydrogen and methane, respectively, have been studied using ab-initio molecular orbital methods at the second-order Møller-Plesset (MP2) perturbation level. The calculations show that such reactions are feasible and that they can in some instances be competitive with an oxidative addition/reductive elimination sequence. A key factor is the presence of an additional lone pair not engaged in the initial bonding of the metal atom with the reacting water or alcohol.

Synthetic, Structural, Spectroscopic, and Theoretical Studies of Structural Isomers of the Cluster Pt(3)(&mgr;-PPh(2))(3)Ph(PPh(3))(2). A Unique Example of Core Isomerism in Phosphine Phosphido-Rich Clusters.

Two isomers of the phosphido-bridged platinum cluster Pt(3)(&mgr;-PPh(2))(3)Ph(PPh(3))(2) (2 and 3) have been isolated, and their structures have been solved by single-crystal X-ray diffraction. Compound 2 crystallizes in the orthorhombic space group Cmc2(1) with a = 22.192(10) Å, b = 17.