SUMMARYFor medical biologists, sequencing has become a commonplace technique to support diagnosis. Rapid changes in this field have led to the generation of large amounts of data, which are not always correctly listed in databases. This is particularly true for data concerning class A β-lactamases, a group of key antibiotic resistance enzymes produced by bacteria. Many genomes have been reported to contain putative β-lactamase genes, which can be compared with representative types. We analyzed several hundred amino acid sequences of class A β-lactamase enzymes for phylogenic relationships, the presence of specific residues, and cluster patterns. A clear distinction was first made between dd-peptidases and class A enzymes based on a small number of residues (S70, K73, P107, 130SDN132, G144, E166, 234K/R, 235T/S, and 236G [Ambler numbering]). Other residues clearly separated two main branches, which we named subclasses A1 and A2. Various clusters were identified on the major branch (subclass A1) on the basis of signature residues associated with catalytic properties (e.g., limited-spectrum β-lactamases, extended-spectrum β-lactamases, and carbapenemases). For subclass A2 enzymes (e.g., CfxA, CIA-1, CME-1, PER-1, and VEB-1), 43 conserved residues were characterized, and several significant insertions were detected. This diversity in the amino acid sequences of β-lactamases must be taken into account to ensure that new enzymes are accurately identified. However, with the exception of PER types, this diversity is poorly represented in existing X-ray crystallographic data.

Histone modifications are fundamental to chromatin structure and transcriptional regulation, and are recognized by a limited number of protein folds. Among these folds are PHD fingers, which are present in most chromatin modification complexes. To date, about 15 PHD finger domains have been structurally characterized, whereas hundreds of different sequences have been identified. Consequently, an important open problem is to predict structural features of a PHD finger knowing only its sequence. Here, we classify PHD fingers into different groups based on the analysis of residue–residue co-evolution in their sequences. We measure the degree to which fixing the amino acid type at one position modifies the frequencies of amino acids at other positions. We then detect those position/amino acid combinations, or ‘conditions’, which have the strongest impact on other sequence positions. Clustering these strong conditions yields four families, providing informative labels for PHD finger sequences. Existing experimental results, as well as docking calculations performed here, reveal that these families indeed show discrepancies at the functional level. Our method should facilitate the functional characterization of new PHD fingers, as well as other protein families, solely based on sequence information.

Background: Identifying the active site of an enzyme is a crucial step in functional studies. While protein sequences and structures can be experimentally characterized, determining which residues build up an active site is not a straightforward process. In the present study a new method for the detection of protein active sites is introduced. This method uses local network descriptors derived from protein three-dimensional structures to determine whether a residue is part of an active site. It thus does not involve any sequence alignment or structure similarity to other proteins. A scoring function is elaborated over a set of more than 220 proteins having different structures and functions, in order to detect protein catalytic sites with a high precision, i.e. with a minimal rate of false positives.

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Background:The dopamine transporter controls the concentration of dopamine at the synapse. Results: Ctr9, formerly identified as a nuclei protein, interacts with the dopamine transporter in the cytoplasmic compartment. Conclusion: This interaction facilitates the targeting of the dopamine transporter to the plasma membrane and increases its activity. Significance: Identifying the complete dopamine transporter interactome is essential to understanding how neurotransmission is regulated.

Bovine dopamine L L-hydroxylase (DbH) was inactivated by hydrogen peroxide and ascorbate in the presence of dioxygen. Both inactivated forms of the enzyme were investigated. We could highlight the presence of a quinone derivative bound to the protein, assumed as being dopa-quinone, that is absent from active enzyme. Such results suggest that a tyrosinyl radical transiently forms during catalysis. Moreover we could show that addition of substrate tyramine to H 2 O 2 incubates is responsible for a partial protection of DbH against inactivation. ß

A number of copolymers on the basis of acrylate or methacrylate copolymers containing nitrogen and of ethylene copolymers containing structural units of N,N-diethyl-2-aminoethyl acrylate and 2,2,6,6-tetramethyl-4-piperidyl acrylate or of the vinyl ester of N,N-dimethyl-6-aminocaproic acid were synthetized. These copolymers wcre added to polypropylene before spinning. The dyeability of stretched fibres with acid dyestuffs was evaluated. Modifikatoren zur Verbesserung der Farbbarkeit von PolypropylenEine Anzahl Copolymere auf Basis von stickstoffhaltigen Acrylat-und Methacrylatcopolymeren sowie von Ethylencopolymeren, die N,N-Diethyl-2-aminoethyl-acrylat-oder 2,2,6,6-Tetramethyl-4-piperidylacrylat-Struktureinheiten enthalten, und auf Basis des Vinylesters der N,N-Dimcthyl-6-aminocapronsaure wurden synthetisiert. Diese Copolymere wurden dem Polypropylen vor dem Verspinnen zugesetzt. Die Anfarbbarkeit der gereckten Fasern mit sauren Farbstoffen wurde gepruft. Modu@utcamopbi d~u~ yAyuzuenuR oKpazuusaeMocmu nofiunponzuteiLaCHHTe3HpOBaH PRH COnOJIHMepOB H a OCHOBe a30TCOAepxta~HX aKpHJIaTHbIX H MeTaKpHJIaTHblX COnOJIHMePOB, a TaKH(e COIIOJIHMepOB 3THJIeHa, KOTOPbIe COAepxtaT CTPYKTYPHbIe 3BeHbR N,N-AHaTHJI-2-aMHH03THJI-aKpmnaTa IlJIH 2,2,6,6-TeTpaMeTHJI-4-nHnepH~HJIaKpHJIaTa H H a OCHOBe BHHHJIOBOrO 3@Hpa N,N-AHMeTHJI-&-aMHHOKanpOHOBO~ KHCJIOTIJ. ~T H cononHMepm 6b1nn ~0 6 a~n e~b 1 K nonnnponnneHy nepen @opMosameM. Mccnenosanacb oKpamusae-MOCTb BbITRHYTblX BOJIOKOH C KHCJIbIMH KpaCIlTeJIHMH.