Robust determination of differential abundance in shotgun proteomics using nonparametric statistics.

Label-free shotgun mass spectrometry enables the detection of significant changes in protein abundance between different conditions. Due to often limited cohort sizes or replication, large ratios of potential protein markers to number of samples, as well as multiple null measurements pose important technical challenges to conventional parametric models. From a statistical perspective, a scenario similar to that of unlabeled proteomics is encountered in genomics when looking for differentially expressed genes.

Two-domain analysis of JmjN-JmjC and PHD-JmjC lysine demethylases: Detecting an inter-domain evolutionary stress.

Residues at different positions of a multiple sequence alignment sometimes evolve together, due to a correlated structural or functional stress at these positions. Co-evolution has thus been evidenced computationally in multiple proteins or protein domains. Here, we wish to study whether an evolutionary stress is exerted on a sequence alignment across protein domains, i.

Identification of family determining residues in Jumonji-C lysine demethylases: A sequence-based, family wide classification.

Histone post-translational modifications play a critical role in the regulation of gene expression. Methylation of lysines at N-terminal tails of histones has been shown to be involved in such regulation. While this modification was long considered to be irreversible, two different classes of enzymes capable of carrying out the demethylation of histone lysines were recently identified: the oxidases, such as LSD1, and the oxygenases (JmjC-containing).

A Structure-Based Classification of Class A β-Lactamases, a Broadly Diverse Family of Enzymes.

For 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.

Ctr9, a Protein in the Transcription Complex Paf1, Regulates Dopamine Transporter Activity at the Plasma Membrane.

Dopamine (DA) is a major regulator of sensorimotor and cognitive functions. The DA transporter (DAT) is the key protein that regulates the spatial and temporal activity of DA release into the synaptic cleft via the rapid reuptake of DA into presynaptic termini. Several lines of evidence have suggested that transporter-interacting proteins may play a role in DAT function and regulation.

Identification of family-determining residues in PHD fingers.

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.

N-Hydroxyguanidines oxidation by a N3S copper-complex mimicking the reactivity of Dopamine beta-Hydroxylase.

N-Aryl-N'-hydroxyguanidines are compounds that display interesting pharmacological properties but their chemical reactivity remains poorly investigated. Some of these compounds are substrates for the heme-containing enzymes nitric-oxide synthases (NOS) and act as reducing co-substrates for the copper-containing enzyme Dopamine beta-Hydroxylase (DBH) [P. Slama, J.

Detection of protein catalytic residues at high precision using local network properties.

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.

Aromatic N-hydroxyguanidines as new reduction cosubstrates for dopamine beta-hydroxylase.

Conversion of neurotransmitter dopamine into norepinephrine is catalyzed by dopamine beta-hydroxylase (DbH). The reaction requires the presence of both molecular oxygen and a reducing cosubstrate, the assumed physiological cosubstrate being ascorbic acid. We have investigated the ability of a new family of molecules, N-aryl-N'-hydroxyguanidines, to serve as cosubstrates for DbH.

Copper-containing monooxygenases: enzymatic and biomimetic studies of the O-atom transfer catalysis.

This review reports our recent studies or the mechanism of O-atom transfer to a benzylic C-H bond promoted by Dopamine beta-Hydroxylase (DBH) and its biomimetic models. We demonstrate that it is possible to carry out parallel and comparative studies on this enzyme (DBH) and its biomimetic models with the same substrate: 2-aminoindane (3). It was chosen because its two stereogenic centers, both in benzylic positions, make it very powerful for studying the stereochemistry of an O-atom transfer reaction.