Enumerating Pathways of Proton Abstraction Based on a Spatial and Electrostatic Analysis of Residues in the Catalytic Site

The pathways of proton abstraction (PA), a key aspect of most catalytic reactions, is often controversial and highly debated. Ultrahigh-resolution diffraction studies, molecular dynamics, quantum mechanics and molecular mechanic simulations are often adopted to gain insights in the PA mechanisms in enzymes. These methods require expertise and effort to setup and can be computationally intensive. We present a push button methodology – Proton abstraction Simulation (PRISM) – to enumerate the possible pathways of PA in a protein with known 3D structure based on the spatial and electrostatic properties of residues in the proximity of a given nucleophilic residue. Proton movements are evaluated in the vicinity of this nucleophilic residue based on distances, potential differences, spatial channels and characteristics of the individual residues (polarity, acidic, basic, etc). Modulating these parameters eliminates their empirical nature and also might reveal pathways that originate from conformational changes. We have validated our method using serine proteases and concurred with the dichotomy in PA in Class A β-lactamases, both of which are hydrolases. The PA mechanism in a transferase has also been corroborated. The source code is made available at www.sanchak.com/prism

Palynological and chemical volatile components of tipically autumnal honeys of the western Mediterranean

[EN] Twenty-five samples of autumnal honeys from the western Mediterranean (Mallorca and Eivissa, Balearic Islands) were examined for pollen content (qualitative and quantitative melissopalynological analysis), moisture, electrical conductivity, colour, sensorial qualities and volatile components. Quantitative analysis showed that the honey contained Maurizio's Class II: 64%, Class III: 28%, Class IV: 4% and Class V: 4%. Fifty-four pollen types, with an average number of 16.68 per sample, were identified, belonging to 29 botanical families. Only two taxa (Ceratonia siliqua and Erica multiflora) were found in all samples. Seventeen samples were unifloral (68%) - ten (40%) of C. siliqua, six (24%) of E. multiflora and one (4%) of Hedera helix. All honeys have a low honeydew index (<?0.09%), while the values for electrical conductivity and water content were high. The major honey volatile components are: cis- and trans-linalool oxides (64.2%) and hotrienol (10.4%) for the carob (C. siliqua) and trans-linalool oxide (13.4%), p-menthane-1,8-diol (11.1%), safranal (9.7%), limonene (5,4%), -pinene (3.7%) and oxoisophorone (3.4%) for the winter heather (E. multiflora).The authors would like to extend their gratitude to the Mallorca Rural 'Leader plus' programme and the beekeepers of Mallorca and Eivissa for their support and friendly collaboration. The authors also thank an anonymous reviewer for useful comments and suggestions on an earlier version of the manuscript.Boi, M.; Llorens Molina, JA.; Cortés, L.; Lladó, G.; Llorens, L. (2013). Palynological and chemical volatile components of tipically autumnal honeys of the western Mediterranean. Grana. 52(2):93-105. doi:10.1080/00173134.2012.744774S93105522Andrade, P. B., Amaral, M. T., Isabel, P., Carvalho, J. C. M. F., Seabra, R. M., & Proença da Cunha, A. (1999). 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Ligand Binding Study of Human PEBP1/RKIP: Interaction with Nucleotides and Raf-1 Peptides Evidenced by NMR and Mass Spectrometry

Background Human Phosphatidylethanolamine binding protein 1 (hPEBP1) also known as Raf kinase inhibitory protein (RKIP), affects various cellular processes, and is implicated in metastasis formation and Alzheimer's disease. Human PEBP1 has also been shown to inhibit the Raf/MEK/ERK pathway. Numerous reports concern various mammalian PEBP1 binding ligands. However, since PEBP1 proteins from many different species were investigated, drawing general conclusions regarding human PEBP1 binding properties is rather difficult. Moreover, the binding site of Raf-1 on hPEBP1 is still unknown. Methods/Findings In the present study, we investigated human PEBP1 by NMR to determine the binding site of four different ligands: GTP, FMN, and one Raf-1 peptide in tri-phosphorylated and non-phosphorylated forms. The study was carried out by NMR in near physiological conditions, allowing for the identification of the binding site and the determination of the affinity constants KD for different ligands. Native mass spectrometry was used as an alternative method for measuring KD values. Conclusions/Significance Our study demonstrates and/or confirms the binding of hPEBP1 to the four studied ligands. All of them bind to the same region centered on the conserved ligand-binding pocket of hPEBP1. Although the affinities for GTP and FMN decrease as pH, salt concentration and temperature increase from pH 6.5/NaCl 0 mM/20°C to pH 7.5/NaCl 100 mM/30°C, both ligands clearly do bind under conditions similar to what is found in cells regarding pH, salt concentration and temperature. In addition, our work confirms that residues in the vicinity of the pocket rather than those within the pocket seem to be required for interaction with Raf-1.METASU

Chromogenic depsipeptide substrates for beta-lactamases and penicillin-sensitive DD-peptidases.

Various ester and thioester derivatives of hippuric acid have been prepared which were substrates of both beta-lactamases and DD-peptidases. The thioesters were more rapidly hydrolysed by nearly all the enzymes. Surprisingly, the enzymes acted rather efficiently on substrates which did not contain any chiral centre

Streptomyces K15 active-site serine DD-transpeptidase: specificity profile for peptide, thiol ester and ester carbonyl donors and pathways of the transfer reactions.

The Streptomyces K15 transferase is a penicillin-binding protein presumed to be involved in bacterial wall peptidoglycan crosslinking. It catalyses cleavage of the peptide, thiol ester or ester bond of carbonyl donors Z-R1-CONH-CHR2-COX-CHR3-COO- (where X is NH, S or O) and transfers the electrophilic group Z-R1-CONH-CHR2-CO to amino acceptors via an acyl-enzyme intermediate. Kinetic data suggest that the amino acceptor behaves as a simple alternative nucleophile at the level of the acyl-enzyme in the case of thiol ester and ester donors, and that it binds to the enzyme.carbonyl donor Michaelis complex and influences the rate of enzyme acylation by the carbonyl donor in the case of amide donors. Depending on the nature of the scissile bond, the enzyme has different requirements for substituents at positions R1, R2 and R3

ACCUMULATION OF ACYL-ENZYME IN DD-PEPTIDASE-CATALYZED REACTIONS WITH ANALOGS OF PEPTIDE-SUBSTRATES

Thioester substrates can be used to study the hydrolysis and transfer reactions catalysed by beta-lactamases and DD-peptidases. With the latter enzymes, accumulation of the acyl-enzyme can be detected directly. The efficiency of various amines as acceptor substrates was in excellent agreement with previous results obtained with peptide substrates of the DD-peptidases. The results indicated the presence of a specific binding site for the acceptor substrates, Although most of the results agreed well with a simple partition model, more elaborate hypotheses will be needed to account for all the data presented