Olfactory proteins mediating chemical communication in the navel orangeworm moth, Amyelois transitella.

BackgroundThe navel orangeworm, Amyelois transitella Walker (Lepidoptera: Pyralidae), is the most serious insect pest of almonds and pistachios in California for which environmentally friendly alternative methods of control--like pheromone-based approaches--are highly desirable. Some constituents of the sex pheromone are unstable and could be replaced with parapheromones, which may be designed on the basis of molecular interaction of pheromones and pheromone-detecting olfactory proteins.MethodologyBy analyzing extracts from olfactory and non-olfactory tissues, we identified putative olfactory proteins, obtained their N-terminal amino acid sequences by Edman degradation, and used degenerate primers to clone the corresponding cDNAs by SMART RACE. Additionally, we used degenerate primers based on conserved sequences of known proteins to fish out other candidate olfactory genes. We expressed the gene encoding a newly identified pheromone-binding protein, which was analyzed by circular dichroism, fluorescence, and nuclear magnetic resonance, and used in a binding assay to assess affinity to pheromone components.ConclusionWe have cloned nine cDNAs encoding olfactory proteins from the navel orangeworm, including two pheromone-binding proteins, two general odorant-binding proteins, one chemosensory protein, one glutathione S-transferase, one antennal binding protein X, one sensory neuron membrane protein, and one odorant receptor. Of these, AtraPBP1 is highly enriched in male antennae. Fluorescence, CD and NMR studies suggest a dramatic pH-dependent conformational change, with high affinity to pheromone constituents at neutral pH and no binding at low pH

Reactivity versus steric effects in fluorinated ketones as esterase inhibitors: a quantum mechanical and molecular dynamics study

12 pages, 10 figures, 3 tables.-- PMID: 20676708 [Pubmed].-- PMCID: PMC3014912.-- NIHMSID: NIHMS250369.-- Printed version published Nov 2010.Carboxylesterases (CEs) are a family of ubiquitous enzymes with broad substrate specificity, and their inhibition may have important implications in pharmaceutical and agrochemical fields. One of the most potent inhibitors both for mammalian and insect CEs are trifluoromethyl ketones (TFMKs), but the mechanism of action of these chemicals is not completely understood. This study examines the balance between reactivity versus steric effects in modulating the activity against human carboxylesterase 1. The intrinsic reactivity of the ketone moiety is determined from quantum mechanical computations, which combine gas phase B3LYP calculations with hydration free energies estimated with the IEF/MST model. In addition, docking and molecular dynamics simulations are used to explore the binding mode of the inhibitors along the deep gorge that delineates the binding site. The results point out that the activity largely depends on the nature of the fluorinated ketone, since the activity is modulated by the balance between the intrinsic electrophilicity of the carbonyl carbon atom and the ratio between keto and hydrate forms. However, the results also suggest that the correct alignment of the alkyl chain in the binding site can exert a large influence on the inhibitory activity, as this effect seems to override the intrinsic reactivity features of the fluorinated ketone. Overall, the results sustain a subtle balance between reactivity and steric effects in modulating the inhibitory activity of TFMK inhibitors.We also gratefully acknowledge the Spanish Ministerio de Ciencia e Innovación (MICINN; projects AGL2006-13489-C02-01/AGR and SAF2008-05595) and the Generalitat de Catalunya (SCG2009 294 and 2009 SGR 871) for financial support. Partial support was provided by National Institute of Environmental Health Sciences R01 ES002710 and Superfund Research Program, P42 ES004699.Peer reviewe

Improved Microwave-Assisted Ring Opening of 1,1,1-Trifluoro-2,3-epoxypropane: Synthesis of New 3-Alkoxy-1,1,1-trifluoropropan-2-ols

A highly efficient and environmentally friendly method for the synthesis of 3-alkoxy-1,1,1-trifluoropropan-2-ols is presented. The approach involves ring-opening reaction of 1,1,1-trifluoro-2,3-epoxypropane with structurally different long-chain alcohols under microwave irradiation at room temperature in the absence of solvent. These chemicals are precursors of the corresponding tri­fluoromethyl ketones, potent inhibitors of human and murine liver microsomes and porcine liver esterase.We are indebted to Miriam Fuentes for technical support and Drs. A. Delgado and A. Messeguer for the use of the microwave oven. We also gratefully acknowledge MICINN for a fellowship to J. Rayó, EU for a contract to L. Muñoz and CICYT (AGL2009-13452-C02-01) for financial support.Peer reviewe

Short-chain reactive probes as tools to unravel the Pseudomonas aeruginosa quorum sensing regulon.

In recent years, the world has seen a troubling increase in antibiotic resistance among bacterial pathogens. In order to provide alternative strategies to combat bacterial infections, it is crucial deepen our understanding into the mechanisms that pathogens use to thrive in complex environments. Most bacteria use sophisticated chemical communication systems to sense their population density and coordinate gene expression in a collective manner, a process that is termed "quorum sensing" (QS). The human pathogen Pseudomonas aeruginosa uses several small molecules to regulate QS, and one of them is N-butyryl-l-homoserine lactone (C4-HSL). Using an activity-based protein profiling (ABPP) strategy, we designed biomimetic probes with a photoreactive group and a 'click' tag as an analytical handle. Using these probes, we have identified previously uncharacterized proteins that are part of the P. aeruginosa QS network, and we uncovered an additional role for this natural autoinducer in the virulence regulon of P. aeruginosa, through its interaction with PhzB1/2 that results in inhibition of pyocyanin production

Cross-linked peptide identification: A computational forest of algorithms

Chemical cross-linking analyzed by mass spectrometry (XL-MS) has become an important tool in unravelling protein structure, dynamics, and complex formation. Because the analysis of cross-linked proteins with mass spectrometry results in specific computational challenges, many computational tools have been developed to identify cross-linked peptides from mass spectra and subsequently interpret the identified cross-links within their structural context. In this review, we will provide an overview of the different tools that are currently available to tackle the computational part of an XL-MS experiment. First, we give an introduction on the computational challenges encountered when processing data from a cross-linking experiment. We then discuss available tools to identify peptides that are linked by intact or MS-cleavable cross-linkers, and we provide an overview of tools to interpret cross-linked peptides in the context of protein structure. Finally, we give an outlook on data management and dissemination challenges and opportunities for cross-linking experiments.status: publishe

Cross-linked peptide identification : a computational forest of algorithms

Chemical cross-linking analyzed by mass spectrometry (XL-MS) has become an important tool in unravelling protein structure, dynamics, and complex formation. Because the analysis of cross-linked proteins with mass spectrometry results in specific computational challenges, many computational tools have been developed to identify cross-linked peptides from mass spectra and subsequently interpret the identified cross-links within their structural context. In this review, we will provide an overview of the different tools that are currently available to tackle the computational part of an XL-MS experiment. First, we give an introduction on the computational challenges encountered when processing data from a cross-linking experiment. We then discuss available tools to identify peptides that are linked by intact or MS-cleavable cross-linkers, and we provide an overview of tools to interpret cross-linked peptides in the context of protein structure. Finally, we give an outlook on data management and dissemination challenges and opportunities for cross-linking experiments

Olfactory proteins mediating chemical communication in the navel orangeworm moth, Amyelois transitella.

BACKGROUND:The navel orangeworm, Amyelois transitella Walker (Lepidoptera: Pyralidae), is the most serious insect pest of almonds and pistachios in California for which environmentally friendly alternative methods of control--like pheromone-based approaches--are highly desirable. Some constituents of the sex pheromone are unstable and could be replaced with parapheromones, which may be designed on the basis of molecular interaction of pheromones and pheromone-detecting olfactory proteins. METHODOLOGY:By analyzing extracts from olfactory and non-olfactory tissues, we identified putative olfactory proteins, obtained their N-terminal amino acid sequences by Edman degradation, and used degenerate primers to clone the corresponding cDNAs by SMART RACE. Additionally, we used degenerate primers based on conserved sequences of known proteins to fish out other candidate olfactory genes. We expressed the gene encoding a newly identified pheromone-binding protein, which was analyzed by circular dichroism, fluorescence, and nuclear magnetic resonance, and used in a binding assay to assess affinity to pheromone components. CONCLUSION:We have cloned nine cDNAs encoding olfactory proteins from the navel orangeworm, including two pheromone-binding proteins, two general odorant-binding proteins, one chemosensory protein, one glutathione S-transferase, one antennal binding protein X, one sensory neuron membrane protein, and one odorant receptor. Of these, AtraPBP1 is highly enriched in male antennae. Fluorescence, CD and NMR studies suggest a dramatic pH-dependent conformational change, with high affinity to pheromone constituents at neutral pH and no binding at low pH

Development and Biological Activity of a New Antagonist of the Pheromone of the Codling Moth Cydia pomonella

A new pheromone antagonist of the codling moth Cydia pomonella is reported. Presaturation of the antennae of the insects with vapors of the antagonist (E,E)-8,10-dodecadienyl trifluoromethyl ketone, analogue of the main component of the pheromone (codlemone), resulted in lower electrophysiological responses to the pheromone relative to untreated insects in the wind tunnel, the compound elicited a remarkable disruptive effect on all types of behavior of males flying toward a source baited with a pheromone antagonist blend in 11, 15, and 11 ratios. The insects displayed erratic flights in the presence of the antagonist, as shown by their flight parameters in comparison to insects attracted to the pheromone alone. In the field, traps baited with mixtures of 11 codlemone antagonist attracted considerably lower numbers of males than the natural attractant. The antagonist, however, did not inhibit the pheromone-degrading enzymes present in male antennae, suggesting that trifluoromethyl ketones are not sufficiently electrophilic to produce a stable intermediate adduct with a cysteine residue of the enzyme, a mechanism previously proposed for oxidase inhibition in insects. Overall and taking into account our previous reports and, of the pheromone of Sesamia nonagrioides (Sole,. ans, A. iho,. oSo,. Bosch,. P. Barrot, Palencia,. astelfii,. Guerrero. A. eduction of dama e by the Mediterrean corn borer, Sesamia nonagrioides, and the European corn borer, Ostrinia nubilalis, in maize fields by a trifluoromethyl ketone pheromone anologue. Entomol. Exp. Appl. 2008, 126, 28-39), the antagonist might be a ne candidate to consider in future strategies to control the codling moth