Publications by authors named "Jean-Pierre Le Caer"

45 Publications

Multimodal Imaging Mass Spectrometry to Identify Markers of Pulmonary Arterial Hypertension in Human Lung Tissue Using MALDI-ToF, ToF-SIMS, and Hybrid SIMS.

Anal Chem 2020 09 17;92(17):12079-12087. Epub 2020 Aug 17.

Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France.

Pulmonary arterial hypertension (PAH) is a rare and deadly disease affecting roughly 15-60 people per million in Europe with a poorly understood pathology. There are currently no diagnostic tools for early detection nor does a curative treatment exist. The lipid composition of arteries in lung tissue samples from human PAH and control patients were investigated using matrix-assisted laser desorption ionization (MALDI) imaging mass spectrometry (IMS) combined with time-of-flight secondary ion mass spectrometry (TOF-SIMS) imaging. Using random forests as an IMS data analysis technique, it was possible to identify the ion at / 885.6 as a marker of PAH in human lung tissue. The / 885.6 ion intensity was shown to be significantly higher around diseased arteries and was confirmed to be a diacylglycerophosphoinositol PI(C18:0/C20:4) via MS/MS using a novel hybrid SIMS instrument. The discovery of a potential biomarker opens up new research avenues which may finally lead to a better understanding of the PAH pathology and highlights the vital role IMS can play in modern biomedical research.
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http://dx.doi.org/10.1021/acs.analchem.0c02815DOI Listing
September 2020

Purification, Toxicity and Functional Characterization of a New Proteinaceous Mussel Biotoxin from Bizerte Lagoon.

Toxins (Basel) 2020 07 30;12(8). Epub 2020 Jul 30.

Institut Pasteur de Tunis, Laboratoire des Venins et Biomolécules Thérapeutiques, Université Tunis El Manar, 13 Place Pasteur, B.P. 74, 1002 Tunis-Belvédère, Tunisia.

The marine environment is known to be occupied by microorganisms. The potential toxicity of some of these marine microorganisms, that are capable of producing unknown biotoxins, has always been underestimated. Indeed, these biotoxins may be a threat to human health through the consumption of contaminated seafood and fish. For more than ten years, recurrent but atypical toxicity has been detected in mussels from Bizerte lagoon (North of Tunisia) during routine tests. In this study, we have isolated and characterized a new proteinaceous marine biotoxin, named Mussel Toxic Peptide (MTP). Using HPLC, electrophoresis and LC/MS studies, we showed that MTP has a protein characteristic UV-spectrum, can be visualized by protein specific reagents such as Coomassie, and has a molecular mass of 6.4 kDa. Patch-clamp experiments performed on cultured N18 neuroblastoma cells revealed that MTP (0.9-18 µM) markedly inhibited voltage-gated Na current, but was about 23 times less active in blocking voltage-gated K current at equimolar concentrations. To the best of our knowledge, this is the first time that a proteinaceous marine biotoxin with relatively high molecular mass is isolated and involved in the contamination of mussels harvested from shellfish farming areas.
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http://dx.doi.org/10.3390/toxins12080487DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7472388PMC
July 2020

Structural and genomic decoding of human and plant myristoylomes reveals a definitive recognition pattern.

Nat Chem Biol 2018 07 11;14(7):671-679. Epub 2018 Jun 11.

Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Gif-sur-Yvette cedex, France.

An organism's entire protein modification repertoire has yet to be comprehensively mapped. N-myristoylation (MYR) is a crucial eukaryotic N-terminal protein modification. Here we mapped complete Homo sapiens and Arabidopsis thaliana myristoylomes. The crystal structures of human modifier NMT1 complexed with reactive and nonreactive target-mimicking peptide ligands revealed unexpected binding clefts and a modifier recognition pattern. This information allowed integrated mapping of myristoylomes using peptide macroarrays, dedicated prediction algorithms, and in vivo mass spectrometry. Global MYR profiling at the genomic scale identified over a thousand novel, heterogeneous targets in both organisms. Surprisingly, MYR involved a non-negligible set of overlapping targets with N-acetylation, and the sequence signature marks for a third proximal acylation-S-palmitoylation-were genomically imprinted, allowing recognition of sequences exhibiting both acylations. Together, the data extend the N-end rule concept for Gly-starting proteins to subcellular compartmentalization and reveal the main neighbors influencing protein modification profiles and consequent cell fate.
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http://dx.doi.org/10.1038/s41589-018-0077-5DOI Listing
July 2018

Targeted Profiling of Subproteomes Illuminates Co- and Posttranslationally N-Terminal Myristoylated Proteins.

Plant Cell 2018 03 16;30(3):543-562. Epub 2018 Feb 16.

Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France

N-terminal myristoylation, a major eukaryotic protein lipid modification, is difficult to detect in vivo and challenging to predict in silico. We developed a proteomics strategy involving subfractionation of cellular membranes, combined with separation of hydrophobic peptides by mass spectrometry-coupled liquid chromatography to identify the myristoylated proteome. This approach identified a starting pool of 8837 proteins in all analyzed cellular fractions, comprising 32% of the Arabidopsis proteome. Of these, 906 proteins contain an N-terminal Gly at position 2, a prerequisite for myristoylation, and 214 belong to the predicted myristoylome (comprising 51% of the predicted myristoylome of 421 proteins). We further show direct evidence of myristoylation in 72 proteins; 18 of these myristoylated proteins were not previously predicted. We found one myristoylation site downstream of a predicted initiation codon, indicating that posttranslational myristoylation occurs in plants. Over half of the identified proteins could be quantified and assigned to a subcellular compartment. Hierarchical clustering of protein accumulation combined with myristoylation and -acylation data revealed that N-terminal double acylation influences redirection to the plasma membrane. In a few cases, MYR function extended beyond simple membrane association. This study identified hundreds of -acylated proteins for which lipid modifications could control protein localization and expand protein function.
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http://dx.doi.org/10.1105/tpc.17.00523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5894833PMC
March 2018

DYRK1A inhibition and cognitive rescue in a Down syndrome mouse model are induced by new fluoro-DANDY derivatives.

Sci Rep 2018 02 12;8(1):2859. Epub 2018 Feb 12.

Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, 91198, Gif-sur-Yvette, France.

Inhibition of DYRK1A kinase, produced by chromosome 21 and consequently overproduced in trisomy 21 subjects, has been suggested as a therapeutic approach to treating the cognitive deficiencies observed in Down syndrome (DS). We now report the synthesis and potent DYRK1A inhibitory activities of fluoro derivatives of 3,5-di(polyhydroxyaryl)-7-azaindoles (F-DANDYs). One of these compounds (3-(4-fluorophenyl)-5-(3,4-dihydroxyphenyl)-1H-pyrrolo[2,3-b]pyridine, 5a) was selected for in vivo studies of cognitive rescuing effects in a standard mouse model of DS (Ts65Dn line). Using the Morris water maze task, Ts65Dn mice treated i.p. with 20 mg/kg of 5a performed significantly better than Ts65Dn mice treated with placebo, confirming the promnesiant effect of 5a in the trisomic mice. Overall, these results demonstrate for the first time that selective and competitive inhibition of DYRK1A kinase by the F-DANDY derivative 5a may provide a viable treatment strategy for combating the memory and learning deficiencies encountered in DS.
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http://dx.doi.org/10.1038/s41598-018-20984-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5809559PMC
February 2018

An Integrative Approach to Decipher the Chemical Antagonism between the Competing Endophytes Paraconiothyrium variabile and Bacillus subtilis.

J Nat Prod 2017 11 15;80(11):2863-2873. Epub 2017 Nov 15.

Unité Molécules de Communication et Adaptation des Micro-organismes (UMR 7245), Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS , CP 54, 57 rue Cuvier, 75005 Paris, France.

An integrative approach combining traditional natural products chemistry, molecular networking, and mass spectrometry imaging has been undertaken to decipher the molecular dialogue between the fungus Paraconiothyrium variabile and the bacterium Bacillus subtilis, which were isolated as endophytes from the conifer Cephalotaxus harringtonia and are characterized by a strong and mutual antibiosis. From this study, we highlight that bacterial surfactins and a fungal tetronic acid are involved in such competition and that the fungus is able to hydrolyze surfactins to fight against the bacterial partner.
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http://dx.doi.org/10.1021/acs.jnatprod.6b01185DOI Listing
November 2017

Affinity labelling in situ of the bL12 protein on E. coli 70S ribosomes by means of a tRNA dialdehyde derivative.

J Biochem 2017 Dec;162(6):437-448

Sorbonne Universités UPMC Univ Paris 06, Unité de Recherche UPMC UR6 "Enzymologie de l'ARN", 4, Place Jussieu, F-75252 Paris Cedex 05, France.

In this report, we have used periodate-oxidized tRNA (tRNAox) as an affinity laleling reagent to demonstrate that: (i) the bL12 protein contacts the CCA-arm of P-site bound tRNA on the Escherichia coli 70S ribosomes; (ii) the stoichiometry of labelling is one molecule of tRNAox bound to one polypeptide chain of endogenous bL12; (iii) cross-linking in situ of bL12 with tRNAox on the ribosomes provokes the loss of activity; (iv) intact tRNA protects bL12 in the 70S ribosomes against cross-linking with tRNAox; (v) both tRNAox and pyridoxal 5'-phosphate (PLP) compete for the same or for proximal cross-linking site(s) on bL12 inside the ribosome; (vi) the stoichiometry of cross-linking of PLP to the recombinant E. coli bL12 protein is one molecule of PLP covalently bound per polypeptide chain; (vii) the amino acid residue of recombinant bL12 cross-linked with PLP is Lys-65; (viii) Lys-65 of E. coli bL12 corresponds to Lys-53 of eL42 which was previously shown to cross-link with P-site bound tRNAox on human 80S ribosomes in situ; (ix) finally, E. coli bL12 and human eL42 proteins display significant primary structure similarities, which argues for evolutionary conservation of these two proteins located at the tRNA-CCA binding site on eubacterial and eukaryal ribosomes.
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http://dx.doi.org/10.1093/jb/mvx055DOI Listing
December 2017

An histidine covalent receptor and butenolide complex mediates strigolactone perception.

Nat Chem Biol 2016 10 1;12(10):787-794. Epub 2016 Aug 1.

Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France.

Strigolactone plant hormones control plant architecture and are key players in both symbiotic and parasitic interactions. They contain an ABC tricyclic lactone connected to a butenolide group, the D ring. The DWARF14 (D14) strigolactone receptor belongs to the superfamily of α/β-hydrolases, and is known to hydrolyze the bond between the ABC lactone and the D ring. Here we characterized the binding and catalytic functions of RAMOSUS3 (RMS3), the pea (Pisum sativum) ortholog of rice (Oryza sativa) D14 strigolactone receptor. Using new profluorescent probes with strigolactone-like bioactivity, we found that RMS3 acts as a single-turnover enzyme that explains its apparent low enzymatic rate. We demonstrated the formation of a covalent RMS3-D-ring complex, essential for bioactivity, in which the D ring was attached to histidine 247 of the catalytic triad. These results reveal an undescribed mechanism of plant hormone reception in which the receptor performs an irreversible enzymatic reaction to generate its own ligand.
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http://dx.doi.org/10.1038/nchembio.2147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5030144PMC
October 2016

An Artificial Enzyme Made by Covalent Grafting of an Fe(II) Complex into β-Lactoglobulin: Molecular Chemistry, Oxidation Catalysis, and Reaction-Intermediate Monitoring in a Protein.

Chemistry 2015 Aug 15;21(34):12188-93. Epub 2015 Jul 15.

Institut de Chimie Moléculaire et des Matériaux d'Orsay, Université Paris Sud, CNRS, 91405, Orsay CEDEX (France).

An artificial metalloenzyme based on the covalent grafting of a nonheme Fe(II) polyazadentate complex into bovine β-lactoglobulin has been prepared and characterized by using various spectroscopic techniques. Attachment of the Fe(II) catalyst to the protein scaffold is shown to occur specifically at Cys121. In addition, spectrophotometric titration with cyanide ions based on the spin-state conversion of the initial high spin (S=2) Fe(II) complex into a low spin (S=0) one allows qualitative and quantitative characterization of the metal center's first coordination sphere. This biohybrid catalyst activates hydrogen peroxide to oxidize thioanisole into phenylmethylsulfoxide as the sole product with an enantiomeric excess of up to 20 %. Investigation of the reaction between the biohybrid system and H2 O2 reveals the generation of a high spin (S=5/2) Fe(III) (η(2) -O2 ) intermediate, which is proposed to be responsible for the catalytic sulfoxidation of the substrate.
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http://dx.doi.org/10.1002/chem.201501755DOI Listing
August 2015

Mammalian frataxin directly enhances sulfur transfer of NFS1 persulfide to both ISCU and free thiols.

Nat Commun 2015 Jan 19;6:5686. Epub 2015 Jan 19.

Institut de Chimie des Substances Naturelles, UPR2301, Centre de Recherche de Gif, Centre National de la Recherche Scientifique, 1 avenue de la terrasse, 91191 Gif Sur Yvette, France.

Friedreich's ataxia is a severe neurodegenerative disease caused by the decreased expression of frataxin, a mitochondrial protein that stimulates iron-sulfur (Fe-S) cluster biogenesis. In mammals, the primary steps of Fe-S cluster assembly are performed by the NFS1-ISD11-ISCU complex via the formation of a persulfide intermediate on NFS1. Here we show that frataxin modulates the reactivity of NFS1 persulfide with thiols. We use maleimide-peptide compounds along with mass spectrometry to probe cysteine-persulfide in NFS1 and ISCU. Our data reveal that in the presence of ISCU, frataxin enhances the rate of two similar reactions on NFS1 persulfide: sulfur transfer to ISCU leading to the accumulation of a persulfide on the cysteine C104 of ISCU, and sulfur transfer to small thiols such as DTT, L-cysteine and GSH leading to persulfuration of these thiols and ultimately sulfide release. These data raise important questions on the physiological mechanism of Fe-S cluster assembly and point to a unique function of frataxin as an enhancer of sulfur transfer within the NFS1-ISD11-ISCU complex.
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http://dx.doi.org/10.1038/ncomms6686DOI Listing
January 2015

Isolation, purification and functional characterization of alpha-BnIA from Conus bandanus venom.

Toxicon 2014 Dec 15;91:155-63. Epub 2014 Oct 15.

CNRS, Centre de Recherche de Gif - FRC3115, Institut de Neurobiologie Alfred Fessard - FRC2118, Laboratoire de Neurobiologie et Développement - UPR3294, F-91198 Gif-sur-Yvette, France. Electronic address:

We report the isolation and characterization by proteomic approach of a native conopeptide, named BnIA, from the crude venom of Conus bandanus, a molluscivorous cone snail species, collected in the South central coast of Vietnam. Its primary sequence was determined by matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry using collision-induced dissociation and confirmed by Edman's degradation of the pure native fraction. BnIA was present in high amounts in the crude venom and the complete sequence of the 16 amino acid peptide was the following GCCSHPACSVNNPDIC*, with C-terminal amidation deduced from Edman's degradation and theoretical monoisotopic mass calculation. Sequence alignment revealed that its -C1C2X4C3X7C4- pattern belongs to the A-superfamily of conopeptides. The cysteine connectivity of BnIA was 1-3/2-4 as determined by partial-reduction technique, like other α4/7-conotoxins, reported previously on other Conus species. Additionally, we found that native α-BnIA shared the same sequence alignment as Mr1.1, from the closely related molluscivorous Conus marmoreus venom, in specimens collected in the same coastal region of Vietnam. Functional studies revealed that native α-BnIA inhibited acetylcholine-evoked currents reversibly in oocytes expressing the human α7 nicotinic acetylcholine receptors, and blocked nerve-evoked skeletal muscle contractions in isolated mouse neuromuscular preparations, but with ∼200-times less potency.
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http://dx.doi.org/10.1016/j.toxicon.2014.10.006DOI Listing
December 2014

Agar-supported cultivation of Halorubrum sp. SSR, and production of halocin C8 on the scale-up prototype Platotex.

Extremophiles 2014 Nov 20;18(6):1049-55. Epub 2014 Aug 20.

Faculty of Biological Sciences, Cellular and Molecular Biology Laboratory, University of Sciences and Technology Houari Boumediene, Bp 32, El Alia, 16111, Bab Ezzouar Algiers, Algeria.

Halorubrum sp. SSR was isolated from a solar saltern in Algeria. The strain exhibited a high antibiotic activity against the indicator strain Natronorubrum aibiense G23, and the bioactive compound showed thermal, acid and alkali stability. SSR was grown on agar-supported cultivation (AgSF) to compare yields and applicability with traditional submerged cultivation. AgSF scale-up was implemented taking benefit from the solid-state cultivation prototype Platotex. This technology leads to high amounts of the target Halocin and facilitate the downstream steps. The antibiotic compound was purified according to a fast efficient procedure including ion exchange chromatography followed by a fractionation on C18 Sep-Pack cartridge. The compound was identified as Halocin C8 according to N-terminal amino acid sequencing and high-resolution mass spectrometry.
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http://dx.doi.org/10.1007/s00792-014-0682-5DOI Listing
November 2014

Optimization and validation of a label-free MRM method for the quantification of cytochrome P450 isoforms in biological samples.

Anal Bioanal Chem 2014 Aug 22;406(20):4861-74. Epub 2014 Jun 22.

Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles, CNRS, Avenue de la Terrasse, 91198, Gif-sur-Yvette Cedex, France.

Cytochromes P450 (CYPs) play critical roles in oxidative metabolism of many endogenous and exogenous compounds. Protein expression levels of CYPs in liver provide relevant information for a better understanding of the importance of CYPs in pharmacology and toxicology. This work aimed at establishing a simple method to quantify six CYPs (CYP3A4, CYP3A5, CYP1A2, CYP2D6, CYP2C9, and CYP2J2) in various biological samples without isotopic labeling. The biological matrix was spiked with the standard peptides prior to the digestion step to realize a label-free quantification by mass spectrometry. The method was validated and applied to quantify these six isoforms in both human liver microsomes and mitochondria, but also in recombinant expression systems such as baculosomes and the HepG2 cell line. The results showed intra-assay and interassay accuracy and precision within 16 % and 5 %, respectively, at the low quality control level, and demonstrated the advantages of the method in terms of reproducibility and cost.
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http://dx.doi.org/10.1007/s00216-014-7928-zDOI Listing
August 2014

Characterization of a novel Conus bandanus conopeptide belonging to the M-superfamily containing bromotryptophan.

Mar Drugs 2014 Jun 5;12(6):3449-65. Epub 2014 Jun 5.

Neurobiology and Development Laboratory, Research Unit # 3294, Institute of Neurobiology Alfred Fessard # 2118, National Center for Scientific Research, Gif sur Yvette Cedex 91198, France.

A novel conotoxin (conopeptide) was biochemically characterized from the crude venom of the molluscivorous marine snail, Conus bandanus (Hwass in Bruguière, 1792), collected in the south-central coast of Vietnam. The peptide was identified by screening bromotryptophan from chromatographic fractions of the crude venom. Tandem mass spectrometry techniques were used to detect and localize different post-translational modifications (PTMs) present in the BnIIID conopeptide. The sequence was confirmed by Edman's degradation and mass spectrometry revealing that the purified BnIIID conopeptide had 15 amino acid residues, with six cysteines at positions 1, 2, 7, 11, 13, and 14, and three PTMs: bromotryptophan, γ-carboxy glutamate, and amidated aspartic acid, at positions "4", "5", and "15", respectively. The BnIIID peptide was synthesized for comparison with the native peptide. Homology comparison with conopeptides having the III-cysteine framework (-CCx1x2x3x4Cx1x2x3Cx1CC-) revealed that BnIIID belongs to the M-1 family of conotoxins. This is the first report of a member of the M-superfamily containing bromotryptophan as PTM.
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http://dx.doi.org/10.3390/md12063449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071585PMC
June 2014

Toxic c17-sphinganine analogue mycotoxin, contaminating tunisian mussels, causes flaccid paralysis in rodents.

Mar Drugs 2013 Nov 28;11(12):4724-40. Epub 2013 Nov 28.

Laboratory of Food Toxins, Pasteur Institute of Tunis, University of Tunis Manar, 13 Place Pasteur, Post-Office Box 74, Tunis-Belvédère 1002, Tunisia.

Severe toxicity was detected in mussels from Bizerte Lagoon (Northern Tunisia) using routine mouse bioassays for detecting diarrheic and paralytic toxins not associated to classical phytoplankton blooming. The atypical toxicity was characterized by rapid mouse death. The aim of the present work was to understand the basis of such toxicity. Bioassay-guided chromatographic separation and mass spectrometry were used to detect and characterize the fraction responsible for mussels' toxicity. Only a C17-sphinganine analog mycotoxin (C17-SAMT), with a molecular mass of 287.289 Da, was found in contaminated shellfish. The doses of C17-SAMT that were lethal to 50% of mice were 750 and 150 μg/kg following intraperitoneal and intracerebroventricular injections, respectively, and 900 μg/kg following oral administration. The macroscopic general aspect of cultures and the morphological characteristics of the strains isolated from mussels revealed that the toxicity episodes were associated to the presence of marine microfungi (Fusarium sp., Aspergillus sp. and Trichoderma sp.) in contaminated samples. The major in vivo effect of C17-SAMT on the mouse neuromuscular system was a dose- and time-dependent decrease of compound muscle action potential amplitude and an increased excitability threshold. In vitro, C17-SAMT caused a dose- and time-dependent block of directly- and indirectly-elicited isometric contraction of isolated mouse hemidiaphragms.
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http://dx.doi.org/10.3390/md11124724DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3877882PMC
November 2013

High accuracy mass spectrometry comparison of Conus bandanus and Conus marmoreus venoms from the South Central Coast of Vietnam.

Toxicon 2013 Dec 21;75:148-59. Epub 2013 Jun 21.

CNRS, Centre de Recherche de Gif - FRC3115, Institut de Neurobiologie Alfred Fessard - FRC2118, Laboratoire de Neurobiologie et Développement - UPR3294, F-91198 Gif-sur-Yvette, France; University of Nha Trang, Institute of Biotechnology and Environment, Nha Trang, Khanh Hoa, Viet Nam. Electronic address:

Cone snail (genus Conus) venoms provide a rich source of small bioactive peptides known as conopeptides or conotoxins, which are highly interesting in pharmacological studies for new drug discovery. Conus species have evolved expressing a variety of conopeptides, adapted to the biological targets of their own specific preys at their living environments. Therefore, the potential proteomic evaluation of Conus venom components, poorly studied, is of great interest. Early studies supposed about 5% overlap in venom peptides from different Conus species. In this study, we compare using nano-liquid chromatography coupled with electrospray ionisation-mass spectrometry and bioinformatics, the molluscivorous Conus bandanus venom to that of its close-relative Conus marmoreus of the South Central Coast of Vietnam. With this approach, we demonstrate with high precision that 92 common conopeptides are present in the venom of the two mollusc-hunting cone snails, representing 24.4% (out of 376 peptides) and 18.4% (out of 499 peptides) of C. bandanus and C. marmoreus components, respectively. The proteomic comparison of the two close-relative interspecies suggests both common and different strategies for mature conopeptide production in the two species. The overall estimation of putative conopeptide disulphide bridges reveals 75% and 61% of "disulphide-rich" peptides in C. bandanus and C. marmoreus venom components, respectively. The same amino acid sequence for Bn1.1 and Mr1.1, determined at the genomic level, was also found in the two venoms, besides other common conopeptides. Confidently, the broader distribution of C. bandanus compared to C. marmoreus guarantee new opportunities for discovering conopeptides with original pharmacological properties.
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http://dx.doi.org/10.1016/j.toxicon.2013.06.005DOI Listing
December 2013

Identification and functional characterization of a novel α-conotoxin (EIIA) from Conus ermineus.

Anal Bioanal Chem 2013 Jun 14;405(15):5341-51. Epub 2013 Apr 14.

Laboratoire des Mécanismes Réactionnels, Département de Chimie, Ecole Polytechnique, CNRS UMR7651, 91128 Palaiseau Cedex, France.

Nicotinic acetylcholine receptors (nAChRs) are one of the most important families in the ligand-gated ion channel superfamily due to their involvement in primordial brain functions and in several neurodegenerative pathologies. The discovery of new ligands which can bind with high affinity and selectivity to nAChR subtypes is of prime interest in order to study these receptors and to potentially discover new drugs for treating various pathologies. Predatory cone snails of the genus Conus hunt their prey using venoms containing a large number of small, highly structured peptides called conotoxins. Conotoxins are classified in different structural families and target a large panel of receptors and ion channels. Interestingly, nAChRs represent the only subgroup for which Conus has developed seven distinct families of conotoxins. Conus venoms have thus received much attention as they could represent a potential source of selective ligands of nAChR subtypes. We describe the mass spectrometric-based approaches which led to the discovery of a novel α-conotoxin targeting muscular nAChR from the venom of Conus ermineus. The presence of several posttranslational modifications complicated the N-terminal sequencing. To discriminate between the different possible sequences, analogs with variable N-terminus were synthesized and fragmented by MS/MS. Understanding the fragmentation pathways in the low m/z range appeared crucial to determine the right sequence. The biological activity of this novel α-conotoxin (α-EIIA) that belongs to the unusual α4/4 subfamily was determined by binding experiments. The results revealed not only its selectivity for the muscular nAChR, but also a clear discrimination between the two binding sites described for this receptor.
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http://dx.doi.org/10.1007/s00216-013-6926-xDOI Listing
June 2013

Immunoproteomic analysis of potentially severe non-graft-versus-host disease hepatitis after allogenic bone marrow transplantation.

Hepatology 2013 Feb 8;57(2):689-99. Epub 2013 Jan 8.

INSERM, Unité 785, Villejuif, France.

Unlabelled: The development of potentially severe non-graft-versus-host disease (GVHD) hepatitis resembling autoimmune hepatitis (AIH) has been reported after bone marrow transplantation (BMT). The aim of this study was to better characterize this form of hepatitis, particularly through the identification of autoantigens recognized by patient sera. Five patients who received an allogeneic BMT for the treatment of hematological diseases developed liver dysfunction with histological features suggestive of AIH. Before and during the onset of hepatic dysfunction, sera were tested on immunoblottings performed with cytosolic, microsomal, mitochondrial, and nuclear proteins from rat liver homogenate and resolved by two-dimensional electrophoresis. Antigenic targets were identified by mass spectrometry. During the year that followed BMT, all patients presented with GVHD. Acute hepatitis then occurred after the withdrawal, or during the tapering, of immunosuppressive therapy. At that time, no patients had a history of liver toxic drug absorption, patent viral infection, or any histopathological findings consistent with GVHD. Immunoreactive spots stained by sera collected at the time of hepatic dysfunction were more numerous and more intensely expressed than those stained by sera collected before. Considerable patient-dependent pattern heterogeneity was observed. Among the 259 spots stained exclusively by sera collected at the time of hepatitis, a total of 240 spots were identified, corresponding to 103 different proteins. Twelve of them were recognized by sera from 3 patients.

Conclusions: This is the first immunological description of potentially severe non-GVHD hepatitis occurring after BMT, determined using a proteomic approach and enabling a discussion of the mechanisms that transform an alloimmune reaction into an autoimmune response. Any decision to withdraw immunosuppression after allogeneic BMT should be made with caution.
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http://dx.doi.org/10.1002/hep.26024DOI Listing
February 2013

Solid-phase hexapeptide ligand libraries open up new perspectives in the discovery of biomarkers in human plasma.

Clin Chim Acta 2011 Apr 8;412(9-10):740-7. Epub 2011 Jan 8.

Inserm, U698, Paris, F-75018 France.

Background: Pre-treatment of plasma with hexapeptide ligand libraries prior to proteomic analysis is well documented. However, the maintenance of biomarker abundance throughout the different pre-analytical steps is required for a potential application of differential proteomics in clinical studies.

Methods: We combined the use of an amino-terminal hexapeptide ligand library and its carboxyl-terminal version with a sequential elution strategy of the proteins/peptides bound to the beads, followed by either mass spectrometry or 2D electrophoresis analyses.

Results: We show the maintenance of C-reactive protein abundance (a marker of inflammation) throughout the process (including hexapeptide bead treatment and proteomic analysis) in patients presenting high and low levels of this protein. In parallel, we assessed the contribution of this workflow to increasing the number of potential biomarkers detected and its suitability for a clinical study on approximately a hundred samples, as well as the reproducibility of the process.

Conclusions: Pre-treatment with hexapeptide ligand libraries opens up new perspectives in the discovery of biomarkers in human plasma by improving the detection of new species while maintaining their original differential abundance. This approach is also suitable for an application in a clinical proteomic study of at least 100 samples.
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http://dx.doi.org/10.1016/j.cca.2010.12.036DOI Listing
April 2011

A region within the C-terminal domain of Ure2p is shown to interact with the molecular chaperone Ssa1p by the use of cross-linkers and mass spectrometry.

FEBS J 2010 Dec 16;277(24):5112-23. Epub 2010 Nov 16.

Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif-sur-Yvette, France.

The propagation of yeast prion phenotypes is highly dependent on molecular chaperones. We previously demonstrated that the molecular chaperone Ssa1p sequesters Ure2p in high molecular weight, assembly incompetent oligomeric species. We also determined the affinity of Ssa1p for Ure2p, and its globular domain. To map the Ure2p-Ssa1p interface, we have used chemical cross-linkers and MS. We demonstrate that Ure2p and Ssa1p form a 1 : 1 complex. An analytical strategy combining in-gel digestion of cross-linked protein complexes, and both MS and MS/MS analysis of proteolytic peptides, allowed us to identify a number of peptides that were modified because they are exposed to the solvent. A difference in the exposure to the solvent of a single lysine residue, lysine 339 of Ure2p, was detected upon Ure2p-Ssa1p complex formation. These observations strongly suggest that lysine 339 and its flanking amino acid stretches are involved in the interaction between Ure2p and Ssa1p. They also reveal that the Ure2p amino-acid stretch spanning residues 327-339 plays a central role in the assembly into fibrils.
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http://dx.doi.org/10.1111/j.1742-4658.2010.07915.xDOI Listing
December 2010

Analysis of human C1q by combined bottom-up and top-down mass spectrometry: detailed mapping of post-translational modifications and insights into the C1r/C1s binding sites.

Mol Cell Proteomics 2010 Apr 14;9(4):593-610. Epub 2009 Dec 14.

Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, CNRS UMR 8587, Université d'Evry-Val-d'Essonne, Evry, France.

C1q is a subunit of the C1 complex, a key player in innate immunity that triggers activation of the classical complement pathway. Featuring a unique structural organization and comprising a collagen-like domain with a high level of post-translational modifications, C1q represents a challenging protein assembly for structural biology. We report for the first time a comprehensive proteomics study of C1q combining bottom-up and top-down analyses. C1q was submitted to proteolytic digestion by a combination of collagenase and trypsin for bottom-up analyses. In addition to classical LC-MS/MS analyses, which provided reliable identification of hydroxylated proline and lysine residues, sugar loss-triggered MS(3) scans were acquired on an LTQ-Orbitrap (Linear Quadrupole Ion Trap-Orbitrap) instrument to strengthen the localization of glucosyl-galactosyl disaccharide moieties on hydroxylysine residues. Top-down analyses performed on the same instrument allowed high accuracy and high resolution mass measurements of the intact full-length C1q polypeptide chains and the iterative fragmentation of the proteins in the MS(n) mode. This study illustrates the usefulness of combining the two complementary analytical approaches to obtain a detailed characterization of the post-translational modification pattern of the collagen-like domain of C1q and highlights the structural heterogeneity of individual molecules. Most importantly, three lysine residues of the collagen-like domain, namely Lys(59) (A chain), Lys(61) (B chain), and Lys(58) (C chain), were unambiguously shown to be completely unmodified. These lysine residues are located about halfway along the collagen-like fibers. They are thus fully available and in an appropriate position to interact with the C1r and C1s protease partners of C1q and are therefore likely to play an essential role in C1 assembly.
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http://dx.doi.org/10.1074/mcp.M900350-MCP200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860232PMC
April 2010

The human large subunit ribosomal protein L36A-like contacts the CCA end of P-site bound tRNA.

Biochimie 2009 Nov-Dec;91(11-12):1420-5. Epub 2009 Jul 31.

Université Pierre et Marie Curie (UPMC, Univ Paris 06), Equipe de Photobiologie Moléculaire, Paris Cedex 05, France.

Periodate-oxidized tRNA (tRNAox), the 2',3'-dialdehyde derivative of tRNA, was used as a zero-length active site-directed affinity labeling reagent, to covalently label proteins at the binding site for the 3'-end of tRNA on human 80S ribosomes. When human 80S ribosomes were reacted with tRNA(Asp)ox positioned at the P-site, in the presence of an appropriate 12 mer mRNA, a set of two tRNAox-labeled ribosomal proteins (rPs) was observed. The majorily labeled protein was identified as the large subunit rP L36a-like (RPL36AL) by means of mass spectrometry. Intact tRNA(Asp) competed with tRNA(Asp)ox for the binding to the P-site, by preventing tRNA-protein cross-linking with RPL36AL. Altogether, the data presented in this report are consistent with the presence of RPL36AL at or near the binding site for the CCA end of the tRNA substrate positioned at the P-site of human 80S ribosomes. It is the first time that a ribosomal protein is found in an intimate contact (i.e. at a zero-distance) with a nucleotide of the conserved CCA terminus of P-site tRNA which is the substrate of peptidyl transferase reaction. RPL36AL which is strongly conserved in eukaryotes belongs to the L44e family of rPs, a representative of which is Haloarcula marismortui RPL44e.
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http://dx.doi.org/10.1016/j.biochi.2009.07.013DOI Listing
April 2010

In situ localisation and quantification of surfactins in a Bacillus subtilis swarming community by imaging mass spectrometry.

Proteomics 2008 Sep;8(18):3682-91

Institut de Chimie des Substances Naturelles, CNRS, UPR 2301, Av. de la Terrasse, Gif-sur-Yvette, France.

Surfactins are a family of heptacyclopeptides in which the C-terminal carbonyl is linked with the beta-hydroxy group of a fatty acid acylating the N-terminal function of a glutamic acid residue. The fatty acyl chain is 12-16 carbon atoms long. These compounds, which are secreted by the Gram-positive bacterium Bacillus subtilis in stationary phase in liquid cultures, play an important role in swarming communities on the surface of agar media in the formation of dendritic patterns. TOF secondary ion MS (TOF-SIMS) imaging was used to map surfactins within 16-17 h swarming patterns, with a 2 mum spatial resolution. Surfactins were mainly located in the central mother colony (the site of initial inoculation), in a 'ring' surrounding the pattern and along the edges of the dendrites. In the mother colony and the interior of the dendrites, surfactins with shorter chain lengths are present, whereas in the ring surrounding the swarm community and between dendrites, surfactins with longer fatty acyl chain lengths were found. A quantitative analysis by MALDI-TOF MS showed a concentration gradient of surfactin from the mother colony to the periphery. The concentration of surfactin was approximately 400 pmol/mL in the mother colony and approximately 10 pmol/mL at the base of the dendrites, decreasing to 2 pmol/mL at their tips.
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http://dx.doi.org/10.1002/pmic.200701025DOI Listing
September 2008

Large-scale study of phosphoproteins involved in long-term potentiation in the rat dentate gyrus in vivo.

Eur J Neurosci 2008 Jun;27(11):2985-98

Laboratoire de Neurobiologie de l'Apprentissage, de la Mémoire et de la Communication, Université Paris-Sud, Orsay, France.

The mechanisms underlying the induction of synaptic plasticity and the formation of long-term memory involve activation of cell-signalling cascades and protein modifications such as phosphorylation and dephosphorylation. Based on a protein candidate strategy, studies have identified several protein kinases and their substrates, which show an altered phosphorylation state during the early phases of long-term potentiation (LTP), yet only a limited number of synaptic phosphoproteins are known to be implicated in LTP. To identify new phosphoproteins associated with LTP, we have undertaken a proteomic study of phosphoproteins at different time points following the induction of LTP in the dentate gyrus in vivo (0, 15 and 90 min). For each time point, proteins from the dentate gyrus were separated by two-dimensional gel electrophoresis and stained with Pro-Q Diamond, a fluorescent stain specific for phosphoproteins. Fourteen proteins whose phosphorylation state varied significantly following LTP were identified using matrix-assisted laser desorption ionization/time of flight mass spectrometry and electrospray ionization-Orbitrap tandem mass spectrometry (MS/MS). They are involved in various cellular functions implicated in synaptic plasticity, such as intracellular signalling, axonal growth, exocytosis, protein synthesis and metabolism. Our results highlight new proteins whose phosphorylation or dephosphorylation is associated with LTP induction or maintenance. Further studies focusing on the regulation of specific phosphorylation sites will lead to greater understanding of the individual implications of these proteins in LTP as well as of their molecular interactions.
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http://dx.doi.org/10.1111/j.1460-9568.2008.06280.xDOI Listing
June 2008

An Sfi1p-like centrin-binding protein mediates centrin-based Ca2+ -dependent contractility in Paramecium tetraurelia.

Eukaryot Cell 2007 Nov 3;6(11):1992-2000. Epub 2007 Aug 3.

Centre de Génétique Moléculaire, UPR 2167, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, France.

The previous characterization and structural analyses of Sfi1p, a Saccharomyces cerevisiae centrin-binding protein essential for spindle pole body duplication, have suggested molecular models to account for centrin-mediated, Ca2+-dependent contractility processes (S. Li, A. M. Sandercock, P. Conduit, C. V. Robinson, R. L. Williams, and J. V. Kilmartin, J. Cell Biol. 173:867-877, 2006). Such processes can be analyzed by using Paramecium tetraurelia, which harbors a large Ca2+ -dependent contractile cytoskeletal network, the infraciliary lattice (ICL). Previous biochemical and genetic studies have shown that the ICL is composed of diverse centrin isoforms and a high-molecular-mass centrin-associated protein, whose reduced size in the démaillé (dem1) mutant correlates with defective organization of the ICL. Using sequences derived from the high-molecular-mass protein to probe the Paramecium genome sequence, we characterized the PtCenBP1 gene, which encodes a 460-kDa protein. PtCenBP1p displays six almost perfect repeats of ca. 427 amino acids (aa) and harbors 89 potential centrin-binding sites with the consensus motif LLX11F/LX2WK/R, similar to the centrin-binding sites of ScSfi1p. The smaller (260-kDa) protein encoded by the dem1 mutant PtCenBP1 allele comprises only two repeats of 427 aa and 46 centrin-binding sites. By using RNA interference and green fluorescent protein fusion experiments, we showed that PtCenBP1p forms the backbone of the ICL and plays an essential role in its assembly and contractility. This study provides the first in vivo demonstration of the role of Sfi1p-like proteins in centrin-mediated Ca2+-dependent contractile processes.
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http://dx.doi.org/10.1128/EC.00197-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168399PMC
November 2007

Hydrogen/deuterium exchange mass spectrometric analysis of conformational changes accompanying the assembly of the yeast prion Ure2p into protein fibrils.

J Mol Biol 2007 Jun 12;369(4):1113-25. Epub 2007 Apr 12.

Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France.

The Ure2 protein from baker's yeast (Saccharomyces cerevisiae) has prion properties. In vitro, at neutral pH, soluble Ure2p forms long, twisted fibrils. Two models have been proposed to account for Ure2p polymerization. The first postulates that a segment of 70 amino acid residues in the flexible N-terminal domain from different Ure2p molecules forms a parallel superpleated beta-structure running along the fibrils. The second hypothesizes that assembly of full-length Ure2p is driven by limited conformational rearrangements and non-native inter- and intramolecular interactions. The knowledge of the three-dimensional structure of the fibrillar form of Ure2p is critical for understanding the molecular events leading to the polymerization of soluble Ure2p into fibrils and hence for the design of inhibitors that might have therapeutic potential as yeast prions possessing domains rich in N and Q residues, similar to huntingtin. Solvent-accessibility studies using hydrogen/deuterium exchange monitored by mass spectrometry (HXMS) can provide insights into the structure of the fibrillar form of Ure2p and characterize at the molecular level the conformational rearrangements that occur upon assembly, in particular through the identification of protected regions and their localization in the overall structure of the protein. We have analyzed the changes in Ure2p structure associated with its assembly into fibrils using HXMS. The deuterium incorporation profile along the sequence allows the identification of the regions that exhibit the most important conformational change. Our data reveal that Ure2p undergoes minor structural changes upon assembly. While polypeptides [82-92] and [13-37] exhibit significant increased and decreased exposure to the solvent, respectively, no marked change was observed for the rest of the protein upon assembly. Our results afford new insights into the conformational rearrangements that lead to the assembly of Ure2p into fibrils and the propagation of the [URE3] element in yeast.
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http://dx.doi.org/10.1016/j.jmb.2007.04.018DOI Listing
June 2007

New mortalin and histidyl tRNA synthetase isoforms point out a pitfall in proteomic analysis of Egr1 genetically modified mice.

Proteomics 2007 Jan;7(2):289-98

Institut de Biochimie et Biophysique Moléculaire et Cellulaire, UMR 8619, CNRS, Université Paris-Sud, Orsay Cedex, France.

Egr1 (Zif268) is an immediate early gene encoding an inducible transcription factor involved in synaptic plasticity and several forms of memory in rodents. Using 2-DE and MS, we compared proteomes of hippocampal subregions and cortex in Egr1-deficient and wild-type littermates. Two significant differences were identified: a shift in the pI of the molecular chaperone mortalin (mtHsp70/PBP74/Grp75) and the apparent disappearance of histidyl tRNA synthetase (HisRS). We found that the pI shift for mortalin in Egr1-deficient mice was caused by a difference in protein sequence: D626G. Using cDNA sequencing, we demonstrated for both mortalin and HisRS that protein differences were not due to a lack of Egr1 but to DNA polymorphism between the C57Bl/6J and 129/Sv strains used to generate the Egr1-deficient mice. Our results show that mortalin and HisRS genes, which map closely to the Egr1 locus, have conserved the 129/Sv haplotype despite numerous back-crossing of the null mice progeny with C57Bl/6J animals. This demonstrates that allelic differences between mouse strains can introduce variations in differential proteomic analyses of genetically modified organisms. Finally, we report the identification of new isoforms of HisRS and mortalin (mot-3) encoded by the 129/Sv haplotype.
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http://dx.doi.org/10.1002/pmic.200600513DOI Listing
January 2007

Fourier transform mass spectrometry: a powerful tool for toxin analysis.

Toxicon 2006 May 30;47(6):715-26. Epub 2006 Mar 30.

Laboratoire des Mécanismes Réactionnels, UMR 7651 CNRS, Ecole Polytechnique, F-91128 Palaiseau, France.

The crude venom of Conus virgo was analyzed by Fourier transform mass spectrometry (FTMS) using both nano-electrospray ionization and MALDI. The analyses were performed directly on the crude venom, without chromatographic separation. The mass fingerprinting of the venom yielded 64 distinct molecular masses in the range 500-4500 Da with two major components at 1328.5142 and 1358.5592 Da. To facilitate the de novo sequencing of these compounds, the disulfide bonds of all components were reduced for the whole venom. The mass accuracy, resolution and sensitivity provided by FTMS were necessary to complete the sequencing of the two new peptides named ViVA and ViVB, that turned out to be conotoxins belonging to the T-superfamily, with the disulfide framework V. The peptides shared 80% similarity and as often observed for this class of compound, they were highly post-translationally modified: amidated C-terminus, pyroglutamic acid residue at the N-terminus and two disulfide bonds. Complementary online nano-LC-nano-ESI-FTMS experiments were undertaken. Among the 130 molecular masses found in the coupling experiments, only 45 were common with those obtained in the direct approach, which means that 21 compounds observed by nano-ESI-FTMS were not detected. This clearly shows that some discriminations against some classes of compounds occur when a chromatographic step is used before mass spectrometry.
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http://dx.doi.org/10.1016/j.toxicon.2006.01.023DOI Listing
May 2006

Major phosphorylation of SF1 on adjacent Ser-Pro motifs enhances interaction with U2AF65.

FEBS J 2006 Feb;273(3):577-87

INSERM, U706, UPMC, Institut du Fer à Moulin, Paris, France.

Protein phosphorylation ensures the accurate and controlled expression of the genome, for instance by regulating the activities of pre-mRNA splicing factors. Here we report that splicing factor 1 (SF1), which is involved in an early step of intronic sequence recognition, is highly phosphorylated in mammalian cells on two serines within an SPSP motif at the junction between its U2AF65 and RNA binding domains. We show that SF1 interacts in vitro with the protein kinase KIS, which possesses a 'U2AF homology motif' (UHM) domain. The UHM domain of KIS is required for KIS and SF1 to interact, and for KIS to efficiently phosphorylate SF1 on the SPSP motif. Importantly, SPSP phosphorylation by KIS increases binding of SF1 to U2AF65, and enhances formation of the ternary SF1-U2AF65-RNA complex. These results further suggest that this phosphorylation event has an important role for the function of SF1, and possibly for the structural rearrangements associated with spliceosome assembly and function.
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http://dx.doi.org/10.1111/j.1742-4658.2005.05091.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1949809PMC
February 2006

Proteomic analysis of the tetraspanin web using LC-ESI-MS/MS and MALDI-FTICR-MS.

Proteomics 2006 Mar;6(5):1437-49

INSERM U602, Institut André Lwoff, Université Paris XI, Hôpital Paul Brousse, Villejuif Cedex, France.

Tetraspanins are integral membrane proteins involved in a variety of physiological and pathological processes. In cancer, clinical and experimental studies have reported a link between tetraspanin expression levels and metastasis. Tetraspanins play a role as organizers of a molecular network of interactions, the "tetraspanin web". Here, we have performed a proteomic characterization of the tetraspanin web using a model of human colon cancer consisting of two cell lines derived from primary tumor and metastasis from the same patient. The tetraspanin complexes were isolated after immunoaffinity purification and the proteins were identified by MS using LC-ESI-MS/MS and MALDI-FTICR. The high resolution and mass accuracy of FTICR MS allowed reliable identification using mass finger printing with only two peptides. Thus, it could be used to resolve the composition of complex peptide mixtures from membrane proteins. Different types of membrane proteins were identified, including adhesion molecules (integrins, Lu/B-CAM, GA733 proteins), receptors and signaling molecules (BAI2, PKC, G proteins), proteases (ADAM10, TADG15), and membrane fusion proteins (syntaxins) as well as poorly characterized proteins (CDCP1, HEM-1, CTL1, and CTL2). Some components were differentially detected in the tetraspanin web of the two cell lines. These differences may be relevant for tumor progression and metastasis.
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http://dx.doi.org/10.1002/pmic.200500180DOI Listing
March 2006