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Home > Scientific Publications

B3S Publications

2018


  • A. Barwinska-Sendra, A. Baslé, K. J. Waldron, and S. Un, “A charge polarization model for the metal-specific activity of superoxide dismutases”, Physical chemistry chemical physics: PCCP, Jan. 2018.
    Abstract: The pathogenicity of Staphylococcus aureus is enhanced by having two superoxide dismutases (SODs): a Mn-specific SOD and another that can use either Mn or Fe. Using 94 GHz electron-nuclear double resonance (ENDOR) and electron double resonance detected (ELDOR)-NMR we show that, despite their different metal-specificities, their structural and electronic similarities extend down to their active-site 1H- and 14N-Mn(ii) hyperfine interactions. However these interactions, and hence the positions of these nuclei, are different in the inactive Mn-reconstituted Escherichia coli Fe-specific SOD. Density functional theory modelling attributes this to a different angular position of the E. coli H171 ligand. This likely disrupts the Mn-H171-E170' triad causing a shift in charge and in metal redox potential, leading to the loss of activity. This is supported by the correlated differences in the Mn(ii) zero-field interactions of the three SOD types and suggests that the triad is important for determining metal specific activity.
    Tags: B3S.

  • D. P. O'Brien, A. C. S. Perez, J. Karst, S. E. Cannella, V. Y. N. Enguéné, A. Hessel, D. Raoux-Barbot, A. Voegele, O. Subrini, M. Davi, J. I. Guijarro, B. Raynal, B. Baron, P. England, B. Hernandez, M. Ghomi, V. Hourdel, C. Malosse, J. Chamot-Rooke, P. Vachette, D. Durand, S. Brier, D. Ladant, and A. Chenal, “Calcium-dependent disorder-to-order transitions are central to the secretion and folding of the CyaA toxin of Bordetella pertussis, the causative agent of whooping cough”, Toxicon: Official Journal of the International Society on Toxinology, Jan. 2018.
    Abstract: The adenylate cyclase toxin (CyaA) plays an essential role in the early stages of respiratory tract colonization by Bordetella pertussis, the causative agent of whooping cough. Once secreted, CyaA invades eukaryotic cells, leading to cell death. The cell intoxication process involves a unique mechanism of translocation of the CyaA catalytic domain directly across the plasma membrane of the target cell. Herein, we review our recent results describing how calcium is involved in several steps of this intoxication process. In conditions mimicking the low calcium environment of the crowded bacterial cytosol, we show that the C-terminal, calcium-binding Repeat-in-ToXin (RTX) domain of CyaA, RD, is an extended, intrinsically disordered polypeptide chain with a significant level of local, secondary structure elements, appropriately sized for transport through the narrow channel of the secretion system. Upon secretion, the high calcium concentration in the extracellular milieu induces the refolding of RD, which likely acts as a scaffold to favor the refolding of the upstream domains of the full-length protein. Due to the presence of hydrophobic regions, CyaA is prone to aggregate into multimeric forms in vitro, in the absence of a chaotropic agent. We have recently defined the experimental conditions required for CyaA folding, comprising both calcium binding and molecular confinement. These parameters are critical for CyaA folding into a stable, monomeric and functional form. The monomeric, calcium-loaded (holo) toxin exhibits efficient liposome permeabilization and hemolytic activities in vitro, even in a fully calcium-free environment. By contrast, the toxin requires sub-millimolar calcium concentrations in solution to translocate its catalytic domain across the plasma membrane, indicating that free calcium in solution is actively involved in the CyaA toxin translocation process. Overall, this data demonstrates the remarkable adaptation of bacterial RTX toxins to the diversity of calcium concentrations it is exposed to in the successive environments encountered in the course of the intoxication process.
    Tags: B3S, Bordetella pertussis, Calcium, CyaA toxin, Disorder-to-order transition, FAAM, Folding, Protein secretion, Whooping cough.

2017


  • A. M. Acuña, C. Lemaire, R. van Grondelle, B. Robert, and I. H. M. van Stokkum, “Energy transfer and trapping in Synechococcus WH 7803”, Photosynthesis Research, 2017.
    Abstract: Excitation energy transfer (EET) and trapping in Synechococcus WH 7803 whole cells and isolated photosystem I (PSI) complexes have been studied by time-resolved emission spectroscopy at room temperature (RT) and at 77 K. With the help of global and target analysis, the pathways of EET and the charge separation dynamics have been identified. Energy absorbed in the phycobilisome (PB) rods by the abundant phycoerythrin (PE) is funneled to phycocyanin (PC645) and from there to the core that contains allophycocyanin (APC660 and APC680). Intra-PB EET rates have been estimated to range from 11 to 68/ns. It was estimated that at RT, the terminal emitter of the phycobilisome, APC680, transfers its energy at a rate of 90/ns to PSI and at a rate of 50/ns to PSII. At 77 K, the redshifted Chl a states in the PSI core were heterogeneous, with maximum emission at 697 and 707 nm. In 72% of the PSI complexes, the bulk Chl a in equilibrium with F697 decayed with a main trapping lifetime of 39 ps.
    Tags: B3S, Excitation energy transfer, Global analysis, LBMS, Light harvesting, LPSM, Target analysis.


  • M. Amjadi, T. Hallaj, H. Asadollahi, Z. Song, M. de Frutos, and N. Hildebrandt, “Facile synthesis of carbon quantum dot/silver nanocomposite and its application for colorimetric detection of methimazole”, Sensors and Actuators B: Chemical, vol. 244, p. 425-432, 2017.


  • H. Azouaoui, C. Montigny, T. Dieudonné, P. Champeil, A. Jacquot, J. L. Vázquez-Ibar, P. Le Maréchal, J. Ulstrup, M. - R. Ash, J. A. Lyons, P. Nissen, and G. Lenoir, “A High and Phosphatidylinositol-4-phosphate (PI4P)-dependent ATPase Activity for the Drs2p/Cdc50p Flippase after Removal of its N- and C-terminal Extensions”, Journal of Biological Chemistry, p. jbc.M116.751487, Mar. 2017.
    Tags: autophosphorylation, B3S, Cdc50 protein, Flippase, inhibition mechanism, limited proteolysis, lipid-protein interaction, LPSM, phosphatidylserine, phosphoinositide.

  • A. Bahloul, E. Pepermans, B. Raynal, N. Wolff, F. Cordier, P. England, S. Nouaille, B. Baron, A. El-Amraoui, J. - P. Hardelin, D. Durand, and C. Petit, “Conformational switch of harmonin, a submembrane scaffold protein of the hair cell mechanoelectrical transduction machinery”, FEBS letters, 2017.
    Abstract: Mutations in the gene encoding harmonin, a multi-PDZ domain-containing submembrane protein, cause Usher syndrome type 1 (congenital deafness and balance disorder, as well as early-onset sight loss). The structure of the protein and biological activities of its three different classes of splice isoforms (a, b, and c) remain poorly understood. Combining biochemical and biophysical analyses, we show that harmonin-a1 can switch between open and closed conformations through intramolecular binding of its C-terminal PDZ-binding motif to its N-terminal supramodule NTD-PDZ1 and a flexible PDZ2-PDZ3 linker. This conformational switch presumably extends to most harmonin isoforms, and is expected to have an impact on the interaction with some binding partners, as shown here for cadherin-related 23, another component of the hair cell mechanoelectrical transduction machinery. This article is protected by copyright. All rights reserved.
    Tags: B3S, conformation switch, FAAM, PDZ domain, Usher syndrome.


  • E. Baquero, A. A. Albertini, H. Raux, A. Abou‐Hamdan, E. Boeri‐Erba, M. Ouldali, L. Buonocore, J. K. Rose, J. Lepault, S. Bressanelli, and Y. Gaudin, “Structural intermediates in the fusion‐associated transition of vesiculovirus glycoprotein”, The EMBO Journal, vol. 36, no. 5, p. 679-692, Mar. 2017.
    Tags: B3S, conformational change, glycoprotein, IMAPP, intermediate structures, membrane fusion, RHABDO, Vesiculovirus, VIRO, VIROEM.

  • L. Benkaidali, F. André, G. Moroy, B. Tangour, F. Maurel, and M. Petitjean, “The Cytochrome P450 3A4 Has Three Major Conformations: New Clues to Drug Recognition by this Promiscuous Enzyme”, Molecular Informatics, 2017.
    Abstract: We computed the channels of the 3A4 isoform of the cytochrome P450 3A4 (CYP) on the basis of 24 crystal structures extracted from the Protein Data Bank (PDB). We identified three major conformations (denoted C, O1 and O2) using an enhanced version of the CCCPP software that we developed for the present work, while only two conformations (C and O(2) ) are considered in the literature. We established the flowchart of definition of these three conformations in function of the structural and physicochemical parameters of the ligand. The channels are characterized with qualitative and quantitative parameters, and not only with their surrounding secondary structures as it is usually done in the literature.
    Tags: active site access channels, B3S, conformations, CYP 3A4 ligands, cytochromes P450, drug-drug interactions, LSOD.


  • S. Bhuckory, E. Hemmer, Y. - T. Wu, A. Yahia-Ammar, F. Vetrone, and N. Hildebrandt, “Core or Shell? Er <sup>3+</sup> FRET Donors in Upconversion Nanoparticles: Core or Shell? Er <sup>3+</sup> FRET Donors in Upconversion Nanoparticles”, European Journal of Inorganic Chemistry, vol. 2017, no. 44, p. 5186-5195, Dec. 2017.

  • D. A. Braun, J. Rao, G. Mollet, D. Schapiro, M. - C. Daugeron, W. Tan, O. Gribouval, O. Boyer, P. Revy, T. Jobst-Schwan, J. M. Schmidt, J. A. Lawson, D. Schanze, S. Ashraf, J. F. P. Ullmann, C. A. Hoogstraten, N. Boddaert, B. Collinet, G. Martin, D. Liger, S. Lovric, M. Furlano, I. C. Guerrera, O. Sanchez-Ferras, J. F. Hu, A. - C. Boschat, S. Sanquer, B. Menten, S. Vergult, N. De Rocker, M. Airik, T. Hermle, S. Shril, E. Widmeier, H. Y. Gee, W. - I. Choi, C. E. Sadowski, W. L. Pabst, J. K. Warejko, A. Daga, T. Basta, V. Matejas, K. Scharmann, S. D. Kienast, B. Behnam, B. Beeson, A. Begtrup, M. Bruce, G. - S. Ch'ng, S. - P. Lin, J. - H. Chang, C. - H. Chen, M. T. Cho, P. M. Gaffney, P. E. Gipson, C. - H. Hsu, J. A. Kari, Y. - Y. Ke, C. Kiraly-Borri, W. - M. Lai, E. Lemyre, R. O. Littlejohn, A. Masri, M. Moghtaderi, K. Nakamura, F. Ozaltin, M. Praet, C. Prasad, A. Prytula, E. R. Roeder, P. Rump, R. E. Schnur, T. Shiihara, M. D. Sinha, N. A. Soliman, K. Soulami, D. A. Sweetser, W. - H. Tsai, J. - D. Tsai, R. Topaloglu, U. Vester, D. H. Viskochil, N. Vatanavicharn, J. L. Waxler, K. J. Wierenga, M. T. F. Wolf, S. - N. Wong, S. A. Leidel, G. Truglio, P. C. Dedon, A. Poduri, S. Mane, R. P. Lifton, M. Bouchard, P. Kannu, D. Chitayat, D. Magen, B. Callewaert, H. van Tilbeurgh, M. Zenker, C. Antignac, and F. Hildebrandt, “Mutations in KEOPS-complex genes cause nephrotic syndrome with primary microcephaly”, Nature Genetics, 2017.
    Abstract: Galloway-Mowat syndrome (GAMOS) is an autosomal-recessive disease characterized by the combination of early-onset nephrotic syndrome (SRNS) and microcephaly with brain anomalies. Here we identified recessive mutations in OSGEP, TP53RK, TPRKB, and LAGE3, genes encoding the four subunits of the KEOPS complex, in 37 individuals from 32 families with GAMOS. CRISPR-Cas9 knockout in zebrafish and mice recapitulated the human phenotype of primary microcephaly and resulted in early lethality. Knockdown of OSGEP, TP53RK, or TPRKB inhibited cell proliferation, which human mutations did not rescue. Furthermore, knockdown of these genes impaired protein translation, caused endoplasmic reticulum stress, activated DNA-damage-response signaling, and ultimately induced apoptosis. Knockdown of OSGEP or TP53RK induced defects in the actin cytoskeleton and decreased the migration rate of human podocytes, an established intermediate phenotype of SRNS. We thus identified four new monogenic causes of GAMOS, describe a link between KEOPS function and human disease, and delineate potential pathogenic mechanisms.
    Tags: ARCHEE, B3S, FAAM, MICROBIO.


  • K. Brettel, M. Byrdin, and M. H. Vos, “Ultrafast Light-Induced Processes in DNA Photolyase and Its Substrate-Bound Complex”, in Ultrafast Dynamics at the Nanoscale: Biomolecules and Supramolecular Assemblies, I. Burghardt and S. Haacke, Eds. Penthouse Level, Suntec Tower 3, 8 Temasek Boulevard, Singapore 038988: Pan Stanford Publishing, 2017, p. 65-90.


  • Ultrafast Dynamics at the Nanoscale: Biomolecules and Supramolecular Assemblies. Penthouse Level, Suntec Tower 3, 8 Temasek Boulevard, Singapore 038988: Pan Stanford Publishing, 2017.

  • C. Caillet-Saguy, A. Toto, R. Guerois, P. Maisonneuve, E. di Silvio, K. Sawyer, S. Gianni, and N. Wolff, “Regulation of the Human Phosphatase PTPN4 by the inter-domain linker connecting the PDZ and the phosphatase domains”, Scientific Reports, vol. 7, no. 1, p. 7875, 2017.
    Abstract: Human protein tyrosine phosphatase non-receptor type 4 (PTPN4) has been shown to prevent cell death. The active form of human PTPN4 consists of two globular domains, a PDZ (PSD-95/Dlg/ZO-1) domain and a phosphatase domain, tethered by a flexible linker. Targeting its PDZ domain abrogates this protection and triggers apoptosis. We previously demonstrated that the PDZ domain inhibits the phosphatase activity of PTPN4 and that the mere binding of a PDZ ligand is sufficient to release the catalytic inhibition. We demonstrate here that the linker connecting the PDZ domain and the phosphatase domain is involved in the regulation of the phosphatase activity in both PDZ-related inhibition and PDZ ligand-related activation events. We combined bioinformatics and kinetic studies to decipher the role of the linker in the PTPN4 activity. By comparing orthologous sequences, we identified a conserved patch of hydrophobic residues in the linker. We showed that mutations in this patch affect the regulation of the PTPN4 bidomain indicating that the PDZ-PDZ ligand regulation of PTPN4 is a linker-mediated mechanism. However, the mutations do not alter the binding of the PDZ ligand. This study strengthens the notion that inter-domain linker can be of functional importance in enzyme regulation of large multi-domain proteins.
    Tags: AMIG, B3S.


  • S. E. Cannella, V. Y. Ntsogo Enguéné, M. Davi, C. Malosse, A. C. Sotomayor Pérez, J. Chamot-Rooke, P. Vachette, D. Durand, D. Ladant, and A. Chenal, “Stability, structural and functional properties of a monomeric, calcium–loaded adenylate cyclase toxin, CyaA, from Bordetella pertussis”, Scientific Reports, vol. 7, p. 42065, Feb. 2017.


  • L. Cao, S. Cantos-Fernandes, and B. Gigant, “The structural switch of nucleotide-free kinesin”, Scientific Reports, vol. 7, p. 42558, Feb. 2017.

  • P. Cardol and A. Krieger-Liszkay, “From light capture to metabolic needs, oxygenic photosynthesis is an ever-expanding field of study in plants, algae and cyanobacteria”, Physiologia Plantarum, 2017.
    Abstract: Understanding of the molecular mechanisms of photosynthetic electron and proton transports and their regulation in plants and algae in response to changes in environmental conditions is an important issue for fundamental research on photosynthesis, and may extend even to practical applications by identifying important sites for improvement of photosynthesis. The significance and often centrality of regulatory mechanisms of photosynthetic electron transport is well established for processes in plant acclimation. In recent years, significant advancements have been achieved in understanding of regulatory processes such as dissipation of excess energy in the antenna systems, state transitions, cyclic electron flow, oxygen reduction by flavodiiron enzymes and many others.
    Tags: B3S, MROP.


  • M. - F. Carlier and S. Shekhar, “Global treadmilling coordinates actin turnover and controls the size of actin networks”, Nature Reviews Molecular Cell Biology, Mar. 2017.


  • L. Celma, C. Corbinais, J. Vercruyssen, X. Veaute, I. L. de la Sierra-Gallay, R. Guérois, D. Busso, A. Mathieu, S. Marsin, S. Quevillon-Cheruel, and J. P. Radicella, “Structural basis for the substrate selectivity of Helicobacter pylori NucT nuclease activity”, PLOS ONE, vol. 12, no. 12, p. e0189049, Dec. 2017.


  • V. Chaptal, F. Delolme, A. Kilburg, S. Magnard, C. Montigny, M. Picard, C. Prier, L. Monticelli, O. Bornert, M. Agez, S. Ravaud, C. Orelle, R. Wagner, A. Jawhari, I. Broutin, E. Pebay-Peyroula, J. - M. Jault, H. R. Kaback, M. le Maire, and P. Falson, “Quantification of Detergents Complexed with Membrane Proteins”, Scientific Reports, vol. 7, p. 41751, Feb. 2017.


  • J. - P. Charbonnier, E. M. van Rikxoort, A. A. A. Setio, C. M. Schaefer-Prokop, B. van Ginneken, and F. Ciompi, “Improving airway segmentation in computed tomography using leak detection with convolutional networks”, Medical Image Analysis, vol. 36, p. 52-60, 2017.

  • A. Chevrel, A. Mesneau, D. Sanchez, L. Celma, S. Quevillon-Cheruel, A. Cavagnino, S. Nessler, I. Li de la Sierra-Gallay, H. van Tilbeurgh, P. Minard, M. Valerio-Lepiniec, and A. Urvoas, “Alpha Repeat proteins (αRep) as expression and crystallization helpers”, Journal of Structural Biology, 2017.
    Abstract: We have previously described a highly diverse library of artificial repeat proteins based on thermostable HEAT-like repeats, named αRep. αReps binding specifically to proteins difficult to crystallize have been selected and in several examples, they made possible the crystallization of these proteins. To further simplify the production and crystallization experiments we have explored the production of chimeric protein corresponding to covalent association between the targets and their specific binders strengthened by a linker. Although chimeric proteins with expression partners are classically used to enhance expression these fusions cannot usually be used for crystallization. With specific expression partners like a cognate αRep this is no longer true, and chimeric proteins can be expressed purified and crystallized. αRep selection by phage display suppose that at least a small amount of the target protein should be produced to be used as a bait for selection and this might, in some cases, be difficult. We have therefore transferred the αRep library in a new construction adapted to selection by protein complementation assay (PCA). This new procedure allows to select specific binders by direct interaction with the target in the cytoplasm of the bacteria and consequently does not require preliminary purification of target protein. αRep binders selected by PCA or by phage display can be used to enhance expression, stability, solubility and crystallogenesis of proteins that are otherwise difficult to express, purify and/or crystallize.
    Tags: artificial repeat proteins, B3S, Crystallization helper, FAAM, Fusion protein, MIP, Protein complementation assay, Protein library.

  • M. Clémancey, T. Cantat, G. Blondin, J. - M. Latour, P. Dorlet, and G. Lefèvre, “Structural Insights into the Nature of Fe(0) and Fe(I) Low-Valent Species Obtained upon the Reduction of Iron Salts by Aryl Grignard Reagents”, Inorganic Chemistry, vol. 56, no. 7, p. 3834-3848, 2017.
    Abstract: Mechanistic studies of the reduction of Fe(III) and Fe(II) salts by aryl Grignard reagents in toluene/tetrahydrofuran mixtures in the absence of a supporting ligand, as well as structural insights regarding the nature of the low-valent iron species obtained at the end of this reduction process, are reported. It is shown that several reduction pathways can be followed, depending on the starting iron precursor. We demonstrate, moreover, that these pathways lead to a mixture of Fe(0) and Fe(I) complexes regardless of the nature of the precursor. Mössbauer and (1)H NMR spectroscopies suggest that diamagnetic 16-electron bisarene complexes such as (η(4)-C6H5Me)2Fe(0) can be formed as major species (85% of the overall iron quantity). The formation of a η(6)-arene-ligated low-spin Fe(I) complex as a minor species (accounting for ca. 15% of the overall iron quantity) is attested by Mössbauer spectroscopy, as well as by continuous-wave electron paramagnetic resonance (EPR) and pulsed-EPR (HYSCORE) spectroscopies. The nature of the Fe(I) coordination sphere is discussed by means of isotopic labeling experiments and density functional theory calculations. It is shown that the most likely low-spin Fe(I) candidate obtained in these systems is a diphenylarene-stabilized species [(η(6)-C6H5Me)Fe(I)Ph2](-) exhibiting an idealized C2v topology. This enlightens the nature of the lowest valence states accommodated by iron during the reduction of Fe(III) and Fe(II) salts by aryl Grignard reagents in the absence of any additional coligand, which so far remained rather unknown. The reactivity of these low-valent Fe(I) and Fe(0) complexes in aryl-heteroaryl Kumada cross-coupling conditions has also been investigated, and it is shown that the zerovalent Fe(0) species can be used efficiently as a precursor in this reaction, whereas the Fe(I) oxidation state does not exhibit any reactivity.
    Tags: B3S, LSOD.

  • C. Corbinais, A. Mathieu, P. P. Damke, T. Kortulewski, D. Busso, M. Prado-Acosta, J. P. Radicella, and S. Marsin, “ComB proteins expression levels determine Helicobacter pylori competence capacity”, Scientific Reports, vol. 7, p. 41495, 2017.
    Abstract: Helicobacter pylori chronically colonises half of the world's human population and is the main cause of ulcers and gastric cancers. Its prevalence and the increase in antibiotic resistance observed recently reflect the high genetic adaptability of this pathogen. Together with high mutation rates and an efficient DNA recombination system, horizontal gene transfer through natural competence makes of H. pylori one of the most genetically diverse bacteria. We show here that transformation capacity is enhanced in strains defective for recN, extending previous work with other homologous recombination genes. However, inactivation of either mutY or polA has no effect on DNA transformation, suggesting that natural competence can be boosted in H. pylori by the persistence of DNA breaks but not by enhanced mutagenesis. The transformation efficiency of the different DNA repair impaired strains correlates with the number of transforming DNA foci formed on the cell surface and with the expression of comB8 and comB10 competence genes. Overexpression of the comB6-B10 operon is sufficient to increase the transformation capacity of a wild type strain, indicating that the ComB complex, present in the bacterial wall and essential for DNA uptake, can be a limiting factor for transformation efficiency.
    Tags: B3S, FAAM.


  • P. Cuniasse, P. Tavares, E. V. Orlova, and S. Zinn-Justin, “Structures of biomolecular complexes by combination of NMR and cryoEM methods”, Current Opinion in Structural Biology, vol. 43, p. 104-113, 2017.


  • L. Dhers, N. Pietrancosta, L. Ducassou, B. Ramassamy, J. Dairou, M. Jaouen, F. André, D. Mansuy, and J. - L. Boucher, “Spectral and 3D model studies of the interaction of orphan human cytochrome P450 2U1 with substrates and ligands”, Biochimica et Biophysica Acta (BBA) - General Subjects, vol. 1861, no. 1, p. 3144-3153, 2017.

  • T. Di Meo, W. Ghattas, C. Herrero, C. Velours, P. Minard, J. - P. Mahy, R. Ricoux, and A. Urvoas, “αRep A3: A versatile artificial scaffold for metalloenzyme design”, Chemistry (Weinheim an Der Bergstrasse, Germany), 2017.
    Abstract: αRep is a new family of artificial proteins based on a thermostable alpha-helical repeated motif. One of its members, αRep A3, forms a stable homo-dimer with a wide cleft that is able to receive metal complexes and thus appears as suitable for generating new artificial biocatalysts. Based on the crystal structure of αRep A3, two positions (F119 and Y26) were chosen and changed independently into cysteine residues. A phenanthroline ligand was covalently attached to the unique cysteine of each protein variant and the corresponding biohybrids were purified and characterized. Once mutated and coupled to phenanthroline, the protein remained folded and dimeric. Copper(II) was bound specifically by the two biohybrids with two different binding modes and, in addition, the holo biohybrid A3F119NPH was found to be able to catalyze enantioselectively the Diels-Alder (D-A) cycloaddition with up to 62% ee. This study validates the choice of the αRep A3 dimer as a protein scaffold and provides a new promising route for the design and production of new enantioselective biohybrids based on entirely artificial proteins issued from a highly diverse library.
    Tags: artificial repeat proteins, B3S, Diels-Alder reaction, Enantioselective Catalysis, MIP, PF, PIM.

  • S. A. Díaz, G. Lasarte Aragonés, S. Buckhout-White, X. Qiu, E. Oh, K. Susumu, J. S. Melinger, A. L. Huston, N. Hildebrandt, and I. L. Medintz, “Bridging Lanthanide to Quantum Dot Energy Transfer with a Short-Lifetime Organic Dye”, The Journal of Physical Chemistry Letters, p. 2182-2188, 2017.
    Abstract: Semiconductor nanocrystals or quantum dots (QDs) should act as excellent Förster resonance energy transfer (FRET) acceptors due to their large absorption cross section, tunable emission, and high quantum yields. Engaging this type of FRET can be complicated due to direct excitation of the QD acceptor along with its longer excited-state lifetime. Many cases of QDs acting as energy transfer acceptors are within time-gated FRET from long-lifetime lanthanides, which allow the QDs to decay before observing FRET. Efficient QD sensitization requires the lanthanide to be in close proximity to the QD. To overcome the lifetime mismatch issues and limited transfer range, we utilized a Cy3 dye to bridge the energy transfer from an extremely long lived terbium emitter to the QD. We demonstrated that short-lifetime dyes can be used as energy transfer relays between extended lifetime components and in this way increased the distance of terbium-QD FRET to ∼14 nm.
    Tags: B3S, NANO.


  • G. Dimchev, A. Steffen, F. Kage, V. Dimchev, J. Pernier, M. - F. Carlier, and K. Rottner, “Efficiency of lamellipodia protrusion is determined by the extent of cytosolic actin assembly”, Molecular Biology of the Cell, p. mbc.E16-05-0334, Mar. 2017.


  • T. Djebaili, S. Abel, M. Marchi, and J. Richardi, “Influence of Force-Field Parameters on the Atomistic Simulations of Metallic Surfaces and Nanoparticles”, The Journal of Physical Chemistry C, vol. 121, no. 49, p. 27758-27765, Dec. 2017.

  • S. Y. Doerflinger, M. Cortese, I. Romero-Brey, Z. Menne, T. Tubiana, C. Schenk, P. A. White, R. Bartenschlager, S. Bressanelli, G. S. Hansman, and V. Lohmann, “Membrane alterations induced by nonstructural proteins of human norovirus”, PLoS pathogens, vol. 13, no. 10, p. e1006705, 2017.
    Abstract: Human noroviruses (huNoV) are the most frequent cause of non-bacterial acute gastroenteritis worldwide, particularly genogroup II genotype 4 (GII.4) variants. The viral nonstructural (NS) proteins encoded by the ORF1 polyprotein induce vesical clusters harboring the viral replication sites. Little is known so far about the ultrastructure of these replication organelles or the contribution of individual NS proteins to their biogenesis. We compared the ultrastructural changes induced by expression of norovirus ORF1 polyproteins with those induced upon infection with murine norovirus (MNV). Characteristic membrane alterations induced by ORF1 expression resembled those found in MNV infected cells, consisting of vesicle accumulations likely built from the endoplasmic reticulum (ER) which included single membrane vesicles (SMVs), double membrane vesicles (DMVs) and multi membrane vesicles (MMVs). In-depth analysis using electron tomography suggested that MMVs originate through the enwrapping SMVs with tubular structures similar to mechanisms reported for picornaviruses. Expression of GII.4 NS1-2, NS3 and NS4 fused to GFP revealed distinct membrane alterations when analyzed by correlative light and electron microscopy. Expression of NS1-2 induced proliferation of smooth ER membranes forming long tubular structures that were affected by mutations in the active center of the putative NS1-2 hydrolase domain. NS3 was associated with ER membranes around lipid droplets (LDs) and induced the formation of convoluted membranes, which were even more pronounced in case of NS4. Interestingly, NS4 was the only GII.4 protein capable of inducing SMV and DMV formation when expressed individually. Our work provides the first ultrastructural analysis of norovirus GII.4 induced vesicle clusters and suggests that their morphology and biogenesis is most similar to picornaviruses. We further identified NS4 as a key factor in the formation of membrane alterations of huNoV and provide models of the putative membrane topologies of NS1-2, NS3 and NS4 to guide future studies.
    Tags: B3S, IMAPP.

  • L. Ducassou, L. Dhers, G. Jonasson, N. Pietrancosta, J. - L. Boucher, D. Mansuy, and F. André, “Membrane-bound human orphan cytochrome P450 2U1: Sequence singularities, construction of a full 3D model, and substrate docking”, Biochimie, vol. 140, p. 166-175, 2017.
    Abstract: BACKGROUND: Human cytochrome P450 2U1 (CYP2U1) is an orphan CYP that exhibits several distinctive characteristics among the 57 human CYPs with a highly conserved sequence in almost all living organisms. METHODS: We compared its protein sequence with those of the 57 human CYPs and constructed a 3D structure of a full-length CYP2U1 model bound to a POPC membrane. We also performed docking experiments of arachidonic acid (AA) and N-arachidonoylserotonin (AS) in this model. RESULTS: The protein sequence of CYP2U1 displayed two unique characteristics when compared to those of the human CYPs, the presence of a longer N-terminal region upstream of the putative trans-membrane helix (TMH) containing 8 proline residues, and of an insert of about 20 amino acids containing 5 arginine residues between helices A' and A. Its N-terminal part upstream of TMH involved an additional short terminal helix, in a manner similar to what was reported in the crystal structure of Saccharomyces cerevisiae CYP51. Our model also showed a specific interaction between the charged residues of insert AA' and phosphate groups of lipid polar heads, suggesting a possible role of this insert in substrate recruitment. Docking of AA and AS in this model showed these substrates in channel 2ac, with the terminal alkyl chain of AA or the indole ring of AS close to the heme, in agreement with the reported CYP2U1-catalyzed AA and AS hydroxylation regioselectivities. MAJOR CONCLUSION AND GENERAL SIGNIFICANCE: This model should be useful to find new endogenous or exogenous CYP2U1 substrates and to interpret the regioselectivity of their hydroxylation.
    Tags: Access channels, Active site topology, Arachidonic acid, B3S, LSOD, Membrane interaction, molecular dynamics, N-arachidonoylserotonin.


  • Y. Duroc, R. Kumar, L. Ranjha, C. Adam, R. Guérois, K. Md Muntaz, M. - C. Marsolier-Kergoat, F. Dingli, R. Laureau, D. Loew, B. Llorente, J. - B. Charbonnier, P. Cejka, and V. Borde, “Concerted action of the MutLβ heterodimer and Mer3 helicase regulates the global extent of meiotic gene conversion”, eLife, vol. 6, Jan. 2017.
    Tags: AMIG, B3S, biochemistry, Chromosomes, genes, INTGEN, Meiosis, mismatch repair, Recombination, S. cerevisiae.

  • N. El Bakkali-Tahéri, S. Tachon, M. Orio, S. Bertaina, M. Martinho, V. Robert, M. Réglier, T. Tron, P. Dorlet, and A. J. Simaan, “Characterization of Cu(II)-reconstituted ACC Oxidase using experimental and theoretical approaches”, Archives of Biochemistry and Biophysics, 2017.
    Abstract: 1-Aminocyclopropane-1-carboxylic acid oxidase (ACCO) is a non heme iron(II) containing enzyme that catalyzes the final step of the ethylene biosynthesis in plants. The iron(II) ion is bound in a facial triad composed of two histidines and one aspartate (H177, D179 and H234). Several active site variants were generated to provide alternate binding motifs and the enzymes were reconstituted with copper(II). Continuous wave (cw) and pulsed Electron Paramagnetic Resonance (EPR) spectroscopies as well as Density Functional Theory (DFT) calculations were performed and models for the copper(II) binding sites were deduced. In all investigated enzymes, the copper ion is equatorially coordinated by the two histidine residues (H177 and H234) and probably two water molecules. The copper-containing enzymes are inactive, even when hydrogen peroxide is used in peroxide shunt approach. EPR experiments and DFT calculations were undertaken to investigate substrate's (ACC) binding on the copper ion and the results were used to rationalize the lack of copper-mediated activity.
    Tags: ACC Oxidase, B3S, Copper, Density functional theory calculations, Electron paramagnetic resonance, Ethylene, LSOD.

  • E. Errasti-Murugarren, A. Rodríguez-Banqueri, and J. L. Vázquez-Ibar, “Split GFP Complementation as Reporter of Membrane Protein Expression and Stability in E. coli: A Tool to Engineer Stability in a LAT Transporter”, Methods in Molecular Biology (Clifton, N.J.), vol. 1586, p. 181-195, 2017.
    Abstract: Obtaining enough quantity of recombinant membrane transport proteins with optimal purity and stability for structural studies is a remarkable challenge. In this chapter, we describe a protocol to engineer SteT, the amino acid transporter of Bacillus subtilis, in order to improve its heterologous expression in Escherichia coli and its stability in detergent micelles. We built a library of 70 SteT mutants, combining a random mutagenesis protocol with a split GFP assay as reporter of protein folding and membrane insertion. Mutagenesis was restricted to residues situated in the transmembrane domains. Improved versions of SteT were successfully identified after analyzing the expression yield and monodispersity in detergent micelles of the library's members.
    Tags: B3S, FSEC, Heterologous expression, LAT, LPSM, Membrane Transport Proteins, Split GFP, SteT.


  • R. Farran, C. Ducloiset, J. Buendia, N. T. Vo, R. Guillot, Z. Halime, P. Dauban, W. Leibl, M. Sircoglou, and A. Aukauloo, “Light-Induced Activation of the Du Bois [Rh <sup>II</sup> <sub>2</sub> (Esp) <sub>2</sub> ] Catalyst for Nitrogen Atom Transfer Reactions”, ChemPhotoChem, vol. 1, no. 12, p. 562-567, 2017.

  • K. Feilke, G. Ajlani, and A. Krieger-Liszkay, “Overexpression of plastid terminal oxidase in Synechocystis sp. PCC 6803 alters cellular redox state”, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 372, no. 1730, 2017.
    Abstract: Cyanobacteria are the most ancient organisms performing oxygenic photosynthesis, and they are the ancestors of plant plastids. All plastids contain the plastid terminal oxidase (PTOX), while only certain cyanobacteria contain PTOX. Many putative functions have been discussed for PTOX in higher plants including a photoprotective role during abiotic stresses like high light, salinity and extreme temperatures. Since PTOX oxidizes PQH2 and reduces oxygen to water, it is thought to protect against photo-oxidative damage by removing excess electrons from the plastoquinone (PQ) pool. To investigate the role of PTOX we overexpressed rice PTOX fused to the maltose-binding protein (MBP-OsPTOX) in Synechocystis sp. PCC 6803, a model cyanobacterium that does not encode PTOX. The fusion was highly expressed and OsPTOX was active, as shown by chlorophyll fluorescence and P700 absorption measurements. The presence of PTOX led to a highly oxidized state of the NAD(P)H/NAD(P)(+) pool, as detected by NAD(P)H fluorescence. Moreover, in the PTOX overexpressor the electron transport capacity of PSI relative to PSII was higher, indicating an alteration of the photosystem I (PSI) to photosystem II (PSII) stoichiometry. We suggest that PTOX controls the expression of responsive genes of the photosynthetic apparatus in a different way from the PQ/PQH2 ratio.This article is part of the themed issue 'Enhancing photosynthesis in crop plants: targets for improvement'.
    Tags: B3S, cellular redox state, chlorophyll fluorescence, LBMS, MROP, NAD(P)H fluorescence, P700 absorption, plastid terminal oxidase, Synechocystis sp. PCC 6803.


  • K. Feilke, G. Ajlani, and A. Krieger-Liszkay, “Correction to ‘Overexpression of plastid terminal oxidase in <i>Synechocystis</i> sp. PCC 6803 alters cellular redox state’”, Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 372, no. 1736, p. 20170277, Dec. 2017.


  • S. Fieulaine, R. Alves de Sousa, L. Maigre, K. Hamiche, M. Alimi, J. - M. Bolla, A. Taleb, A. Denis, J. - M. Pagès, I. Artaud, T. Meinnel, and C. Giglione, “Corrigendum: A unique peptide deformylase platform to rationally design and challenge novel active compounds”, Scientific Reports, vol. 7, p. 39365, Jan. 2017.

  • V. R. Figliuolo, L. E. B. Savio, H. Safya, H. Nanini, C. Bernardazzi, A. Abalo, H. S. P. de Souza, J. Kanellopoulos, P. Bobé, C. M. L. M. Coutinho, and R. Coutinho-Silva, “P2X7 receptor promotes intestinal inflammation in chemically induced colitis and triggers death of mucosal regulatory T cells”, Biochimica Et Biophysica Acta, 2017.
    Abstract: P2X7 receptor activation contributes to inflammation development in different pathologies. We previously reported that the P2X7 receptor is over-expressed in the gut mucosa of patients with inflammatory bowel disease, and that P2X7 inhibition protects against chemically induced colitis. Here, we investigated in detail the role of the P2X7 receptor in inflammatory bowel disease development, by treating P2X7 knockout (KO) and WT mice with two different (and established) colitis inductors. P2X7 KO mice were protected against gut inflammation induced by 2,4,6-trinitrobenzenesulfonic acid or oxazolone, with no weight loss or gut histological alterations after treatment. P2X7 receptor knockout induced regulatory T cell accumulation in the colon, as evaluated by qRT-PCR for FoxP3 expression and immunostaining for CD90/CD45RB(low). Flow cytometry analysis of mesenteric lymph node cells showed that P2X7 activation (by ATP) triggered regulatory T cell death. In addition, such cells from P2X7 KO mice expressed more CD103, suggesting increased migration of regulatory T cells to the colon (relative to the WT). Our results show that the P2X7 has a key role during inflammation development in inflammatory bowel disease, by triggering the death and retention in the mesenteric lymph nodes of regulatory T cells that would otherwise promote immune system tolerance in the gut.
    Tags: ATP, B3S, colitis, MIP, P2X7 receptor, regulatory T cells.

  • G. Folpini, T. Siebert, M. Woerner, S. Abel, D. Laage, and T. Elsaesser, “Water Librations in the Hydration Shell of Phospholipids”, The Journal of Physical Chemistry Letters, p. 4492-4497, 2017.
    Abstract: The hydrophilic phosphate moiety in the headgroup of phospholipids forms strong hydrogen bonds with water molecules in the first hydration layer. Time-domain terahertz spectroscopy in a range from 100 to 1000 cm(-1) reveals the influence of such interactions on rotations of water molecules. We determine librational absorption spectra of water nanopools in phospholipid reverse micelles for a range from w0 = 2 to 16 waters per phospholipid molecule. A pronounced absorption feature with maximum at 830 cm(-1) is superimposed on a broad absorption band between 300 and 1000 cm(-1). Molecular dynamics simulations of water in the reverse micelles suggest that the feature at 830 cm(-1) arises from water molecules forming one or two strong hydrogen bonds with phosphate groups, while the broad component comes from bulk-like environments. This behavior is markedly different from water interacting with less polar surfaces.
    Tags: B3S, LBMS.


  • G. Gaibelet, F. Tercé, S. Allart, C. Lebrun, X. Collet, N. Jamin, and S. Orlowski, “Fluorescent probes for detecting cholesterol-rich ordered membrane microdomains: entangled relationships between structural analogies in the membrane and functional homologies in the cell”, AIMS Biophysics, vol. 4, no. 1, p. 121-151, 2017.


  • J. M. Zwier and N. Hildebrandt, “Time-Gated FRET Detection for Multiplexed Biosensing”, in Reviews in Fluorescence 2016, C. D. Geddes, Eds. Cham: Springer International Publishing, 2017, p. 17-43.

  • R. Grzela, J. Nusbaum, S. Fieulaine, F. Lavecchia, W. V. Bienvenut, C. Dian, T. Meinnel, and C. Giglione, “The C-terminal residue of phage Vp16 PDF, the smallest peptide deformylase, acts as an offset element locking the active conformation”, Scientific Reports, vol. 7, no. 1, p. 11041, 2017.
    Abstract: Prokaryotic proteins must be deformylated before the removal of their first methionine. Peptide deformylase (PDF) is indispensable and guarantees this mechanism. Recent metagenomics studies revealed new idiosyncratic PDF forms as the most abundant family of viral sequences. Little is known regarding these viral PDFs, including the capacity of the corresponding encoded proteins to ensure deformylase activity. We provide here the first evidence that viral PDFs, including the shortest PDF identified to date, Vp16 PDF, display deformylase activity in vivo, despite the absence of the key ribosome-interacting C-terminal region. Moreover, characterization of phage Vp16 PDF underscores unexpected structural and molecular features with the C-terminal Isoleucine residue significantly contributing to deformylase activity both in vitro and in vivo. This residue fully compensates for the absence of the usual long C-domain. Taken together, these data elucidate an unexpected mechanism of enzyme natural evolution and adaptation within viral sequences.
    Tags: B3S, DBG, IMAPP, PROMTI.

  • R. Grzela, J. Nusbaum, S. Fieulaine, F. Lavecchia, M. Desmadril, N. Nhiri, A. Van Dorsselaer, S. Cianferani, E. Jacquet, T. Meinnel, and C. Giglione, “Peptide deformylases from Vibrio parahaemolyticus phage and bacteria display similar deformylase activity and inhibitor binding clefts”, Biochimica Et Biophysica Acta, Oct. 2017.
    Abstract: Unexpected peptide deformylase (PDF) genes were recently retrieved in numerous marine phage genomes. While various hypotheses dealing with the occurrence of these intriguing sequences have been made, no further characterization and functional studies have been described thus far. In this study, we characterize the bacteriophage Vp16 PDF enzyme, as representative member of the newly identified C-terminally truncated viral PDFs. We show here that conditions classically used for bacterial PDFs lead to an enzyme exhibiting weak activity. Nonetheless, our integrated biophysical and biochemical approaches reveal specific effects of pH and metals on Vp16 PDF stability and activity. A novel purification protocol taking in account these data allowed strong improvement of Vp16 specific activity to values similar to those of bacterial PDFs. We next show that Vp16PDF is as sensitive to the natural inhibitor compound of PDFs, actinonin, as bacterial PDFs. Comparison of the 3D structures of Vp16 and E. coli PDFs bound to actinonin also reveals that both PDFs display identical substrate binding mode. We conclude that bacteriophage Vp16 PDF protein has functional peptide deformylase activity and we suggest that encoded phage PDFs might be important for viral fitness.
    Tags: B3S, DBG, Enzyme mechanism, IMAPP, N-terminal methionine excision, Peptide deformylase, PF, PIM, PROMTI, structure, Virus.


  • M. Guettari, A. Belaidi, S. Abel, and T. Tajouri, “Polyvinylpyrrolidone Behavior in Water/Ethanol Mixed Solvents: Comparison of Modeling Predictions with Experimental Results”, Journal of Solution Chemistry, vol. 46, no. 7, p. 1404-1417, 2017.

  • S. Hadpech, S. Nangola, K. Chupradit, K. Fanhchaksai, W. Furnon, A. Urvoas, M. Valerio-Lepiniec, P. Minard, P. Boulanger, S. - S. Hong, and C. Tayapiwatana, “Alpha-helicoidal HEAT-like Repeat Proteins (αRep) Selected as Interactors of HIV-1 Nucleocapsid Negatively Interfere with Viral Genome Packaging and Virus Maturation”, Scientific Reports, vol. 7, no. 1, p. 16335, 2017.
    Abstract: A new generation of artificial proteins, derived from alpha-helicoidal HEAT-like repeat protein scaffolds (αRep), was previously characterized as an effective source of intracellular interfering proteins. In this work, a phage-displayed library of αRep was screened on a region of HIV-1 Gag polyprotein encompassing the C-terminal domain of the capsid, the SP1 linker and the nucleocapsid. This region is known to be essential for the late steps of HIV-1 life cycle, Gag oligomerization, viral genome packaging and the last cleavage step of Gag, leading to mature, infectious virions. Two strong αRep binders were isolated from the screen, αRep4E3 (32 kDa; 7 internal repeats) and αRep9A8 (28 kDa; 6 internal repeats). Their antiviral activity against HIV-1 was evaluated in VLP-producer cells and in human SupT1 cells challenged with HIV-1. Both αRep4E3 and αRep9A8 showed a modest but significant antiviral effects in all bioassays and cell systems tested. They did not prevent the proviral integration reaction, but negatively interfered with late steps of the HIV-1 life cycle: αRep4E3 blocked the viral genome packaging, whereas αRep9A8 altered both virus maturation and genome packaging. Interestingly, SupT1 cells stably expressing αRep9A8 acquired long-term resistance to HIV-1, implying that αRep proteins can act as antiviral restriction-like factors.
    Tags: B3S, MIP.


  • N. Hildebrandt, C. M. Spillmann, W. R. Algar, T. Pons, M. H. Stewart, E. Oh, K. Susumu, S. A. Díaz, J. B. Delehanty, and I. L. Medintz, “Energy Transfer with Semiconductor Quantum Dot Bioconjugates: A Versatile Platform for Biosensing, Energy Harvesting, and Other Developing Applications”, Chemical Reviews, vol. 117, no. 2, p. 536-711, Jan. 2017.

  • J. Ho, E. Kish, D. D. Méndez-Hernández, K. WongCarter, S. Pillai, G. Kodis, J. Niklas, O. G. Poluektov, D. Gust, T. A. Moore, A. L. Moore, V. S. Batista, and B. Robert, “Triplet-triplet energy transfer in artificial and natural photosynthetic antennas”, Proceedings of the National Academy of Sciences of the United States of America, 2017.
    Abstract: In photosynthetic organisms, protection against photooxidative stress due to singlet oxygen is provided by carotenoid molecules, which quench chlorophyll triplet species before they can sensitize singlet oxygen formation. In anoxygenic photosynthetic organisms, in which exposure to oxygen is low, chlorophyll-to-carotenoid triplet-triplet energy transfer (T-TET) is slow, in the tens of nanoseconds range, whereas it is ultrafast in the oxygen-rich chloroplasts of oxygen-evolving photosynthetic organisms. To better understand the structural features and resulting electronic coupling that leads to T-TET dynamics adapted to ambient oxygen activity, we have carried out experimental and theoretical studies of two isomeric carotenoporphyrin molecular dyads having different conformations and therefore different interchromophore electronic interactions. This pair of dyads reproduces the characteristics of fast and slow T-TET, including a resonance Raman-based spectroscopic marker of strong electronic coupling and fast T-TET that has been observed in photosynthesis. As identified by density functional theory (DFT) calculations, the spectroscopic marker associated with fast T-TET is due primarily to a geometrical perturbation of the carotenoid backbone in the triplet state induced by the interchromophore interaction. This is also the case for the natural systems, as demonstrated by the hybrid quantum mechanics/molecular mechanics (QM/MM) simulations of light-harvesting proteins from oxygenic (LHCII) and anoxygenic organisms (LH2). Both DFT and electron paramagnetic resonance (EPR) analyses further indicate that, upon T-TET, the triplet wave function is localized on the carotenoid in both dyads.
    Tags: artificial photosynthesis, B3S, DFT calculations, LBMS, Photoprotection, Resonance Raman, triplet–triplet energy transfer.

  • C. Houriez, M. Meot-Ner Mautner, and M. Masella, “Solvation of the Guanidinium Ion in Pure Aqueous Environments: A Theoretical Study from an "Ab Initio"-Based Polarizable Force Field”, The Journal of Physical Chemistry. B, vol. 121, no. 50, p. 11219-11228, Dec. 2017.
    Abstract: We report simulation results regarding the hydration process of the guanidinium cation in water droplets and in bulk liquid water, at a low concentration of 0.03 M, performed using a polarizable approach to model both water/water and ion/water interactions. In line with earlier theoretical studies, our simulations show a preferential orientation of guanidinium at water-vacuum interfaces, i.e., a parallel orientation of the guanidinium plane to the aqueous surface. In an apparent contradiction with earlier simulation studies, we show also that guanidinium has a stronger propensity for the cores of aqueous systems than the ammonium cation. However, our bulk simulation conditions correspond to weaker cation concentrations than in earlier studies, by 2 orders of magnitude, and that the same simulations performed using a standard nonpolarizable force field leads to the same conclusion. From droplet data, we extrapolate the guanidinium single hydration enthalpy value to be -82.9 ± 2.2 kcal mol-1. That is about half as large as the sole experimental estimate reported to date, about -144 kcal mol-1. Our result yields a guanidinium absolute bulk hydration free energy at ambiant conditions to be -78.4 ± 2.6 kcal mol-1, a value smaller by 3 kcal mol-1 compared to ammonium. The relatively large magnitude of our guanidinium hydration free energy estimate suggests the Gdm+ protein denaturing properties to result from a competition between the cation hydration effects and the cation/protein interactions, a competition that can be modulated by weak differences in the protein or in the cation chemical environment.
    Tags: B3S, INTGEN.

  • C. Houriez, V. Vallet, F. Réal, M. Meot-Ner Mautner, and M. Masella, “Organic ion association in aqueous phase and ab initio-based force fields: The case of carboxylate/ammonium salts”, The Journal of Chemical Physics, vol. 147, no. 16, p. 161720, Oct. 2017.
    Abstract: We performed molecular dynamics simulations of carboxylate/methylated ammonium ion pairs solvated in bulk water and of carboxylate/methylated ammonium salt solutions at ambient conditions using an ab initio-based polarizable force field whose parameters are assigned to reproduce only high end quantum computations, at the Møller-Plesset second-order perturbation theory/complete basis set limit level, regarding single ions and ion pairs as isolated and micro-hydrated in gas phase. Our results agree with the available experimental results regarding carboxylate/ammonium salt solutions. For instance, our force field approach predicts the percentage of acetate associated with ammonium ions in CH3COO(-)/CH3NH3(+) solutions at the 0.2-0.8M concentration scale to range from 14% to 35%, in line with the estimates computed from the experimental ion association constant in liquid water. Moreover our simulations predict the number of water molecules released from the ion first hydration shell to the bulk upon ion association to be about 2.0 ± 0.6 molecules for acetate/protonated amine ion pairs, 3.1 ± 1.5 molecules for the HCOO(-)/NH4(+) pair and 3.3 ± 1.2 molecules for the CH3COO(-)/(CH3)4N(+) pair. For protonated amine-based ion pairs, these values are in line with experiment for alkali/halide pairs solvated in bulk water. All these results demonstrate the promising feature of ab initio-based force fields, i.e., their capacity in accurately modeling chemical systems that cannot be readily investigated using available experimental techniques.
    Tags: B3S, INTGEN.

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