Task 2: Membrane dynamics

1.         Angius, F., Ilioaia, O., Amrani, A., Suisse, A., Rosset, L., Legrand, A., Abou-Hamdan, A., Uzan, M., Zito, F. and Miroux, B. (2018) A novel regulation mechanism of the T7 RNA polymerase based expression system improves overproduction and folding of membrane proteins. Sci Rep, 8, 8572. http://www.ncbi.nlm.nih.gov/pubmed/29872064

2.         Angius, F., Ilioaia, O., Uzan, M. and Miroux, B. (2016) In Mus-Veteau, I. (ed.), In Heterologous Expression of Membrane Proteins. Springer New York, Vol. 1432, pp. 37-52.

3.         Belgareh-Touze, N., Cavellini, L. and Cohen, M.M. (2017) Ubiquitination of ERMES components by the E3 ligase Rsp5 is involved in mitophagy. Autophagy, 13, 114-132. http://www.ncbi.nlm.nih.gov/pubmed/27846375

4.         Boniello, G., Tribet, C., Marie, E., Croquette, V. and Zanchi, D. (2018) Rolling and Ageing in T-Ramp Soft Adhesion. Phys Rev. E 97, 012609.

5.         Brandt, T., Cavellini, L., Kuhlbrandt, W. and Cohen, M.M. (2016) A mitofusin-dependent docking ring complex triggers mitochondrial fusion in vitro. Elife, 5. http://www.ncbi.nlm.nih.gov/pubmed/27253069

6.         Bujaldon, S., Kodama, N., Rappaport, F., Subramanyam, R., de Vitry, C., Takahashi, Y. and Wollman, F.A. (2017) Functional Accumulation of Antenna Proteins in Chlorophyll b-Less Mutants of Chlamydomonas reinhardtii. Mol Plant, 10, 115-130. http://www.ncbi.nlm.nih.gov/pubmed/27742488

7.         Carranza, G., Angius, F., Ilioaia, O., Solgadi, A., Miroux, B. and Arechaga, I. (2017) Cardiolipin plays an essential role in the formation of intracellular membranes in Escherichia coli. Biochim Biophys Acta, 1859, 1124-1132. http://www.ncbi.nlm.nih.gov/pubmed/28284722

8.         Casiraghi, M., Damian, M., Lescop, E., Baneres, J.L. and Catoire, L.J. (2018) Illuminating the Energy Landscape of GPCRs: The Key Contribution of Solution-State NMR Associated with Escherichia coli as an Expression Host. Biochemistry, 57, 2297-2307. http://www.ncbi.nlm.nih.gov/pubmed/29607648

9.         Casiraghi, M., Damian, M., Lescop, E., Point, E., Moncoq, K., Morellet, N., Levy, D., Marie, J., Guittet, E., Baneres, J.L. et al. (2016) Functional Modulation of a G Protein-Coupled Receptor Conformational Landscape in a Lipid Bilayer. J Am Chem Soc, 138, 11170-11175. http://www.ncbi.nlm.nih.gov/pubmed/27489943

10.       Catoire, L.J., Warnet, X.L. and Warschawski, D.E. (2014) In Mus-Veteau, I. (ed.), Membrane Proteins Production for Structural Analysis. Springer New York, pp. 315-345.

11.       Cavellini, L., Meurisse, J., Findinier, J., Erpapazoglou, Z., Belgareh-Touze, N., Weissman, A.M. and Cohen, M.M. (2017) An ubiquitin-dependent balance between mitofusin turnover and fatty acids desaturation regulates mitochondrial fusion. Nat Commun, 8, 15832. http://www.ncbi.nlm.nih.gov/pubmed/28607491

12.       Chipot, C., Dehez, F., Schnell, J.R., Zitzmann, N., Pebay-Peyroula, E., Catoire, L.J., Miroux, B., Kunji, E.R.S., Veglia, G., Cross, T.A. et al. (2018) Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies. Chem Rev, 118, 3559-3607. http://www.ncbi.nlm.nih.gov/pubmed/29488756

13.       Corey, R.A., Pyle, E., Allen, W.J., Watkins, D.W., Casiraghi, M., Miroux, B., Arechaga, I., Politis, A. and Collinson, I. (2018) Specific cardiolipin-SecY interactions are required for proton-motive force stimulation of protein secretion. Proc Natl Acad Sci U S A, 115, 7967-7972. https://www.ncbi.nlm.nih.gov/pubmed/30012626

14.       Dalier, F., Dubacheva, G.V., Coniel, M., Zanchi, D., Galtayries, A., Piel, M., Marie, E. and Tribet, C. (2018) Mixed Copolymer Adlayers Allowing Reversible Thermal Control of Single Cell Aspect Ratio. ACS Appl Mater Interfaces, 10, 2253-2258. http://www.ncbi.nlm.nih.gov/pubmed/29314825

15.       Dalier, F., Eghiaian, F., Scheuring, S., Marie, E. and Tribet, C. (2016) Temperature-Switchable Control of Ligand Display on Adlayers of Mixed Poly(lysine)-g-(PEO) and Poly(lysine)-g-(ligand-modified poly-N-isopropylacrylamide). Biomacromolecules, 17, 1727-1736. http://www.ncbi.nlm.nih.gov/pubmed/27011022

16.       Damodaran, S.P., Eberhard, S., Boitard, L., Rodriguez, J.G., Wang, Y., Bremond, N., Baudry, J., Bibette, J. and Wollman, F.A. (2015) A millifluidic study of cell-to-cell heterogeneity in growth-rate and cell-division capability in populations of isogenic cells of Chlamydomonas reinhardtii. PLoS One, 10, e0118987. http://www.ncbi.nlm.nih.gov/pubmed/25760649

17.       De Vecchis, D., Cavellini, L., Baaden, M., Henin, J., Cohen, M.M. and Taly, A. (2017) A membrane-inserted structural model of the yeast mitofusin Fzo1. Sci Rep, 7, 10217. http://www.ncbi.nlm.nih.gov/pubmed/28860650

18.       Della Pia, E.A., Hansen, R.W., Zoonens, M. and Martinez, K.L. (2014) Functionalized amphipols: a versatile toolbox suitable for applications of membrane proteins in synthetic biology. J Membr Biol, 247, 815-826. http://www.ncbi.nlm.nih.gov/pubmed/24728227

19.       Della Pia, E.A., Holm, J.V., Lloret, N., Le Bon, C., Popot, J.L., Zoonens, M., Nygard, J. and Martinez, K.L. (2014) A step closer to membrane protein multiplexed nanoarrays using biotin-doped polypyrrole. ACS Nano, 8, 1844-1853. http://www.ncbi.nlm.nih.gov/pubmed/24476392

20.       Dilworth, M.V., Piel, M.S., Bettaney, K.E., Ma, P., Luo, J., Sharples, D., Poyner, D.R., Gross, S.R., Moncoq, K., Henderson, P.J.F. et al. (2018) Microbial expression systems for membrane proteins. Methods. http://www.ncbi.nlm.nih.gov/pubmed/29656078

21.       Dreher, M., Prevoteau-Jonquet, J., Trellet, M., Piuzzi, M., Baaden, M., Raffin, B., Ferey, N., Robert, S. and Limet, S. (2014) ExaViz: a flexible framework to analyse, steer and interact with molecular dynamics simulations. Faraday Discuss, 169, 119-142. http://www.ncbi.nlm.nih.gov/pubmed/25340956

22.       Feinstein, H.E., Tifrea, D., Sun, G., Popot, J.L., de la Maza, L.M. and Cocco, M.J. (2014) Long-term stability of a vaccine formulated with the amphipol-trapped major outer membrane protein from Chlamydia trachomatis. J Membr Biol, 247, 1053-1065. http://www.ncbi.nlm.nih.gov/pubmed/24942817

23.       Fernandez, A., Le Bon, C., Baumlin, N., Giusti, F., Cremel, G., Popot, J.L. and Bagnard, D. (2014) In vivo characterization of the biodistribution profile of amphipol A8-35. J Membr Biol, 247, 1043-1051. http://www.ncbi.nlm.nih.gov/pubmed/24898094

24.       Ferrandez, Y., Dezi, M., Bosco, M., Urvoas, A., Valerio-Lepiniec, M., Le Bon, C., Giusti, F., Broutin, I., Durand, G., Polidori, A. et al. (2014) Amphipol-mediated screening of molecular orthoses specific for membrane protein targets. J Membr Biol, 247, 925-940. http://www.ncbi.nlm.nih.gov/pubmed/25086771

25.       Frka-Petesic, B., Zanchi, D., Martin, N., Carayon, S., Huille, S. and Tribet, C. (2016) Aggregation of Antibody Drug Conjugates at Room Temperature: SAXS and Light Scattering Evidence for Colloidal Instability of a Specific Subpopulation. Langmuir, 32, 4848-4861. http://www.ncbi.nlm.nih.gov/pubmed/27129612

26.       Giusti, F., Kessler, P., Hansen, R.W., Della Pia, E.A., Le Bon, C., Mourier, G., Popot, J.L., Martinez, K.L. and Zoonens, M. (2015) Synthesis of a Polyhistidine-bearing Amphipol and its Use for Immobilizing Membrane Proteins. Biomacromolecules, 16, 3751-3761. http://www.ncbi.nlm.nih.gov/pubmed/26492302

27.       Giusti, F., Rieger, J., Catoire, L.J., Qian, S., Calabrese, A.N., Watkinson, T.G., Casiraghi, M., Radford, S.E., Ashcroft, A.E. and Popot, J.L. (2014) Synthesis, characterization and applications of a perdeuterated amphipol. J Membr Biol, 247, 909-924. http://www.ncbi.nlm.nih.gov/pubmed/24652511

28.       Gold, V.A., Brandt, T., Cavellini, L., Cohen, M.M., Ieva, R. and van der Laan, M. (2017) Analysis of Mitochondrial Membrane Protein Complexes by Electron Cryo-tomography. Methods Mol Biol, 1567, 315-336. http://www.ncbi.nlm.nih.gov/pubmed/28276027

29.       Hattab, G., Suisse, A.Y.T., Ilioaia, O., Casiraghi, M., Dezi, M., Warnet, X.L., Warschawski, D.E., Moncoq, K., Zoonens, M. and Miroux, B. (2014) In Mus-Veteau, I. (ed.), Membrane Proteins Production for Structural Analysis. Springer, New York, pp. 87-106.

30.       Hattab, G., Warschawski, D.E., Moncoq, K. and Miroux, B. (2015) Escherichia coli as host for membrane protein structure determination: a global analysis. Scientific Reports, 5, 12097. http://dx.doi.org/10.1038/srep12097

31.       Hirst, J.D., Glowacki, D.R. and Baaden, M. (2014) Molecular simulations and visualization: introduction and overview. Faraday Discuss, 169, 9-22. http://www.ncbi.nlm.nih.gov/pubmed/25285906

32.       Jabrani, A., Makamte, S., Moreau, E., Gharbi, Y., Plessis, A., Bruzzone, L., Sanial, M. and Biou, V. (2017) Biophysical characterisation of the novel zinc binding property in Suppressor of Fused. Sci Rep, 7, 11139. http://www.ncbi.nlm.nih.gov/pubmed/28894158

33.       Kocsis, I., Sorci, M., Vanselous, H., Murail, S., Sanders, S.E., Licsandru, E., Legrand, Y.M., van der Lee, A., Baaden, M., Petersen, P.B. et al. (2018) Oriented chiral water wires in artificial transmembrane channels. Sci Adv, 4, eaao5603. http://www.ncbi.nlm.nih.gov/pubmed/29582016

34.       Laurent, B., Chavent, M., Cragnolini, T., Dahl, A.C., Pasquali, S., Derreumaux, P., Sansom, M.S. and Baaden, M. (2015) Epock: rapid analysis of protein pocket dynamics. Bioinformatics, 31, 1478-1480. http://www.ncbi.nlm.nih.gov/pubmed/25505095

35.       Laurent, B., Murail, S., Shahsavar, A., Sauguet, L., Delarue, M. and Baaden, M. (2016) Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel. Structure, 24, 595-605. http://www.ncbi.nlm.nih.gov/pubmed/27021161

36.       Le Bon, C., Della Pia, E.A., Giusti, F., Lloret, N., Zoonens, M., Martinez, K.L. and Popot, J.L. (2014) Synthesis of an oligonucleotide-derivatized amphipol and its use to trap and immobilize membrane proteins. Nucleic Acids Res, 42, e83. http://www.ncbi.nlm.nih.gov/pubmed/24744236

37.       Le Bon, C., Marconnet, A., Masscheleyn, S., Popot, J.L. and Zoonens, M. (2018) Folding and stabilizing membrane proteins in amphipol A8-35. Methods. http://www.ncbi.nlm.nih.gov/pubmed/29678587

38.       Le Bon, C., Popot, J.L. and Giusti, F. (2014) Labeling and functionalizing amphipols for biological applications. J Membr Biol, 247, 797-814. http://www.ncbi.nlm.nih.gov/pubmed/24696186

39.       Lev, B., Murail, S., Poitevin, F., Cromer, B.A., Baaden, M., Delarue, M. and Allen, T.W. (2017) String method solution of the gating pathways for a pentameric ligand-gated ion channel. Proc Natl Acad Sci U S A, 114, E4158-E4167. http://www.ncbi.nlm.nih.gov/pubmed/28487483

40.       Ma, D., Martin, N., Tribet, C. and Winnik, F.M. (2014) Quantitative characterization by asymmetrical flow field-flow fractionation of IgG thermal aggregation with and without polymer protective agents. Anal Bioanal Chem, 406, 7539-7547. http://www.ncbi.nlm.nih.gov/pubmed/25323742

41.       Malinge, J., Mousseau, F., Zanchi, D., Brun, G., Tribet, C. and Marie, E. (2016) Tailored stimuli-responsive interaction between particles adjusted by straightforward adsorption of mixed layers of Poly(lysine)-g-PEG and Poly(lysine)-g-PNIPAM on anionic beads. J Colloid Interface Sci, 461, 50-55. http://www.ncbi.nlm.nih.gov/pubmed/26397909

42.       Marie, E., Sagan, S., Cribier, S. and Tribet, C. (2014) Amphiphilic macromolecules on cell membranes: from protective layers to controlled permeabilization. J Membr Biol, 247, 861-881. http://www.ncbi.nlm.nih.gov/pubmed/24903487

43.       Martin, N., Costa, N., Wien, F., Winnik, F.M., Ortega, C., Herbet, A., Boquet, D. and Tribet, C. (2017) Refolding of Aggregation-Prone ScFv Antibody Fragments Assisted by Hydrophobically Modified Poly(sodium acrylate) Derivatives. Macromol Biosci, 17. http://www.ncbi.nlm.nih.gov/pubmed/27548824

44.       Martin, N., Ma, D., Herbet, A., Boquet, D., Winnik, F.M. and Tribet, C. (2014) Prevention of thermally induced aggregation of IgG antibodies by noncovalent interaction with poly(acrylate) derivatives. Biomacromolecules, 15, 2952-2962. http://www.ncbi.nlm.nih.gov/pubmed/25019321

45.       Martin, N., Ruchmann, J. and Tribet, C. (2015) Prevention of aggregation and renaturation of carbonic anhydrase via weak association with octadecyl- or azobenzene-modified poly(acrylate) derivatives. Langmuir, 31, 338-349. http://www.ncbi.nlm.nih.gov/pubmed/25495869

46.       Opacic, M., Durand, G., Bosco, M., Polidori, A. and Popot, J.L. (2014) Amphipols and photosynthetic light-harvesting pigment-protein complexes. J Membr Biol, 247, 1031-1041. http://www.ncbi.nlm.nih.gov/pubmed/25107304

47.       Opacic, M., Giusti, F., Popot, J.L. and Broos, J. (2014) Isolation of Escherichia coli mannitol permease, EIImtl, trapped in amphipol A8-35 and fluorescein-labeled A8-35. J Membr Biol, 247, 1019-1030. http://www.ncbi.nlm.nih.gov/pubmed/24952466

48.       Ozeir, M., Pelosi, L., Ismail, A., Mellot-Draznieks, C., Fontecave, M. and Pierrel, F. (2015) Coq6 is responsible for the C4-deamination reaction in coenzyme Q biosynthesis in Saccharomyces cerevisiae. J Biol Chem, 290, 24140-24151. http://www.ncbi.nlm.nih.gov/pubmed/26260787

49.       Pérez-Martin, M., Pérez-Pérez, M.E., Lemaire, S.D. and Crespo, J.L. (2014) Oxidative stress contributes to autophagy induction in response to endoplasmic reticulum stress in Chlamydomonas reinhardtii. Plant Physiol, 166, 997-1008. http://www.ncbi.nlm.nih.gov/pubmed/25143584

50.       Pérez-Pérez, M.E., Lemaire, S.D. and Crespo, J.L. (2016) Control of Autophagy in Chlamydomonas Is Mediated through Redox-Dependent Inactivation of the ATG4 Protease. Plant Physiol, 172, 2219-2234. http://www.ncbi.nlm.nih.gov/pubmed/27756818

51.       Pérez-Pérez, M.E., Zaffagnini, M., Marchand, C.H., Crespo, J.L. and Lemaire, S.D. (2014) The yeast autophagy protease Atg4 is regulated by thioredoxin. Autophagy, 10, 1953-1964. http://www.ncbi.nlm.nih.gov/pubmed/25483965

52.       Planchard, N., Point, E., Dahmane, T., Giusti, F., Renault, M., Le Bon, C., Durand, G., Milon, A., Guittet, E., Zoonens, M. et al. (2014) The use of amphipols for solution NMR studies of membrane proteins: advantages and constraints as compared to other solubilizing media. J Membr Biol, 247, 827-842. http://www.ncbi.nlm.nih.gov/pubmed/24676477

53.       Polovinkin, V., Balandin, T., Volkov, O., Round, E., Borshchevskiy, V., Utrobin, P., von Stetten, D., Royant, A., Willbold, D., Arzumanyan, G. et al. (2014) Nanoparticle surface-enhanced Raman scattering of bacteriorhodopsin stabilized by amphipol A8-35. J Membr Biol, 247, 971-980. http://www.ncbi.nlm.nih.gov/pubmed/25192978

54.       Polovinkin, V., Gushchin, I., Sintsov, M., Round, E., Balandin, T., Chervakov, P., Shevchenko, V., Utrobin, P., Popov, A., Borshchevskiy, V. et al. (2014) High-resolution structure of a membrane protein transferred from amphipol to a lipidic mesophase. J Membr Biol, 247, 997-1004. http://www.ncbi.nlm.nih.gov/pubmed/25192977

55.       Puvanendran, D., Cece, Q. and Picard, M. (2017) Reconstitution of the activity of RND efflux pumps: a "bottom-up" approach. Res Microbiol. http://www.ncbi.nlm.nih.gov/pubmed/29217371

56.       Sauvageot, N., Mokhtari, A., Joyet, P., Budin-Verneuil, A., Blancato, V.S., Repizo, G.D., Henry, C., Pikis, A., Thompson, J., Magni, C. et al. (2017) Enterococcus faecalis Uses a Phosphotransferase System Permease and a Host Colonization-Related ABC Transporter for Maltodextrin Uptake. J Bacteriol, 199. http://www.ncbi.nlm.nih.gov/pubmed/28242718

57.       Serra-Batiste, M., Tolchard, J., Giusti, F., Zoonens, M. and Carulla, N. (2018) Stabilization of a Membrane-Associated Amyloid-beta Oligomer for Its Validation in Alzheimer's Disease. Front Mol Biosci, 5, 38. http://www.ncbi.nlm.nih.gov/pubmed/29725595

58.       Shai, N., Yifrach, E., van Roermund, C.W.T., Cohen, N., Bibi, C., Ijlst, L., Cavellini, L., Meurisse, J., Schuster, R., Zada, L. et al. (2018) Systematic mapping of contact sites reveals tethers and a function for the peroxisome-mitochondria contact. Nature Communications, In Press.

59.       Sterpone, F., Derreumaux, P. and Melchionna, S. (2015) Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics. J Chem Theory Comput, 11, 1843-1853. http://www.ncbi.nlm.nih.gov/pubmed/26574390

60.       Sun, J., Jia, L., Emond, M., Li, M.-H., Marie, E., Jullien, L. and Tribet, C. (2014) Photocontrolled Ionization in the Corona of Rodlike Assemblies of Diblock Copolymers. Macromolecules, 47, 1684-1692. https://doi.org/10.1021/ma402591y

61.       Sverzhinsky, A., Qian, S., Yang, L., Allaire, M., Moraes, I., Ma, D., Chung, J.W., Zoonens, M., Popot, J.L. and Coulton, J.W. (2014) Amphipol-trapped ExbB-ExbD membrane protein complex from Escherichia coli: a biochemical and structural case study. J Membr Biol, 247, 1005-1018. http://www.ncbi.nlm.nih.gov/pubmed/24862870

62.       Tehei, M., Perlmutter, J.D., Giusti, F., Sachs, J.N., Zaccai, G. and Popot, J.L. (2014) Thermal fluctuations in amphipol A8-35 particles: a neutron scattering and molecular dynamics study. J Membr Biol, 247, 897-908. http://www.ncbi.nlm.nih.gov/pubmed/25204390

63.       Trellet, M., Ferey, N., Flotynski, J., Baaden, M. and Bourdot, P. (2018) Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data. J Integr Bioinform, 15. http://www.ncbi.nlm.nih.gov/pubmed/29982236

64.       Wang, F., Qi, Y., Malnoe, A., Choquet, Y., Wollman, F.A. and de Vitry, C. (2017) The High Light Response and Redox Control of Thylakoid FtsH Protease in Chlamydomonas reinhardtii. Mol Plant, 10, 99-114. http://www.ncbi.nlm.nih.gov/pubmed/27702692

65.       Warnet, X.L., Arnold, A.A., Marcotte, I. and Warschawski, D.E. (2015) In-Cell Solid-State NMR: An Emerging Technique for the Study of Biological Membranes. Biophys J, 109, 2461-2466. http://www.ncbi.nlm.nih.gov/pubmed/26682804

66.       Warnet, X.L., Laadhari, M., Arnold, A.A., Marcotte, I. and Warschawski, D.E. (2016) A (2)H magic-angle spinning solid-state NMR characterisation of lipid membranes in intact bacteria. Biochim Biophys Acta, 1858, 146-152. http://www.ncbi.nlm.nih.gov/pubmed/26518520

67.       Zambolin, S., Clantin, B., Chami, M., Hoos, S., Haouz, A., Villeret, V. and Delepelaire, P. (2016) Structural basis for haem piracy from host haemopexin by Haemophilus influenzae. Nat Commun, 7, 11590. http://www.ncbi.nlm.nih.gov/pubmed/27188378

68.       Zoonens, M., Comer, J., Masscheleyn, S., Pebay-Peyroula, E., Chipot, C., Miroux, B. and Dehez, F. (2013) Dangerous liaisons between detergents and membrane proteins. The case of mitochondrial uncoupling protein 2. J Am Chem Soc, 135, 15174-15182. http://www.ncbi.nlm.nih.gov/pubmed/24021091


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