DNA self-assembly of single molecules with deterministic position and orientation

Authors: Adamczyk, Aleksandra K., Huijben, Teun A. P. M., Sison, Miguel, di Luca, Andrea, Chiarelli, Germán, Vanni, Stefano, Brasselet, Sophie, Mortensen, Kim, Stefani, Fernando D., Pilo-Pais, Mauricio, Acuna, Guillermo P.

Subject Terms: Condensed Matter - Soft Condensed Matter, Physics - Chemical Physics

Access URL: http://arxiv.org/abs/2207.06472

An in silico osmotic pressure approach allows characterization of pressure–area isotherms of lipid monolayers at low molecular areasElectronic supplementary information (ESI) available: Fig. S1: Showing a snapshot of the simulation box for the POPC-lipid monolayer. Fig. S2: Surface pressure–molecular area isotherms of CG POPC lipid monolayers on aqueous sub-phase at 298 K through compression and expansion. Fig. S3: Showing the liquid-expanded (LE) phases in POPC and DOPC-lipid monolayers. Fig. S4: Showing the unstable DPPC-lipid monolayer at molecular area ∼ 50 Å2. Fig. S5: Implying the phase coexistence region (LC/LE phase) in DPPC monolayers at 310 K (molecular area ∼ 60 Å2). Fig. S6: Showing the coexistence of disordered LE) and ordered (LC) phase close to the phase transition point (molecular area ∼ 65 Å2). Fig. S7: Showing the comparison of simulation vs. experimental isotherm of DPPC at 323 K. Fig. S8: Fitting plot for POPC at 298 K. Tables S1 and S2 list details about simulated lipid monolayer systems to obtain surface pressure–area (Π–A) isotherms using a pressure tensor method and the osmotic pressure method respectively. See DOI: https://doi.org/10.1039/d2sm01419j

Authors: Prabhu, Janak, Singh, Akhil Pratap, Vanni, Stefano

Source: Soft matter. 19(18):3377-3385

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100182251150.0x000001&indx=1&recIds=ETOCvdc_100182251150.0x000001

Development of a coarse-grained model for surface-functionalized gold nanoparticles: towards an accurate description of their aggregation behaviorElectronic supplementary information (ESI) available. See DOI: https://doi.org/10.1039/d3sm00094j

Authors: Petretto, Emanuele, Campomanes, Pablo, Vanni, Stefano

Source: Soft matter. 19(18):3290-3300

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100182251229.0x000001&indx=1&recIds=ETOCvdc_100182251229.0x000001

Compensatory recruitment allows amphibian population persistence in anthropogenic habitats

Authors: Cayuela, Hugo, Monod-Broca, Benjamin, Lemaître, Jean-François, Besnard, Aurélien, Gippet, Jérôme M. W., Schmidt, Benedikt R., Romano, Antonio, Hertach, Thomas, Angelini, Claudio, Canessa, Stefano, Rosa, Giacomo, Vignoli, Leonardo, Venchi, Alberto, Carafa, Marco, Giachi, Filippo, Tiberi, rea, Hantzschmann, Alena M., Sinsch, Ulrich, Tournier, Emilie, Bonnaire, Eric, Gollmann, Günter, Gollmann, Birgit, Spitzen-van der Sluijs, Annemarieke, Buschmann, Holger, Kinet, Thierry, Laudelout, Arnaud, Fonters, Remi, Bunz, Yoann, Corail, Marc, Biancardi, Carlo, Di Cerbo, Anna R., Langlois, Dominique, Thirion, Jean-Marc, Bernard, Laurent, Boussiquault, Elodie, Doré, Florian, Leclerc, Titouan, Enderlin, Nadine, Laurenceau, Florian, Morin, Lucy, Skrzyniarz, Mégane, Barrioz, Mickael, Morizet, Yohan, Cruickshank, Sam S., Pichenot, Julian, Maletzky, Andreas, Delsinne, Thibaut, Henseler, Dominik, Aumaître, Damien, Gailledrat, Miguel, Moquet, Julien, Veen, Robert, Krijnen, Peter, Rivière, Laurent, Trenti, Matteo, Endrizzi, Sonia, Pedrini, Paolo, Biaggini, Marta, Vanni, Stefano, Dudgeon, David, Gaillard, Jean-Michel, Léna, Jean-Paul

Source: Proceedings of the National Academy of Sciences of the United States of America, 2022 Sep . 119(38), 1-8.

Access URL: https://www.jstor.org/stable/27207135

Computational modeling of membrane trafficking processes: From large molecular assemblies to chemical specificity

Authors: Álvarez, Daniel, Sapia, Jennifer, Vanni, Stefano

Source: In Current Opinion in Cell Biology August 2023 83

The conformational plasticity of structurally unrelated lipid transport proteins correlates with their mode of action.

Authors: Srinivasan, Sriraksha¹, Di Luca, Andrea¹, Álvarez, Daniel^1,2, John Peter, Arun T.¹, Gehin, Charlotte³, Lone, Museer A.⁴, Hornemann, Thorsten⁴, D'Angelo, Giovanni³, Vanni, Stefano^1,5, stefano.vanni@unifr.ch

Source: PLoS Biology; 8/19/2024, Vol. 22 Issue 8, p1-24, 24p

Monovalent ion-mediated charge–charge interactions drive aggregation of surface-functionalized gold nanoparticlesElectronic supplementary information (ESI) available. See DOI: https://doi.org/10.1039/d2nr02824g

Authors: Petretto, Emanuele, Ong, Quy K., Olgiati, Francesca, Mao, Ting, Campomanes, Pablo, Stellacci, Francesco, Vanni, Stefano

Source: Nanoscale. 14(40):15181-15192

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100163078990.0x000001&indx=1&recIds=ETOCvdc_100163078990.0x000001

RNA Order Regulates Its Interactions with Zwitterionic Lipid Bilayers.

Authors: Singh, Akhil Pratap, Prabhu, Janak, Vanni, Stefano

Source: Nano Letters; 1/8/2025, Vol. 25 Issue 1, p77-83, 7p

Seipin accumulates and traps diacylglycerols and triglycerides in its ring-like structure

Authors: Zoni, Valeria, Khaddaj, Rasha, Lukmantara, Ivan, Shinoda, Wataru, Yang, Hongyuan, Schneiter, Roger, Vanni, Stefano

Source: Proceedings of the National Academy of Sciences of the United States of America, 2021 Mar 01. 118(10), 1-11.

Access URL: https://www.jstor.org/stable/27027466

Recharging your fats: CHARMM36 parameters for neutral lipids triacylglycerol and diacylglycerol

Authors: Campomanes, Pablo, Prabhu, Janak, Zoni, Valeria, Vanni, Stefano

Source: In Biophysical Reports 8 December 2021 1(2)

Structure of the yeast ceramide synthase

Authors: Schäfer, Jan-Hannes, Clausmeyer, Lena, Körner, Carolin, Esch, Bianca M., Wolf, Verena N., Sapia, Jennifer, Ahmed, Yara, Walter, Stefan, Vanni, Stefano, Januliene, Dovile, Moeller, Arne, Fröhlich, Florian

Source: Nature Structural and Molecular Biology; March 2025, Vol. 32 Issue: 3 p441-449, 9p

Theoretical and experimental comparisons of simple peptide–membrane systems; towards defining the reaction space: general discussion

Authors: Aguilar, Marie-Isabel, Al Nahas, Kareem, Barrera, Francisco N., Bassereau, Patricia, Bechinger, Burkhard, Brand, Izabella, Chattopadhyay, Amitabha, Clarke, Ronald J., DeGrado, William F., Deplazes, Evelyne, Fletcher, Marcus, Fraternali, Franca, Fuchs, Patrick, Garcia-Saez, Ana J., Gilbert, Robert, Hoogenboom, Bart W., Jarin, Zack, O'Shea, Paul, Pabst, Georg, Pal, Sreetama, Sanderson, John M., Seddon, John M., Sengupta, Durba, Siegel, David P., Srivastava, Anand, Tieleman, D. Peter, Tripathy, Madhusmita, Utterström, Johanna, Vácha, Robert, Vanni, Stefano, Voth, Gregory A.

Source: Faraday discussions. 232:149-171

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100137225240.0x000001&indx=1&recIds=ETOCvdc_100137225240.0x000001

Estimating the accuracy of the MARTINI model towards the investigation of peripheral protein–membrane interactionsElectronic supplementary information (ESI) available. See DOI: 10.1039/d0fd00058b

Authors: Srinivasan, Sriraksha, Zoni, Valeria, Vanni, Stefano

Source: Faraday discussions. 232:131-148

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100137225202.0x000001&indx=1&recIds=ETOCvdc_100137225202.0x000001

Investigating the structural properties of hydrophobic solvent-rich lipid bilayers

Authors: Zoni, Valeria, Campomanes, Pablo, Vanni, Stefano

Source: Soft matter. 17(21):5329-5335

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100121406456.0x000001&indx=1&recIds=ETOCvdc_100121406456.0x000001

Unbiased MD simulations identify lipid binding sites in lipid transfer proteins.

Authors: Srinivasan, Sriraksha¹, Álvarez, Daniel^1,2, Peter, Arun T. John¹, Vanni, Stefano^1,3

Source: Journal of Cell Biology; 11/4/2024, Vol. 223 Issue 11, p1-S8, 25p

Yop1 stability and membrane curvature generation propensity are controlled by its oligomerisation interface.

Authors: Chandran, Anu V., Álvarez, Daniel, Vanni, Stefano, Schnell, Jason R.

Source: Biochemical Journal; 10/15/2024, Vol. 481 Issue 20, p1437-1448, 12p

Subject Terms: FAMILIAL spastic paraplegia, MOTOR neuron diseases, MISSENSE mutation, MEMBRANE proteins, ENDOPLASMIC reticulum

Conserved Functions of Ether Lipids and Sphingolipids in the Early Secretory Pathway

Authors: Jiménez-Rojo, Noemi, Leonetti, Manuel D., Zoni, Valeria, Colom, Adai, Feng, Suihan, Iyengar, Namrata R., Matile, Stefan, Roux, Aurélien, Vanni, Stefano, Weissman, Jonathan S., Riezman, Howard

Source: In Current Biology 5 October 2020 30(19):3775-3787

Pliocene colonization of the Mediterranean by Great White Shark inferred from fossil records, historical jaws, phylogeographic and divergence time analyses

Authors: Leone, Agostino, Puncher, Gregory N., Ferretti, Francesco, Sperone, Emilio, Tripepi, Sandro, Micarelli, Primo, Gambarelli, Andrea, Sarà, Maurizio, Arculeo, Marco, Doria, Giuliano, Garibaldi, Fulvio, Bressi, Nicola, Dall'Asta, Andrea, Minelli, Daniela, Cilli, Elisabetta, Vanni, Stefano, Serena, Fabrizio, Díaz‐Jaimes, Píndaro, Baele, Guy, Cariani, Alessia, Tinti, Fausto

Source: Journal of biogeography. 47(5):1119-1129

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100106884835.0x000001&indx=1&recIds=ETOCvdc_100106884835.0x000001

Cryo-EM architecture of a near-native stretch-sensitive membrane microdomain.

Authors: Kefauver, Jennifer M., Hakala, Markku, Zou, Luoming, Alba, Josephine, Espadas, Javier, Tettamanti, Maria G., Gajić, Jelena, Gabus, Caroline, Campomanes, Pablo, Estrozi, Leandro F., Sen, Nesli E., Vanni, Stefano, Roux, Aurélien, Desfosses, Ambroise, Loewith, Robbie

Source: Nature; Aug2024, Vol. 632 Issue 8025, p664-671, 8p

Rescaling protein-protein interactions improves Martini 3 for flexible proteins in solution.

Authors: Thomasen, F. Emil, Skaalum, Tórur, Kumar, Ashutosh, Srinivasan, Sriraksha, Vanni, Stefano, Lindorff-Larsen, Kresten

Source: Nature Communications; 8/5/2024, Vol. 15 Issue 1, p1-17, 17p

Subject Terms: MOLECULAR dynamics, PROTEIN-protein interactions, MEMBRANE lipids, CARRIER proteins, MEMBRANE proteins