S. Vanni publications

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Li, D., Rocha-Roa, C., Schilling, M. A., Reinisch, K. M., & Vanni, S. (2024). Lipid scrambling is a general feature of protein insertases. PNAS (DOI: https://doi.org/10.1073/pnas.2319476121)



Yamada, T., Miyazaki, Y., Harada, S., Kumar, A., Vanni, S., & Shinoda, W. (2023). Improved protein model in SPICA force field. Journal of Chemical Theory and Computation (DOI: https://doi.org/10.1021/acs.jctc.3c01016)

Borges-Araújo, L., Patmanidis, I., Singh, A. P., Santos, L. H., Sieradzan, A. K., Vanni, S., ... & Souza, P. C. (2023). Pragmatic coarse-graining of proteins: models and applications. Journal of Chemical Theory and Computation (DOI: https://doi.org/10.1021/acs.jctc.3c00733)

Li, D., Rocha-Roa, C., Schilling, M. A., Reinisch, K. M., & Vanni, S. (2023). Lipid scrambling is a general feature of protein insertases. bioRxiv (DOI: https://doi.org/10.1101%2F2023.09.01.555937)

Nicastro, R., Brohée, L., Alba, J., Nüchel, J., Figlia, G., Kipschull, S., ... Vanni, S., ... & Demetriades, C. (2023). Malonyl-CoA is a conserved endogenous ATP-competitive mTORC1 inhibitor. Nature Cell Biology (DOI: https://doi.org/10.1016/j.ceb.2023.102205)

Álvarez, D., Sapia, J., & Vanni, S. (2023). Computational modeling of membrane trafficking processes: From large molecular assemblies to chemical specificity. Current Opinion in Cell Biology (DOI: https://doi.org/10.1016/j.ceb.2023.102205)

Wozny, M. R., Di Luca, A., Morado, D. R., Picco, A., Khaddaj, R., Campomanes, P., ... Vanni, S. & Kukulski, W. (2023). In situ architecture of the ER–mitochondria encounter structure. Nature (DOI: https://doi.org/10.1038/s41586-023-06050-3)

Srinivasan, S., Alvarez Lorenzo, D., & Vanni, S. (2023). Unbiased MD simulations characterize lipid binding pockets in lipid transfer proteins. bioRxiv (DOI: https://doi.org/10.1101/2023.11.24.568550)

Kefauver, J. M., Hakala, M., Zou, L., Alba, J., Espadas Moreno, J., Tettamanti, M. G., ... Vanni, S., ... & Loewith, R. (2023). CryoEM architecture of a native stretch-sensitive membrane microdomain. bioRxiv (DOI: https://doi.org/10.1101/2023.08.25.554800)

Thomasen, F. E., Skaalum, T., Kumar, A., Srinivasan, S., Vanni, S., & Lindorff-Larsen, K. (2023). Recalibration of protein interactions in Martini 3. bioRxiv (DOI: https://doi.org/10.1101/2023.05.29.542689)

Petretto, E., Campomanes, P., & Vanni, S. (2023). Development of a coarse-grained model for surface-functionalized gold nanoparticles: towards an accurate description of their aggregation behavior. Soft Matter (DOI: https://doi.org/10.1039/D3SM00094J)

Prabhu, J., Singh, A. P., & Vanni, S. (2023). An in silico osmotic pressure approach allows characterization of pressure–area isotherms of lipid monolayers at low molecular areas. Soft Matter (DOI: https://doi.org/10.1039/D2SM01419J)

Srinivasan, S., DiLuca, A., Peter, A. T. J., Gehin, C., Lone, M. A., Hornemann, T. A., ... & Vanni, S. (2023). Conformational dynamics of lipid transfer domains provide a general framework to decode their functional mechanism. bioRxiv (DOI: https://doi.org/10.1101/2023.04.11.536463)



S Rogers, L Gui, A Kovalenko, V Zoni,...Campomanes P,...Vanni S, Nicastro D, Henne M (2022). Triglyceride lipolysis triggers liquid crystalline phases in lipid droplets and alters the LD proteome. JCB (DOI: https://doi.org/10.1083/jcb.202205053

AK Adamczyk, TAPM Huijben, M Sison, A Di Luca, G Chiarelli, S Vanni, ...(2022). DNA self-assembly of single molecules with deterministic position and orientation. ACS Nano (DOI: https://pubs.acs.org/doi/10.1021/acsnano.2c06936)

S Sotillos, I von der Decken, ID Mercadé, S Srinivasan, S Vanni,...(2022). DLC3/Cv-c function in testis development in humans and Drosophila: implication for variants of sex development. bioRxiv (DOI: https://doi.org/10.1101/2022.07.28.501838)

MR Wozny, A Di Luca,...S Vanni, Kukulski W (2022). Supramolecular architecture of the ER-mitochondria encounter structure in its native environment. bioRxiv (DOI: https://doi.org/10.1101/2022.04.12.488000)

AM Milosevic, ..., S Vanni, ...(2022). The Choice of Nanoparticle Surface‐Coupled Fluorescent Dyes Impacts Cellular Interaction. ChemNanoMat (DOI: https://doi.org/10.1002/cnma.202100443



Srinivasan S, Vanni S (2021). Computational Approaches to Investigate and Design Lipid-binding Domains for Membrane Biosensing. CHIMIA International Journal for Chemistry (DOI: https://doi.org/10.2533/chimia.2021.1031)

Milosevic AM, Haeni L, Hirschi LA, Vanni S, Campomanes P, Rothen‐Rutishauser B, Rodriguez‐Lorenzo L, Petri‐Fink A (2021). The Choice of Nanoparticle Surface‐Coupled Fluorescent Dyes Impacts Cellular Interaction. ChemNanoMat (DOI: https://doi.org/10.1002/cnma.202100443)

Campomanes P, Prabhu J, Zoni V, Vanni S (2021). Recharging your fats: CHARMM36 parameters for neutral lipids triacylglycerol and diacylglycerol. Biophysical Reports (DOI: https://doi.org/10.1016/j.bpr.2021.100034)

Petretto E, Ong QK, Olgiati F, Ting M, Campomanes P, Stellacci F, Vanni S (2021). Ion-mediated charge-charge interactions drive aggregation of surface-functionalized gold nanoparticles. Chemrxiv (DOI: 10.26434/chemrxiv-2021-kq8f0)

Zoni V, Khaddaj R, Lukmantara I, Shinoda W, Yang H, Schneiter R, Vanni S (2021). Seipin accumulates and traps diacylglycerols and triglycerides in its ring-like structure. PNAS (DOI: https://doi.org/10.1073/pnas.2017205118)

Zoni V, Khaddaj R, Campomanes P, Thiam AR, Schneiter R, Vanni S (2021). Pre-existing bilayer stresses modulate triglyceride accumulation in the ER versus lipid droplets. Elife (DOI: https://doi.org/10.7554/eLife.62886)

Campomanes P, Zoni V, Vanni S (2021). Protonation Equilibrium in the Active Site of the Photoactive Yellow Protein. Molecules (DOI: https://doi.org/10.3390/molecules26072025)

Zoni V, Campomanes P, Vanni S (2021). Investigating the structural properties of hydrophobic solvent-rich lipid bilayers. Soft Matter (DOI: 10.1039/D0SM02270E)

Srinivasan S, Zoni V, Vanni S (2021). Estimating the accuracy of the MARTINI model towards the investigation of Peripheral Protein-Membrane Interactions. Faraday Discussions. (DOI: 10.1039/D0FD00058B)




Rodriguez-Gallardo S, Kurokawa K, ..., Zoni V, ... Vanni S, Nakano A, Muñiz M (2020). Ceramide chain length–dependent protein sorting into selective endoplasmic reticulum exit sites. Science advances (DOI: 10.1126/sciadv.aba8237)

Ardham VR, Zoni V, Adamowicz S, Campomanes P,  Vanni S (2020). Accurate Estimation of Membrane Capacitance from Atomistic Molecular Dynamics Simulations of Zwitterionic Lipid Bilayers. The Journal of Physical Chemistry B,  Accepted Manuscript (DOI: 10.1021/acs.jpcb.0c03145)

West A, Zoni V, Teague Jr, Leonard AN, Vanni S, Gawrisch K, Tristram-Nagle S, Sachs JN, Klauda JB (2020). How Do Ethanolamine Plasmalogens Contribute to Order and Structure of Neurological Membranes? The Journal of Physical Chemistry B, 124, 5, 828–839 (DOI: 10.1021/acs.jpcb.9b08850)

Jiménez-Rojo N, Leonetti MD, Zoni V, Colom A, Feng S, Iyengar NR, Matile S, Roux A, Vanni S, Weissman JS, Riezman H (2020). Conserved function of ether lipids and sphingolipids in the early secretory pathway. Current Biology. (DOI: https://doi.org/10.1016/j.cub.2020.07.059)



Zoni V, Nieto V, Endter LJ, Risselada HJ, Monticelli L, Vanni S (2019). To bud or not to bud: a perspective on molecular simulations of lipid droplet budding. Frontiers in Molecular Biosciences 6, 124

Zoni VCampomanes P, Khaddaj R, Thiam AR, Schneiter R, Vanni S (2019). Lipid droplet biogenesis is a liquid phase separation spatially regulated by seipin and membrane curvature. BioRxiv, 777466

Soste M, Charmpi K, Lampert F, Gerez JA, van Oostrum M, Malinovska L, Boersema PJ, Prymaczok NC, Riek R, Peter M, Vanni S, Beyer A, Picotti P (2019).Proteomics-Based Monitoring of Pathway Activity Reveals that Blocking Diacylglycerol Biosynthesis Rescues from Alpha-Synuclein Toxicity. Cell Systems

Vanni S, Riccardi L, Palermo G, DeVivo M (2019). Structure and Dynamics of the Acyl Chains in the Membrane Trafficking and Enzymatic Processing of Lipids. Accounts of Chemical Research

Campomanes P, Zoni V, Vanni S (2019). Local accumulation of diacylglycerol alters membrane properties non-linearly due to its transbilayer activity. Communications Chemistry, 2, 72.

Petretto E, Campomanes P, Stellacci F, Rothen-Rutishauser B, Petri-Fink A, Vanni S (2019). An Atomistic Look into Bio-inspired Nanoparticles and their Molecular Interactions with Cells. CHIMIA, 73 (1), 78-80

Fennouri A, List J, Dupasquier J ,Haeni L, Vanni S, Rothen-Rutishauser B, Mayer M (2019). Templated Assembly of Pore-forming Peptides in Lipid Membranes. CHIMIA, 73 (1), 59-62.



Friedman R, Khalid S, ..., Vanni S, Zeppelin T, Zoni V, Bondar A-N, Domene C (2018). Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology. Journal of Membrane Biology, 251(5-6), 609-631.

Pinot M, Vanni S, Ambroggio E, Guet D, Goud B, Manneville JB (2018). Feedback between membrane tension, lipid shape and curvature in the formation of packing defects. bioRxiv, 389627

Gautier R, Bacle A, Tiberti ML, Fuchs PF, Vanni S, Antonny B (2018). PackMem: A Versatile Tool to Compute and Visualize Interfacial Packing Defects in Lipid Bilayers. Biophysical Journal 115 (3), 436-444



Vanni S (2017). Intracellular lipid droplets: from structure to function. Lipid Insights 10: 1178635317745518.

Soares TA, Vanni S, Milano G & Cascella M (2017). Toward chemically resolved computer simulations of dynamics and remodeling of biological membranes. Journal of Physical Chemistry Letters 8: 3586–3594.

Ben M'barek K, Ajjaji D, Chorlay A, Vanni S, Forêt L & Thiam AR (2017). ER membrane phospholipids and surface tension control cellular lipid droplet formation. Developmental Cell 41: 591-604.

Bacle A, Gautier R, Jackson CL, Fuchs PFJ & Vanni S (2017). Interdigitation between triglycerides and lipids modulates surface properties of lipid droplets. Biophysical Journal 112 1417-1430 (http://www.cell.com/biophysj/abstract/S0006-3495(17)30246-1).



Magdeleine M, Gautier R, Gounon P, Barelli H, Vanni S & Antonny B (2016). A filter at the entrance of the Golgi that selects vesicles according to size and bulk lipid composition. Elife e16988 (DOI: 10.7554/eLife.16988).

Cascella M & Vanni S (2016). Toward accurate coarse-graining approaches for protein and membrane simulations in "SPR- Chemical Modelling" Vol. 12, Royal Society of Chemistry, pp. 1-52.

Antonny B, Vanni S, Shindou H & Ferreira T (2016). From zero to six double bonds: phospholipid unsaturation and organelle function. Trends in Cell Biology 25:427-436.



Moser von Filseck J, Vanni S, Mesmin B, Antonny B & Drin G (2015). A phosphatidylinositol-4-phosphate powered exchange mechanism to create a lipid gradient between membranes. Nature Communications 6: 6671 (doi:10.1038/ncomms7671).

Cournia Z ,Allen TW, Andricioaei I, Antonny B, Baum D, Brannigan G, Buchete N-V, Deckman JT, Delemotte L, del Val C, Friedmann R, Gkeka P, Hege H-C, Hénin J, Kasimova MA, Kolocouris A, Klein ML, Khalid S, Lemieux MJ, Lindow N, Roy M, Selent J, Tarek M, Tofoleanu F, Vanni S, Urban S, Wales DJ, Smith JC, & Bonda A-N (2015). Membrane protein structure, function, and dynamics: a perspective from experiments and theory. J Membrane Biol 248: 611-640 (doi:10.1007/s00232-015-9802-0).

Garten M, Prévost C, Cadart C, Gautier R, Bousset L, Melki R, Bassereau P & Vanni S (2015). Methyl-branched lipids promote the membrane adsorption of α-synuclein by enhancing shallow lipid-packing defects. Phys. Chem. Chem. Phys. 7: 15589-15597 (DOI: 10.1039/C5CP00244C).

Moser von Filseck J, Copic A, Delfosse V, Vanni S, Jackson CL, Bourguet W & Drin G (2015). Phosphatidylserine transport by ORP/Osh proteins is driven by phosphatidylinositol 4-phosphate. Science 349, 432-436 (DOI: 10.1126/science.aab1346).



Vanni S, Hirose H, Barelli H, Antonny B & Gautier R (2014). A sub-nanometre view of how membrane curvature and composition modulate lipid packing and protein recruitment. Nature Communications 5: 4916 (doi:10.1038/ncomms5916).

Campomanes P, Neri M, Horta BAC, Röhrig UF, Vanni S, Tavernelli I & Ursula Rothlisberger U (2014). Origin of the spectral shifts among the early intermediates of the Rhodopsin photo cycle. J. Am. Chem. Soc. 136: 3842–3851 (DOI: 10.1021/ja411303v).

Pinot M, Vanni S, Pagnotta S, Lacas-Gervais S, Payet L-A, Ferreira T, Gautier R, Goud B, Antonny B & Barelli H (2014). Polyunsaturated phospholipids facilitate membrane deformation and fission by endocytic proteins. Science 345: 693-697 (DOI: 10.1126/science.1255288).



Vanni S, Vamparys L, Gautier R, Drin G, Etchebest C, Fuchs PFJ & Bruno Antonny B (2013). Amphipathic lipid packing sensor motifs: probing bilayer defects with hydrophobic residues. Biophysical Journal 104: 575-584 (http://dx.doi.org/10.1016/j.bpj.2012.11.3837).

Vamparys L, Gautier R, Vanni S, Bennett WFD, Tieleman DP, Antonny B, Etchebest C & Fuchs PFL (2013). Biophysical Journal 104: 585-593 (http://dx.doi.org/10.1016/j.bpj.2012.11.3836).



Vanni S & Rothlisberger U (2012). A closer look into G protein coupled receptor activation: X-Ray crystallography and long-scale molecular dynamics simulations. Current Medicinal Chemistry 19: 1135-1145.



Annibale P, Vanni S, Scarselli M, Rothlisberger U & Radenovic A (2011). Identification of clustering artifacts in photoactivated localisation microscopy. Nature Methods 8: 527-528 (doi:10.1038/nmeth.1627).

Curchod BFE, Campomanes P; Laktionov A, Neri M, Penfold TJ, Vanni S, Tavernelli I & Rothlisberger U (2011). Mechanical (QM/MM) simulations of adiabatic and nonadiabatic ultrafast phenomena. Chimia 65: 330-333.

Vanni S, Neri M, Tavernelli I, Rothlisberger U (2011). Predicting novel binding modes of agonists to β adrenergic receptors using all-atom molecular dynamics simulations. PLoS Comput Biol 7: e1001053 (doi:10.1371/journal.pcbi.1001053).

Brunk E, Negar A, Prashanth A, Campomanes P, de Carvalho FF, Curchod BFE Basile, Polydefkis D, Doemer M, Garrec J, Laktionov A, Micciarelli M, Neri M, Palermo G, Penfold TJ, Vanni S, Tavernelli I & Rothlisberger U (2011). Pushing the frontiers of first-principles based computer simulations of chemical and biological systems. Chimia 65: 667-671.

Annibale P, Vanni S, Scarselli M , Rothlisberger U & Radenovic A (2011). Quantitative photo activated localization microscopy: unraveling the effects of photo blinking. PLoS ONE 6: e22678 (doi:10.1371/journal.pone.0022678).



Vanni S, Neri M, Tavernelli I & Rothlisberger U (2010). A conserved protonation-induced switch can trigger “Ionic-Lock” formation in adrenergic receptors. Journal Molecular Biology 397: 1339-1349.

Neri M, Vanni S, Tavernelli I & Rothlisberger U (2010). Role of aggregation in Rhodopsin signal transduction. Biochemistry 49: 4827–4832 (DOI: 10.1021/bi100478j).



Vanni S, Neri M, Tavernelli I & Rothlisberger U (2009). Observation of “Ionic Lock” formation in molecular dynamics simulations of wild-type β1 and β2 adrenergic receptors. Biochemistry 48: 4789-4797 (DOI: 10.1021/bi900299f).



Vanni S, Garavelli M & Robb MA (2008). A new formulation of the phase change approach in the theory of conical intersections. Chemical Physics 347: 46-56 (http://dx.doi.org/10.1016/j.chemphys.2007.09.055).