The Molecular Dynamics of Membrane Contact Sites

Project Information

MCS-MD

Grant agreement ID: 803952

DOI

10.3030/803952

Project closed

EC signature date 17 October 2018

Start date 1 June 2019

End date 31 December 2024

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 497 719,00

EU contribution

€ 1 497 719,00

Coordinated by

UNIVERSITE DE FRIBOURG
Switzerland

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (17)

Estimating the accuracy of the MARTINI model towards the investigation of Peripheral Protein-Membrane Interactions

Author(s): Sriraksha Srinivasan, Valeria Zoni, Stefano Vanni
Published in: Faraday Discussions, 2020, ISSN 1359-6640
Publisher: Royal Society of Chemistry
DOI: 10.1039/d0fd00058b

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

Author(s): Pablo Campomanes, Janak Prabhu, Valeria Zoni, Stefano Vanni
Published in: Biophysical Reports, Issue 1, 2021, Page(s) 100034, ISSN 2667-0747
Publisher: Elsevier
DOI: 10.1016/j.bpr.2021.100034

Structure of the yeast ceramide synthase

Author(s): Jan-Hannes Schäfer, Lena Clausmeyer, Carolin Körner, Bianca M. Esch, Verena N. Wolf, Jennifer Sapia, Yara Ahmed, Stefan Walter, Stefano Vanni, Dovile Januliene, Arne Moeller, Florian Fröhlich
Published in: Nature Structural & Molecular Biology, 2024, ISSN 1545-9993
Publisher: Nature Publishing Group
DOI: 10.1038/s41594-024-01415-2

Pragmatic Coarse-Graining of Proteins: Models and Applications

Author(s): Luís Borges-Araújo; Ilias Patmanidis; Akhil P. Singh; Lucianna H. S. Santos; Adam K. Sieradzan; Stefano Vanni; Cezary Czaplewski; Sergio Pantano; Wataru Shinoda; Luca Monticelli; Adam Liwo; Siewert J. Marrink; Paulo C. T. Souza
Published in: Journal of Chemical Theory and Computation, 2023, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.3c00733

Computational Approaches to Investigate and Design Lipid-binding Domains for Membrane Biosensing

Author(s): Sriraksha Srinivasan, Stefano Vanni
Published in: CHIMIA, Issue 75, 2021, Page(s) 1031-36, ISSN 0009-4293
Publisher: Schweizerische Chemische Gedellschaft
DOI: 10.2533/chimia.2021.1031

An S-acylated N-terminus and a conserved loop regulate the activity of the ABHD17 deacylase

Author(s): Sydney Holme, Jennifer Sapia, Michael Davey, Stefano Vanni, Elizabeth Conibear
Published in: Journal of Cell Biology, Issue 224, 2025, ISSN 0021-9525
Publisher: Rockefeller University Press
DOI: 10.1083/jcb.202405042

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

Author(s): Sriraksha Srinivasan, Andrea Di Luca, Daniel Álvarez, Arun T. John Peter, Charlotte Gehin, Museer A. Lone, Thorsten Hornemann, Giovanni D’Angelo, Stefano Vanni
Published in: PLOS Biology, Issue 22, 2024, Page(s) e3002737, ISSN 1545-7885
Publisher: PLOS
DOI: 10.1371/journal.pbio.3002737

Lipid scrambling is a general feature of protein insertases

Author(s): Dazhi Li, Cristian Rocha-Roa, Matthew A. Schilling, Karin M. Reinisch, Stefano Vanni
Published in: Proceedings of the National Academy of Sciences, Issue 121, 2024, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2319476121

In situ architecture of the ER–mitochondria encounter structure

Author(s): Michael R. Wozny, Andrea Di Luca, Dustin R. Morado, Andrea Picco, Rasha Khaddaj, Pablo Campomanes, Lazar Ivanović, Patrick C. Hoffmann, Elizabeth A. Miller, Stefano Vanni and Wanda Kukulski
Published in: Nature, 2023, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-023-06050-3

A conserved function of Human DLC3 and Drosophila Cv-c in testis development

Author(s): Sol Sotillos, Isabel von der Decken, Ivan Domenech Mercadé, Sriraksha Srinivasan, Dmytro Sirokha, Ludmila Livshits, Stefano Vanni, Serge Nef, Anna Biason-Lauber, Daniel Rodríguez Gutiérrez, James Castelli-Gair Hombría
Published in: eLife, Issue 11, 2023, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.82343

An <i>in silico</i> osmotic pressure approach allows characterization of pressure–area isotherms of lipid monolayers at low molecular areas

Author(s): Janak Prabhu; Akhil Pratap Singh; Stefano Vanni
Published in: Soft Matter, 2023, ISSN 1744-683X
Publisher: Royal Society of Chemistry
DOI: 10.1039/d2sm01419j

A Coarse-Grained SPICA Makeover for Solvated and Bare Sodium and Chloride Ions

Author(s): Janak Prabhu, Matteo Frigerio, Emanuele Petretto, Pablo Campomanes, Stefan Salentinig, Stefano Vanni
Published in: Journal of Chemical Theory and Computation, Issue 20, 2024, Page(s) 7624-7634, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.4c00529

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

Author(s): F. Emil Thomasen, Tórur Skaalum, Ashutosh Kumar, Sriraksha Srinivasan, Stefano Vanni, Kresten Lindorff-Larsen
Published in: Nature Communications, Issue 15, 6645, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/2023.05.29.542689

Molecular dynamics simulations of intracellular lipid droplets: a new tool in the toolbox

Author(s): Jennifer Sapia, Stefano Vanni
Published in: FEBS Letters, Issue 598, 2024, Page(s) 1143-1153, ISSN 0014-5793
Publisher: Elsevier BV
DOI: 10.1002/1873-3468.14879

Unbiased MD simulations identify lipid binding sites in lipid transfer proteins

Author(s): Sriraksha Srinivasan, Daniel Álvarez, Arun T. John Peter, Stefano Vanni
Published in: Journal of Cell Biology, Issue 223, 2024, ISSN 0021-9525
Publisher: Rockefeller University Press
DOI: 10.1083/jcb.202312055

DNA Self-Assembly of Single Molecules with Deterministic Position and Orientation

Author(s): Aleksandra K. Adamczyk; Teun A. P. M. Huijben; Miguel Sison; Andrea Di Luca; Germán Chiarelli; Stefano Vanni; Sophie Brasselet; Kim I. Mortensen; Fernando D. Stefani; Mauricio Pilo-Pais; Guillermo P. Acuna
Published in: Nano letters, 2022, ISSN 1530-6984
Publisher: American Chemical Society
DOI: 10.1021/acsnano.2c06936

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

Author(s): Jennifer Sapia, Daniel Alvarez, Stefano Vanni
Published in: Current Opinion in Cell Biology, 2023, ISSN 0955-0674
Publisher: Elsevier BV
DOI: 10.1016/j.ceb.2023.102205

Other (3)

Amphipathic helices sense the inner nuclear membrane environment through lipid packing defects

Author(s): Shoken Lee, Anabel-Lise Le Roux, Mira Mors, Stefano Vanni, Pere Roca-Cusachs, Shirin Bahmanyar
Published in: BioRxiv, 2024
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.11.14.623600

Pex30-dependent membrane contacts sites maintain ER lipid homeostasis

Author(s): Joana Veríssimo Ferreira, Yara Ahmed, Tiaan Heunis, Aamna Jain, Errin Johnson, Markus Raeschle, Robert Ernst, Stefano Vanni, Pedro Carvalho
Published in: BioRxiv, 2025
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.02.12.637848

Dietary control of peripheral adipose storage capacity through membrane lipid remodelling

Author(s): Marcus J. Tol, Yuta Shimanaka, Alexander H. Bedard, Jennifer Sapia, Liujuan Cui, Mariana Colaço-Gaspar, Peter Hofer, Alessandra Ferrari, Kevin Qian, John P. Kennelly, Stephen D. Lee, Yajing Gao, Xu Xiao, Jie Gao, Julia J. Mack, Thomas A. Weston, Calvin Pan, Aldons J. Lusis, Kevin J. Williams, Baolong Su, Daniel P. Pike, Alex Reed, Natalia Milosevich, Benjamin F. Cravatt, Makoto Arita, Stephen G.
Published in: BioRxiv, 2024
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.10.25.620374