Computational Microscopy of Crowded Membranes

Project Information

COMP-MICR-CROW-MEM

Grant agreement ID: 669723

DOI

10.3030/669723

Project closed

EC signature date 29 June 2015

Start date 1 November 2015

End date 31 October 2020

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 396 584,57

EU contribution

€ 2 396 584,57

Coordinated by

RIJKSUNIVERSITEIT GRONINGEN
Netherlands

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 (16)

Martini 3: a general purpose force field for coarse-grained molecular dynamics

Author(s): Paulo C. T. Souza, Riccardo Alessandri, Jonathan Barnoud, Sebastian Thallmair, Ignacio Faustino, Fabian Grünewald, Ilias Patmanidis, Haleh Abdizadeh, Bart M. H. Bruininks, Tsjerk A. Wassenaar, Peter C. Kroon, Josef Melcr, Vincent Nieto, Valentina Corradi, Hanif M. Khan, Jan Domański, Matti Javanainen, Hector Martinez-Seara, Nathalie Reuter, Robert B. Best, Ilpo Vattulainen, Luca Monticelli, Xavi
Published in: Nature Methods, Issue 18/4, 2021, Page(s) 382-388, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-021-01098-3

Computational Modeling of Realistic Cell Membranes

Author(s): Siewert J. Marrink, Valentina Corradi, Paulo C.T. Souza, Helgi I. Ingólfsson, D. Peter Tieleman, Mark S.P. Sansom
Published in: Chemical Reviews, Issue 119/9, 2019, Page(s) 6184-6226, ISSN 0009-2665
Publisher: American Chemical Society
DOI: 10.1021/acs.chemrev.8b00460

Titratable Martini model for constant pH simulations

Author(s): Fabian Grünewald, Paulo C. T. Souza, Haleh Abdizadeh, Jonathan Barnoud, Alex H. de Vries, Siewert J. Marrink
Published in: The Journal of Chemical Physics, Issue 153/2, 2020, Page(s) 024118, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/5.0014258

Computational Lipidomics of the Neuronal Plasma Membrane

Author(s): Helgi I. Ingólfsson, Timothy S. Carpenter, Harsh Bhatia, Peer-Timo Bremer, Siewert J. Marrink, Felice C. Lightstone
Published in: Biophysical Journal, Issue 113/10, 2017, Page(s) 2271-2280, ISSN 0006-3495
Publisher: Biophysical Society
DOI: 10.1016/j.bpj.2017.10.017

Lipid–Protein Interactions Are Unique Fingerprints for Membrane Proteins

Author(s): Valentina Corradi, Eduardo Mendez-Villuendas, Helgi I. Ingólfsson, Ruo-Xu Gu, Iwona Siuda, Manuel N. Melo, Anastassiia Moussatova, Lucien J. DeGagné, Besian I. Sejdiu, Gurpreet Singh, Tsjerk A. Wassenaar, Karelia Delgado Magnero, Siewert J. Marrink, D. Peter Tieleman
Published in: ACS Central Science, Issue 4/6, 2018, Page(s) 709-717, ISSN 2374-7943
Publisher: American Chemical Society
DOI: 10.1021/acscentsci.8b00143

Lipid phase separation in the presence of hydrocarbons in giant unilamellar vesicles

Author(s): Rianne Bartelds, Jonathan Barnoud, Arnold J. Boersma, Siewert J. Marrink, Bert Poolman
Published in: AIMS Biophysics, Issue 4/4, 2017, Page(s) 528-542, ISSN 2377-9098
Publisher: AIMS
DOI: 10.3934/biophy.2017.4.528

Molecular Dynamics of the Association of L-Selectin and FERM Regulated by PIP2

Author(s): Fude Sun, Carsten F.E. Schroer, Lida Xu, Huiwei Yin, Siewert J. Marrink, Shi-Zhong Luo
Published in: Biophysical Journal, Issue 114/8, 2018, Page(s) 1858-1868, ISSN 0006-3495
Publisher: Biophysical Society
DOI: 10.1016/j.bpj.2018.02.034

Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations

Author(s): Ruo-Xu Gu, Helgi I. Ingólfsson, Alex H. de Vries, Siewert J. Marrink, D. Peter Tieleman
Published in: The Journal of Physical Chemistry B, Issue 121/15, 2017, Page(s) 3262-3275, ISSN 1520-6106
Publisher: American Chemical Society
DOI: 10.1021/acs.jpcb.6b07142

Structural insights into K48-linked ubiquitin chain formation by the Pex4p-Pex22p complex

Author(s): Matthew R. Groves, Carsten F.E. Schroer, Adam J. Middleton, Sergey Lunev, Natasha Danda, Ameena M. Ali, Siewert J. Marrink, Chris Williams
Published in: Biochemical and Biophysical Research Communications, Issue 496/2, 2018, Page(s) 562-567, ISSN 0006-291X
Publisher: Academic Press
DOI: 10.1016/j.bbrc.2017.12.150

Computational ‘microscopy’ of cellular membranes

Author(s): Helgi I. Ingólfsson, Clément Arnarez, Xavier Periole, Siewert J. Marrink
Published in: Journal of Cell Science, Issue 129/2, 2016, Page(s) 257-268, ISSN 0021-9533
Publisher: The Company of Biologists Ltd.
DOI: 10.1242/jcs.176040

Molecular Mechanism of Lipid Nanodisk Formation by Styrene-Maleic Acid Copolymers

Author(s): Minmin Xue, Lisheng Cheng, Ignacio Faustino, Wanlin Guo, Siewert J. Marrink
Published in: Biophysical Journal, Issue 115/3, 2018, Page(s) 494-502, ISSN 0006-3495
Publisher: Biophysical Society
DOI: 10.1016/j.bpj.2018.06.018

Multiscale Simulation of Protein Hydration Using the SWINGER Dynamical Clustering Algorithm

Author(s): Julija Zavadlav, Siewert J. Marrink, Matej Praprotnik
Published in: Journal of Chemical Theory and Computation, Issue 14/3, 2018, Page(s) 1754-1761, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.7b01129

Molecular mechanism of cardiolipin-mediated assembly of respiratory chain supercomplexes

Author(s): C. Arnarez, S. J. Marrink, X. Periole
Published in: Chemical Science, Issue 7/7, 2016, Page(s) 4435-4443, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/C5SC04664E

CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides

Author(s): Pin-Chia Hsu, Bart M. H. Bruininks, Damien Jefferies, Paulo Cesar Telles de Souza, Jumin Lee, Dhilon S. Patel, Siewert J. Marrink, Yifei Qi, Syma Khalid, Wonpil Im
Published in: Journal of Computational Chemistry, Issue 38/27, 2017, Page(s) 2354-2363, ISSN 0192-8651
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/jcc.24895

Adaptive Resolution Simulation of Supramolecular Water: The Concurrent Making, Breaking, and Remaking of Water Bundles

Author(s): Julija Zavadlav, Siewert J. Marrink, Matej Praprotnik
Published in: Journal of Chemical Theory and Computation, Issue 12/8, 2016, Page(s) 4138-4145, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.6b00536

Protein–ligand binding with the coarse-grained Martini model

Author(s): Paulo C. T. Souza, Sebastian Thallmair, Paolo Conflitti, Carlos Ramírez-Palacios, Riccardo Alessandri, Stefano Raniolo, Vittorio Limongelli, Siewert J. Marrink
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-17437-5

Book chapters (1)

Protocol for Simulations of PEGylated Proteins with Martini 3

Author(s): Fabian Grünewald, Peter C. Kroon, Paulo C. T. Souza, Siewert J. Marrink
Published in: Structural Genomics - General Applications, Issue 2199, 2021, Page(s) 315-335, ISBN 978-1-0716-0891-3
Publisher: Springer US
DOI: 10.1007/978-1-0716-0892-0_18