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COMP-MICR-CROW-MEM SIGNED

Computational Microscopy of Crowded Membranes

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EC-Contrib. €

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Project "COMP-MICR-CROW-MEM" data sheet

The following table provides information about the project.

Coordinator
RIJKSUNIVERSITEIT GRONINGEN 

Organization address
address: Broerstraat 5
city: GRONINGEN
postcode: 9712CP
website: www.rug.nl

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Netherlands [NL]
 Project website http://cgmartini.nl
 Total cost 2˙396˙584 €
 EC max contribution 2˙396˙584 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2014-ADG
 Funding Scheme ERC-ADG
 Starting year 2015
 Duration (year-month-day) from 2015-11-01   to  2020-10-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    RIJKSUNIVERSITEIT GRONINGEN NL (GRONINGEN) coordinator 2˙396˙584.00

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 Project objective

Cell membranes form a highly complex and heterogeneous mixture of membrane proteins and lipids. Understanding the protein-lipid interplay that gives rise to the lateral organisation principles of cell membranes is essential for life and health. Thus, investigations of these crowded membranes is emerging as a new and exceptionally exciting frontier at the crossroads of biology, life sciences, physics, and chemistry.

However, our current understanding of the detailed organisation of cellular membranes remains rather elusive. Characterisation of the structural heterogeneity in-vivo remains very challenging, owing to the lack of experimental methods suitable for studying these fluctuating nanoscale assemblies of lipids and proteins with the required spatio-temporal resolution. In recent years, computer simulations have become a unique investigatory tool for understanding the driving forces governing the lateral organisation of cellular membrane components and this “computational microscopy” has become indispensible as a complement to traditional microscopy methods.

In this ERC project I will, using advanced computational microscopy, study the interaction of lipids and proteins in complex, crowded, membrane patches, to enable the driving forces of membrane protein sorting and clustering to be unravelled at conditions closely mimicking real cellular membranes. The specific objectives are:

• To develop a novel computational microscopy framework for simulating biomolecular processes at multiple resolutions. • To use this new computational microscopy framework to investigate the driving forces of membrane protein sorting and clustering. • To provide a molecular view of realistic, crowded, biological membranes composed of hundreds of different lipids and proteins.

The outcomes will enable subsequent studies of many different types of cell membranes based on forthcoming lipidomics studies and progress in structural characterisation of membrane proteins.

 Publications

year authors and title journal last update
List of publications.
2017 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
CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides
published pages: 2354-2363, ISSN: 0192-8651, DOI: 10.1002/jcc.24895
Journal of Computational Chemistry 38/27 2020-03-20
2016 Helgi I. Ingólfsson, Clément Arnarez, Xavier Periole, Siewert J. Marrink
Computational ‘microscopy’ of cellular membranes
published pages: 257-268, ISSN: 0021-9533, DOI: 10.1242/jcs.176040
Journal of Cell Science 129/2 2020-03-20
2017 Ruo-Xu Gu, Helgi I. Ingólfsson, Alex H. de Vries, Siewert J. Marrink, D. Peter Tieleman
Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations
published pages: 3262-3275, ISSN: 1520-6106, DOI: 10.1021/acs.jpcb.6b07142
The Journal of Physical Chemistry B 121/15 2020-03-20
2017 Rianne Bartelds, Jonathan Barnoud, Arnold J. Boersma, Siewert J. Marrink, Bert Poolman
Lipid phase separation in the presence of hydrocarbons in giant unilamellar vesicles
published pages: 528-542, ISSN: 2377-9098, DOI: 10.3934/biophy.2017.4.528
AIMS Biophysics 4/4 2020-03-20
2017 Helgi I. Ingólfsson, Timothy S. Carpenter, Harsh Bhatia, Peer-Timo Bremer, Siewert J. Marrink, Felice C. Lightstone
Computational Lipidomics of the Neuronal Plasma Membrane
published pages: 2271-2280, ISSN: 0006-3495, DOI: 10.1016/j.bpj.2017.10.017
Biophysical Journal 113/10 2020-03-20
2016 Julija Zavadlav, Siewert J. Marrink, Matej Praprotnik
Adaptive Resolution Simulation of Supramolecular Water: The Concurrent Making, Breaking, and Remaking of Water Bundles
published pages: 4138-4145, ISSN: 1549-9618, DOI: 10.1021/acs.jctc.6b00536
Journal of Chemical Theory and Computation 12/8 2020-03-20
2018 Matthew R. Groves, Carsten F.E. Schroer, Adam J. Middleton, Sergey Lunev, Natasha Danda, Ameena M. Ali, Siewert J. Marrink, Chris Williams
Structural insights into K48-linked ubiquitin chain formation by the Pex4p-Pex22p complex
published pages: 562-567, ISSN: 0006-291X, DOI: 10.1016/j.bbrc.2017.12.150
Biochemical and Biophysical Research Communications 496/2 2020-03-20
2018 Fude Sun, Carsten F.E. Schroer, Lida Xu, Huiwei Yin, Siewert J. Marrink, Shi-Zhong Luo
Molecular Dynamics of the Association of L-Selectin and FERM Regulated by PIP2
published pages: 1858-1868, ISSN: 0006-3495, DOI: 10.1016/j.bpj.2018.02.034
Biophysical Journal 114/8 2020-03-20
2016 C. Arnarez, S. J. Marrink, X. Periole
Molecular mechanism of cardiolipin-mediated assembly of respiratory chain supercomplexes
published pages: 4435-4443, ISSN: 2041-6520, DOI: 10.1039/C5SC04664E
Chemical Science 7/7 2020-03-20
2018 Julija Zavadlav, Siewert J. Marrink, Matej Praprotnik
Multiscale Simulation of Protein Hydration Using the SWINGER Dynamical Clustering Algorithm
published pages: 1754-1761, ISSN: 1549-9618, DOI: 10.1021/acs.jctc.7b01129
Journal of Chemical Theory and Computation 14/3 2020-03-20
2018 Minmin Xue, Lisheng Cheng, Ignacio Faustino, Wanlin Guo, Siewert J. Marrink
Molecular Mechanism of Lipid Nanodisk Formation by Styrene-Maleic Acid Copolymers
published pages: 494-502, ISSN: 0006-3495, DOI: 10.1016/j.bpj.2018.06.018
Biophysical Journal 115/3 2020-03-20
2018 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
Lipid–Protein Interactions Are Unique Fingerprints for Membrane Proteins
published pages: 709-717, ISSN: 2374-7943, DOI: 10.1021/acscentsci.8b00143
ACS Central Science 4/6 2020-03-20

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