Floris van Eerden

Floris Van Eerden Specially-Appointed Researcher fvaneerden [at] ifrec.osaka-u.ac.jp


Structural dynamics of the T cell receptor

The T cell receptor is an intriguing part of the immune system. Although a vital part in the detection of pathogens, its functioning is not fully understood. I am trying to undestand its mechanism a bit better, by deploying large scale simulations.

During my PhD I applied large scale simulations to study another complex protein, Photosystem II. A small movie of my research can be seen below.

Excerpt from a half mili second simulation in which plastoquinone is seen entering Photosystem II, one of the major findings from my PhD.


Year Authors Title Publication Cites
2014 HI Ingólfsson, MN Melo, FJ Van Eerden, C Arnarez, CA Lopez, ... Lipid organization of the plasma membrane JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2014, 136, 14554-14559 477
2013 CA López, Z Sovova, FJ van Eerden, AH de Vries, SJ Marrink Martini force field parameters for glycolipids JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2013, 9, 1694-1708 128
2015 FJ van Eerden, DH de Jong, AH de Vries, TA Wassenaar, SJ Marrink Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations BIOCHIMICA ET BIOPHYSICA ACTA (BBA)-BIOMEMBRANES, 2015, 1848, 1319-1330 92
2017 FJ Van Eerden, MN Melo, PWJM Frederix, X Periole, SJ Marrink Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex NATURE COMMUNICATIONS, 2017, 8, 1-8 40
2017 B Liu, C Åberg, FJ van Eerden, SJ Marrink, B Poolman, AJ Boersma Design and properties of genetically encoded probes for sensing macromolecular crowding BIOPHYSICAL JOURNAL, 2017, 112, 1929-1939 31
2017 FJ Van Eerden, T Van Den Berg, PWJM Frederix, DH De Jong, X Periole, ... Molecular dynamics of photosystem II embedded in the thylakoid membrane THE JOURNAL OF PHYSICAL CHEMISTRY B, 2017, 121, 3237-3249 25
2017 FJ Van Eerden, MN Melo, PWJM Frederix, SJ Marrink Prediction of thylakoid lipid binding sites on photosystem II BIOPHYSICAL JOURNAL, 2017, 113, 2669-2681 17
2018 R Friedman, S Khalid, C Aponte-Santamaría, E Arutyunova, M Becker, ... Understanding conformational dynamics of complex lipid mixtures relevant to biology THE JOURNAL OF MEMBRANE BIOLOGY 251 (5-6), 2018, 609-631 14
2019 S Li, J Wilamowski, S Teraguchi, FJ van Eerden, J Rozewicki, A Davila, ... Structural modeling of lymphocyte receptors and their antigens IN VITRO DIFFERENTIATION OF T-CELLS, 2019, 207-229 2
2020 S Teraguchi, DS Saputri, MA Llamas-Covarrubias, A Davila, D Diez, ... Methods for sequence and structural analysis of B and T cell receptor repertoires COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 2020 0
2020 DS Saputri, S Li, FJ Van Eerden, J Rozewicki, Z Xu, HS Ismanto, A Davila, ... Flexible, functional and familiar: characteristics of SARS-CoV-2 spike protein evolution FRONTIERS IN MICROBIOLOGY, 2020, 11, 2112-2112 0
2016 FJ van Eerden Photosynthesis in Silico: Simulations of Photosystem II and the Thylakoid Membrane RIJKSUNIVERSITEIT GRONINGEN, 2016 0
2014 FJ van Eerden, DH de Jong, X Periole, SJ Marrink Simulation of Photosystem Ii Dynamics in the Thylakoid Membrane BIOPHYSICAL JOURNAL 106 (2), 181A, 2014 0
2009 FJ van Eerden Differential Scanning Calorimetry and Protein Stability FACULTY OF SCIENCE AND ENGINEERING, 2009 0