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