About

We were chosen as the Centre of Excellence (CoE) in Biological Barrier Mechanics and Disease by the Academy of Finland for 2022-2029. The Centre is comprised of five groups, one of them being our computational and theoretical team directed by Ilpo Vattulainen, the others being directed by Academy Prof. Johanna Ivaska (chair, Univ Turku), Prof. Sara Wickström (Univ Helsinki), Prof. Pipsa Saharinen (Univ Helsinki), and Academy Prof. Pekka Lappalainen (Univ Helsinki).

 

 

Biological physics, as many people call this discipline nowadays, is an excellent example of a cross-disciplinary field of science that bridges people with various backgrounds to work on problems whose proper understanding is crucial for life. Although much has been done, we are still on our early days of understanding the underlying physical principles that govern the behavior of biological systems.

The Biological Physics and Soft Matter Group focuses on the theory and modeling of biologically relevant soft and condensed matter systems. The work includes the development of theoretical and computational techniques for multiscale modeling, and applications of these methods to study physicochemical properties of soft and condensed matter systems over a multitude of scales.

 

The group concentrates on computational and theoretical biological sciences (biological physics), with an aim to strengthen the understanding of biological processes on a cellular level to promote health. The research focuses on lipids, membrane proteins, lipid transfer proteins, lipid-protein interactions, signaling, tear films, drugs, and glycocalyx. The research topics are related to outstanding issues such as cardiovascular disease, type-2 diabetes, dry eye syndrome, and cancer. The group focuses on high gain projects done together with experimental teams in, e.g., biomedicine, cell biology, pharmacology, structural biology, and biophysics. Through these collaborations the group works on cross-disciplinary problems in the fields where the traditional borderlines between physics, chemistry, and computational and medical sciences tend to vanish.

Recent highlights

  • Lilja, J., Kaivola, J., Conway, J.R.W., Vuorio, J., Parkkola, H., Roivas, P., Dibus, M., Chastney, M.R., Varila, T., Jacquemet, G., Peuhu, E., Wang, E., Pentikäinen, U., Posada, I.M.D., Hamidi, H., Najumudeen, A.K., Sansom, O.J., Barsukov, I.L., Abankwa, D., Vattulainen, I., Salmi, M., and Ivaska, J. SHANK3 depletion leads to ERK signalling overdose and cell death in KRAS-mutant cancers. Nature Communications 15, 8002 (2024). DOI: https://doi.org/10.1038/s41467-024-52326-1
  • Abraham, B.G., Haikarainen, T., Vuorio, T., Girych, M., Virtanen, A.T., Kurttila, A., Karathanasis, Ch., Heilemann, M., Sharma, V., Vattulainen, I., and Silvennoinen, O. Molecular basis of JAK2 activation in erythropoietin receptor and pathogenic JAK2 signaling. Science Advances 10, eadl2097 (2024). DOI: https://doi.org/10.1126/sciadv.adl2097
  • Goellner, S., Enkavi, G., Prasad, V., Denolly, S., Eu, S., Mizzon, G., Witte, L., Kulig, W., Uckeley, Z.M., Lavacca, T.M., Haselmann, U., Lozach, P.-Y., Brügger, B., Vattulainen, I., and Bartenschlager, R. Zika virus prM protein contains cholesterol binding motifs required for virus entry and assembly. Nature Communications 14, 7344 (2023). DOI: https://doi.org/10.1038/s41467-023-42985-x
  • McDowell, M.A., Heimes, M., Enkavi, G., Farkas, Á., Saar, D., Wild, K., Schwappach, B., Vattulainen, I., and Sinning, I. The GET insertase exhibits conformational plasticity and induces membrane thinning. Nature Communications 14, 7355 (2023). DOI: https://doi.org/10.1038/s41467-023-42867-2
  • Moliner, R., Girych, M., Brunello, C.A., Kovaleva, V., Biojone, C., Enkavi, G., Antenucci, L., Kot, E.F., Goncharuk, S.A., Kaurinkoski, K., Kuutti, M., Fred, S.M., Elsilä, L.V., Sakson, S., Cannarozzo, C., Diniz, C.R.A.F., Seiffert, N., Rubiolo, A., Haapaniemi, H., Meshi, E., Nagaeva, E., Öhman, T., Róg, T., Kankuri, E., Vilar, M., Varjosalo, M., Korpi, E.R., Permi, P., Mineev, K.S., Saarma, M., Vattulainen, I., Casarotto, P.C., and Castrén, E. Psychedelics promote plasticity by directly binding to BDNF receptor TrkB. Nature Neuroscience 26, 1032–1041 (2023). DOI: https://doi.org/10.1038/s41593-023-01316-5
  • Dumesnil, C., Vanharanta, L., Prasanna, X., Omrane, M., Carpentier, M., Bhapkar, A., Enkavi, G., Salo, V.T., Vattulainen, I., Ikonen, E., and Thiam, A.R. Cholesterol esters form supercooled lipid droplets whose nucleation is facilitated by triacylglycerols. Nature Communications 14, 915 (2023). DOI: https://doi.org/10.1038/s41467-023-36375-6
  • Lolicato, F., Saleppico, R., Griffo, A., Meyer, A., Scollo, F., Pokrandt, B., Müller, H.-M., Ewers, H., Hähl, H.,  Fleury, J.-B., Seemann, R., Hof, M., Brügger, B., Jacobs, K., Vattulainen, I., and Nickel, W. Cholesterol promotes clustering of PI(4,5)P2 driving unconventional secretion of FGF2. Journal of Cell Biology 221, e202106123 (2022). DOI: https://doi.org/10.1083/jcb.202106123
  • Serdiuk, T., Manna M., Zhang, Ch., Mari, S.A., Kulig, W., Pluhackova, K., Kobilka, B.K., Vattulainen, I., and Müller, D.J. A cholesterol analog stabilizes the human beta2-adrenergic receptor nonlinearly with temperature. Science Signaling 15, eabi7031 (2022). DOI: https://doi.org/10.1126/scisignal.abi7031
  • Souza, P.C.T., Alessandri, R., Barnoud, J., Thallmair, S., Faustino, I., Grünewald, F., Patmanidis, I., Abdizadeh, H., Bruininks, B.M.H., Wassenaar, T.A., Kroon, P.C., Melcr, J., Nieto, V., Corradi, V., Khan, H.M., Domański, J., Javanainen, M., Martinez-Seara, H., Reuter, N., Best, R.B., Vattulainen, I., Monticelli, L., Periole, X., Tieleman, D.P., de Vries, A.H., and Marrink, S.J. Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nature Methods 18, 382–388 (2021). DOI: https://doi.org/10.1038/s41592-021-01098-3
  • Casarotto, P.C., Girych, M., Fred, S.M., Kovaleva, V., Moliner, R., Enkavi, G., Biojone, C., Cannarozzo, C., Sahu, M.P., Kaurinkoski, K., Brunello, C.A., Steinzeig, A., Winkel, F., Patil, S., Vestring, S., Serchov, T., Diniz, C.R.A.F., Laukkanen, L., Cardon, I., Antila, H., Róg, T., Piepponen, T.P., Bramham, C.R., Normann, C., Lauri, S.E., Saarma, M., Vattulainen, I., and Castrén, E. Antidepressant drugs act by directly binding to TRKB neurotrophin receptors. Cell 184, 1299-1313.e19 (2021). DOI: https://doi.org/10.1016/j.cell.2021.01.034
  • Wilmes, S., Hafer, M., Vuorio, J., Tucker, J.A., Winkelmann, H., Lochte, S., Stanly, T.A., Pulgar Prieto, K.D., Poojari, Ch., Sharma, V., Richter, Ch.P., Kurre, R., Hubbard, S.R., Garcia, K.Ch., Moraga, I., Vattulainen, I., Hitchcock, I.S., and Piehler, J. Mechanism of homodimeric cytokine receptor activation and dysregulation by oncogenic mutations. Science 367, 643-652 (2020). DOI: https://doi.org/10.1126/science.aaw3242
  • Gutmann, T., Schäfer, I.B., Poojari, Ch., Brankatschk, B., Vattulainen, I., Strauss, M., and Coskun, Ü. Cryo-EM structure of the complete and ligand-saturated insulin receptor ectodomain. Journal of Cell Biology 219, e201907210 (2020). DOI: https://doi.org/10.1083/jcb.201907210
  • Lucendo, E., Sancho, M., Lolicato, F., Javanainen, M., Kulig, W., Leiva, D., Duart, G., Andreu-Fernández, V., Mingarro, V., and Orzáez, M. Mcl-1 and Bok transmembrane domains: Unexpected players in the modulation of apoptosis. Proceedings of the National Academy of Sciences 117, 27980-27988 (2020). DOI: https://doi.org/10.1073/pnas.2008885117
  • Li, S., Prasanna, X., Salo, V.T., Vattulainen, I., and Ikonen, E. An efficient auxin-inducible degron system with low basal degradation in human cells. Nature Methods 16, 866–869 (2019). DOI: https://doi.org/10.1038/s41592-019-0512-x
  • Enkavi, G., Javanainen, M., Kulig, W., Róg, T., and Vattulainen, I. Multiscale simulations of biological membranes: The challenge to understand biological phenomena in a living substance. Chemical Reviews 119, 5607-5774 (2019). DOI: https://doi.org/10.1021/acs.chemrev.8b00538
  • Kotila, T., Kogan, K., Enkavi, G., Guo, S., Vattulainen, I., Goode B. L., and Lappalainen, P. Structural basis of actin monomer recharging by cyclase-associated protein. Nature Communications, 9, 1892 (2018). DOI: https://doi.org/10.1038/s41467-018-04231-7
  • Manna, M., Niemela, M., Tynkkynen, J., Javanainen, M., Kulig, W., Muller, D. J., Rog, T. and Vattulainen, I. Mechanism of allosteric regulation of β2-adrenergic receptor by cholesterol. eLife 5 18432 (2016). DOI: https://doi.org/10.7554/eLife.18432
  • Jeon, J.-H., Javanainen, M., Martinez-Seara, H., Metzler, R. and Vattulainen, I. Protein Crowding in Lipid Bilayers Gives Rise to Non-Gaussian Anomalous Lateral Diffusion of Phospholipids and Proteins. Physical Review X 6, 021006 (2016). DOI: https://doi.org/10.1103/PhysRevX.6.021006