About

Our team is the host to the ERC Advanced Grant Project CROWDED-PRO-LIPIDS granted to us by the European Research Council for 2012-2017.

We were chosen as the Centre of Excellence (CoE) in Biomembrane Research by the Academy of Finland for 2014-2019. The Centre is comprised of three groups, one of them being our computational and theoretical team directed by Ilpo Vattulainen (vice-chair of the CoE), the others being directed by Academy Prof. Elina Ikonen (chair, Univ Helsinki) and Prof. Pekka Lappalainen (partner, Univ Helsinki).

Cholera toxin.

 

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.

Gold nanoparticle.

 

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

  • 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: 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: 10.1083/jcb.201907210
  • Chronopoulos, A., Thorpe, S.D., Cortes, E., Lachowski, D., Rice, A.J., Mykuliak, V.V., Róg, T., Lee, D.A., Hytonen, V.P., and del Río Hernández, A.E. Syndecan-4 tunes cell mechanics by activating the kindlin-integrin-RhoA pathway. Nature Materials 19, 669–678 (2020). DOI: 10.1038/s41563-019-0567-1
  • 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: 10.1073/pnas.2008885117
  • Kotila, T., Wioland, H., Enkavi, G., Kogan, K., Vattulainen, I., Jégou, A., Romet-Lemonne, G., and Lappalainen, P. Mechanism of synergistic actin filament pointed end depolymerization by cyclase-associated protein and cofilin. Nature Communications 10, 5320 (2019). DOI: 10.1038/s41467-019-13213-2
  • 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: 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: 10.1021/acs.chemrev.8b00538
  • Zhou, K., Dichlberger, A., Martinez-Seara, H., Nyholm, T.K.M.,  Li, S.,  Kim, Y.A., Vattulainen, I., Ikonen, E., and Blom T. Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction. ACS Central Science 4, 548-558 (2018). DOI: 10.1021/acscentsci.7b00582
  • 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:  10.1038/s41467-018-04231-7
  • Senju, Y., Kalimeri, M., Koskela, E. V., Somerharju, P., Zhao, H., Vattulainen, I. and Lappalainen, P. Mechanistic principles underlying regulation of the actin cytoskeleton by phosphoinositides. Proceedings of the National Academy of Sciences 114, E8977–E8986 (2017). DOI: 10.1073/pnas.1705032114
  • Steringer, J. P., Lange, S., Cujova, S., Sachl, R., Poojari, Ch., Lolicato, F., Beutel, O., Muller, H.-M., Unger, S., Coskun, U., Honigmann, A., Vattulainen, I., Hof, M., Freund, Ch., and Nickel, W. Key steps in unconventional secretion of fibroblast growth factor 2 reconstituted with purified components. eLife 6 e28985 (2017). DOI: 10.7554/eLife.28985
  • 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: 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: 10.1103/PhysRevX.6.021006
  • Kaszuba, K., Grzybek, M., Orlowski, A., Danne, R., Rog, T., Simons, K., Coskun, U. and Vattulainen, I. N-Glycosylation as determinant of epidermal growth factor receptor conformation in membranes. Proceedings of the National Academy of Sciences 112, 4334–4339 (2015). DOI: 10.1073/pnas.1503262112
  • Sharma, V., Enkavi, G., Vattulainen, I., Rog, T. and Wikstrom, M. Proton-coupled electron transfer and the role of water molecules in proton pumping by cytochrome. Proceedings of the National Academy of Sciences 112, 2040–2045 (2015). DOI: 10.1073/pnas.1409543112
  • Aijanen, T., Koivuniemi, A., Javanainen, M., Rissanen, S., Rog, T. and Vattulainen, I. How Anacetrapib Inhibits the Activity of the Cholesteryl Ester Transfer Protein? Perspective through Atomistic Simulations. PLoS Computational Biology 10, e1003987 (2014). DOI:10.1371/journal.pcbi.1003987
  • Koivuniemi, A., Vuorela, T., Kovanen, P. T., Vattulainen, I., and Hyvonen, M. Lipid exchange mechanism of the cholesteryl ester transfer protein clarified by atomistic and coarse-grained simulations. PLoS Computational Biology 8, e1002299 (2012). DOI: 10.1371/journal.pcbi.1002299
  • Lingwood, D., Binnington, B., Rog, T., Vattulainen, I., Grzybek, M., Coskun, U., Lingwood, C. A., and Simons, K. Cholesterol modulates glycolipid conformation and receptor activity. Nature Chemical Biology 7, 260-262 (2011). DOI: 10.1038/nchembio.551
  • Kaiser, H. J., Orlowski, A., Rog, T., Chai, W., Feizi, T., Lingwood, D., Vattulainen, I., and Simons, K. Lateral sorting in model membranes by cholesterol-mediated hydrophobic matching. Proceedings of the National Academy of Sciences 108, 16628-16633 (2011). DOI:10.1073/pnas.1103742108