Bio- ja ympäristötieteiden laitos

Spectroscopy for detecting dynamics of biomolecules

Research topic: Spectroscopy on biomolecules

The group of Janne Ihalainen (JYU/NSC) started at the division of Cell and Molecular Biology in January 2009. The research interests of the group lay at the intersection of biology, chemistry and physics. The general aim is to detect fast molecular time-scale processes in nature, which facilitates understanding of the mechanism of biological reactions. Our group has two main research objectives: 1) New strategies for detecting light-activated structural and chemical changes of red light photosensory proteins and 2) development of vibrational spectroscopic tools for detecting uncoating processes of viral particles.

Last years we have progressed our research considerably. The biggest breakthrough was achieved when we detected crystal and solution structures from resting and active states of red light photosensor protein (bacteriophytochromes) in a kinetic manner. For this, a novel technique time-resolved X-ray solution scattering, together with X-ray crystallography, was utilized. After this, we have been able to show that the large scale structural changes are ubiquitous in many bacteriophytochrome systems. By combining spectroscopic experimental observations with the X-ray scattering data, we have characterized the structural changes of the full-length bacteriophytochromes and their monomeric counterparts. Furthermore, we have reported about interdimeric interactions of the subunits and the influence of the quaternary structures to the thermal reversion from the illuminated state to the dark adapted state. In addition, we have been able to characterize the excited state reactions of biliverdin and advanced the know-how about new and potential phytochrome-based red fluorescent proteins. In terms of virus research, we have revealed measures from the virus uncoacting process by detecting Raman spectroscopic signals in its native and disrupted states of Echovirus 1. In addition, we collaborate closely with several other groups in NSC and abroad and contribute their objectives by spectroscopic experiments.

Structural changes of phytochrome proteins. The resting state (Pr) appears in the darkness. After absorbing red light (600-700 nm) phytochromes transfers via several intermediate states to a so-called Pfr state.



Joining our group: If you got interested in research topics, just contact We have projects for post docs, PhD-students, as well as undergraduates.

Selected publications:

Photosensor research

H. Takala*, S. Niebling, O. Berntsson, A. Björling, H. Lehtivuori, H. Häkkänen, M. Panman, E. Gustavsson, M. Hoernke, G. Newby, F. Zontone, M. Wulff, A. Menzel, J.A. Ihalainen, and S. Westenhoff*: Light-induced Structural Changes in a Monomeric Bacteriophytochrome. Structural Dynamics 2016, In Press.

A. Björling, O. Berntsson, H. Lehtivuori, H. Takala, A. J. Hughes, M. Panman, M. Hoernke, S. Niebling, L. Henry, R. Henning, I. Kosheleva, V. Chukharev, N. V. Tkachenko, A. Menzel, G. Newby, D. Khakhulin, M. Wulff, J.A. Ihalainen*, S. Westenhoff*: Structural photoactivation of a full-length bacterial phytochrome. Science Advances 2, e1600920 (2016).

A. Björling, O. Berntsson, H. Takala, K.D. Gallagher, H. Patel, E. Gustavsson, R. St. Peter, P. Duong, A. Nugent, F. Zhang, P. Berntsen, R. Appio, I. Rajkovic, H. Lehtivuori, M. Hoernke, S. Niebling, R. Harimoorthy, T. Lamparter, E. A. Stojkovic, J.A. Ihalainen* and S. Westenhoff*: Ubiquitous structural signalling in bacterial phytochromes, J. Phys. Chem. Lett. 6, 3379-3383 (2015).

H. Takala, A. Björling, M. Linna, S. Westenhoff*, and J.A. Ihalainen*: Light-induced Changes in the Dimerization Interface of Bacteriophytochromes. J. Biol. Chem. 290, 16383 – 16392 (2015).

J.A. Ihalainen*, H. Takala, H. Lehtivuori: Fast photochemistry of canonical Bacteriophytochrome proteins – a species-specific comparison, Frontiers of Science 2, 75 (2015).(See Also)

H. Takala, A. Björling, O. Berntsson, H. Lehtivuori, S. Niebling, M. Hoernke, I. Kosheleva, R. Henning, A. Menzel, J.A. Ihalainen, and S. Westenhoff: Signal amplification and transduction in phytochrome photosensors, Nature 509, 245-249, (2014).

H. Lehtivuori, I. Rissanen, H. Takala, J. Bamford, N.V. Tkachenko, and J.A. Ihalainen: Excited state properties of chromophore-binding domain of bacteriophytochrome from Deinococcus radiodurans, J. Phys. Chem. B 117, 11049-11057 (2013).

S. Bhattacharya, M. E. Auldridge, H. Lehtivuori, J.A. Ihalainen, and K.T. Forest: Origins of Fluorescence in Evolved Bacteriophytochromes, J. Biol. Chem. 289, 32144-32152 (2014).

H. Takala, H. Lehtivuori, H. Hammaren, V.P. Hytönen, and J.A. Ihalainen: Connection between Absorption Properties and Conformational Changes in Deinococcus radiodurans Phytochrome, Biochemistry 53, 7076-7085 (2014)

Virus research

P. Ruokola, E. Dadu, A. Kazmertsuk, H. Häkkänen, V. Marjomäki, and J.A. Ihalainen: Raman spectroscopic signatures of echovirus 1 uncoating. J. Virol 88, 8504-8513 (2014).

A. Pawlowski*, A. Moilanen, I. Rissanen, J. Määttä, V. Hytönen, J.A. Ihalainen, and J. Bamford*: The minor capsid protein VP11 of thermophilic bacteriophage P23-77 facilitates virus assembly using lipid-protein interactions, J. Virol. 89, 7593-7603 (2015).


O. Jurček, P. Bonakdarzadeh, E. Kalenius, J.M. Linnanto, M. Groessl, R. Knochenmuss, J.A. Ihalainen, and K. Rissanen*: Superchiral Pd3L6 Coordination Barrel and Its Reversible Structural Conversion into Pd3L3Cl6 Metallocycle. Angewandte Chemie 54, 15462-15467 (2015).

M. Ojansivu*, S. Vanhatupa, L. Björkvik, H. Häkkänen, M. Kellomäki, R. Autio, J.A. Ihalainen, L. Hupa and S. Miettinen: Bioactive Glass Ions as Strong Enhancers of Osteogenic Differentiation in Human Adipose Stem Cells. Acta Biomaterialia 21, 190-203 (2015).

T.-R. Tero, K. Salorinne, H. Lehtivuori, J.A. Ihalainen, and M. Nissinen, “The structural diversity of benzofuran Resorcinarene leads to enhanced fluorescence”, Chemistry an Asian J. 9, 1860-1867 (2014).

S. Baieva, J.A. Ihalainen, J.J. Toppari, “Strong coupling between surface plasmon polaritons and β-carotene in nanolayered system”, J. Chem. Phys. 138, 044707 (2013).