Mechanobiology
Protein conformation can be modulated in response to chemical and physical stimulus arising from interactions with other molecules and as result of chemical modifications. The Protein Dynamics group uses state of the art experimental and computational methods to elucidate the relations between protein conformation and function. One of the focus points of our studies involves the structural dynamics of the proteins in cellular adhesion sites. In particular, we aim for a more complete understanding of the mechanisms behind cellular mechanosensing. The tools and techniques used in our studies involve cellular models, tailored hydrogel substrates for cell adhesion studies, protein engineering and molecular dynamics simulations. Collaborations with the University of Geneva and the Imperial College of London are essential for the project.

Vaccine development
Enteroviruses are responsible for symptoms ranging from mild respiratory illnesses, such as common cold, to more severe conditions, such as neonatal sepsis-like disease and acute flaccid paralysis. In the genus of Enteroviruses, vaccines are currently available only against the poliovirus. We are developing novel diagnostic tools and vaccines against enteroviruses, with a focus on virus forms associated with type 1 diabetes. Our project is conducted in close collaboration with the Karolinska Institutet.

Methodology
We utilize a broad set of biophysical characterization methods, including calorimetry, biosensors and spectroscopic methods. Recombinant proteins and protein engineering are used routinely in our research and our gained expertise is geared towards the development of novel biofunctionalized materials, including nanocellulose and bioactive glass.

Our group is active within Biocenter Finland infrastructure network (About research infrastructure / Biocenter Finland).

Researchgate (laboratory): Hytonens-lab
Researchgate (profile): Vesa_Hytönen

Recent results

Restricted unfolding of talin rod subdomain modulates cellular mechanosignaling

The force-regulated unfolding of protein domains in the adhesion protein talin has proved to be a critical regulator of cell adhesion structure and function. In collaboration with the research group of professor Armando del Rio at the Imperial College, London, we investigated the role of the force-regulated unfolding of talin R8 subdomain in the regulation of tumor-suppressor protein DLC1. By restricting the unfolding of the R8 subdomain, we were able to demonstrate that the unfolding of talin regulates the mobility of DLC1 in cell adhesions, which is reflected to the activity of RhoA and cell contractility. The results of this study demonstrate the presence of a novel mechanically regulated signaling switch in cells and shed light on the mechanisms acting in talin-mediated cellular mechanosensing.

Haining et al. Mechanotransduction in talin through the interaction of the R8 domain with DLC1. PLOS Biology 2018, 16, e2005599 https://doi.org/10.1371/journal.pbio.2005599

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Stable 3-helix intermediates in talin and α-catenin

Talin and α-catenin are two key mechanoregulated molecules in focal adhesions and adherens junctions, respectively. Using atomistic steered molecular dynamics simulations we show that talin rod α-helix bundles as well as α-catenin α-helix domains unfold through stable 3-helix intermediates. Single-molecule atomic force microscopy experiments were carried out, and they are in agreement with the findings of the computational simulations. As a result, multiple discrete unfolding intermediate states in the talin and α-catenin unfolding pathway were discovered.

Mykuliak et al.
Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin.
PLOS Computational Biology, 2018
https://doi.org/10.1371/journal.pcbi.1006126

 

Optical monitoring of DNA conformation controlled by electric field

In collaboration with University of Jyväskylä, we have devised a nanoactuator system, where gold nanoparticle tethered on a conducting surface is moved reversibly using electric field, while monitoring its position optically via changes of its plasmon resonance (particle color). Forces induced by the nanoparticle can be therefore used to change and study the conformation of the DNA. This method could be suitable for manipulation of other molecules, such as proteins.

Tapio et al.
DNA-nanoparticle actuator enabling optical monitoring of nanoscale movements induced by electric field
Nanoscale, in press.
http://dx.doi.org/10.1039/C8NR05535A

Press release: In EnglishSuomeksi

Antibodies for detection of enteroviral proteases

Enteroviruses are common human pathogens, which cause severe diseases including meningitis, myocarditis and neonatal sepsis. Enteroviruses encode two proteases (2Apro and 3Cpro), which perform the proteolytic cleavage of the enterovirus polyprotein but also cleave host cell proteins to facilitate viral replication. For example, the 2Apro cause direct damage to the infected heart and therefore tools to investigate 2Apro and 3Cpro expression may contribute new knowledge on virus-induced pathologies. We developed new antibodies to enterovirus-encoded proteases that were able to detect a wide spectrum of enterovirus species B viruses in multiple applications of infected cell and animal tissue samples.

Laitinen et al.
New Coxsackievirus 2Apro and 3Cpro protease antibodies for virus detection and discovery of pathogenic mechanisms
J Virol Methods. 2018, 255:29-37.
https://www.sciencedirect.com/science/article/pii/S0166093417307164

Coxsackievirus vaccine protects against virus-induced diabetes

Epidemiological studies suggest a role for Coxsackievirus B (CVB) serotypes in the pathogenesis of type 1 diabetes, but their actual contribution remains elusive. We produced a CVB1 vaccine to test whether vaccination against CVBs can prevent virus-induced diabetes in an experimental mouse model. CVB1 vaccine protected efficiently against both CVB1 infection and CVB1-induced diabetes. This preclinical proof of concept study provided a base for further studies aimed at developing a vaccine to be used in elucidating the role of enteroviruses in human type 1 diabetes and other CVB associated diseases.

Stone et al.
A Coxsackievirus B vaccine protects against virus-induced diabetes in an experimental mouse model of type 1 diabetes
Diabetologia 2018, 61, 476-481

https://link.springer.com/article/10.1007/s00125-017-4492-z

StructureMapper algorithm

The StructureMapper algorithm provides automated, high-throughput mapping of primary sequence amino acids to existing three-dimensional protein structures in the PDB database. The StuctureMapper analyzes the properties of the identified structural locations (e.g. surface accessibility) and can construct any defined biological assemblies for proteins to identify amino acids located at protein-protein interfaces (PPIs). In our study, we have used the StructureMapper to profile the structural locations of 354 781 post-translational modifications sites and to discover novel, potential phosphoswitches.

Nurminen et al.
StructureMapper: a high-throughput algorithm for analyzing protein sequence locations in structural data
Bioinformatics, 2018

https://doi.org/10.1093/bioinformatics/bty086

Note: This article is available under theCreative Commons CC-BY-NC https://creativecommons.org/licenses/license and permits non-commercial use, distribution and reproduction in any medium, provided the original work is properly cited.

New monoclonal enterovirus antibody

Enteroviruses are a group of RNA viruses that frequently infect humans, with symptoms varying from a mild rash to paralytic poliomyelitis. While enteroviruses are common, there are only a handful of reliable methods for their detection and identification. In this study, we describe a new monoclonal antibody, 3A6, which detects a broad range of enteroviruses and works in multiple applications.

Saarinen et al.
A novel rat CVB1-VP1 monoclonal antibody 3A6 detects a broad range of enteroviruses.
Sci. Rep. 2018, 8(1):33

https://www.nature.com/articles/s41598-017-18495-4

Protein interplay in atherosclerosis

Increased expression of histone deacetylase 9 (HDAC9) and matrix metalloprotease 12 (MMP12) in carotid artery wall has been linked to the development of atherosclerosis and adverse clinical outcome of its treatment. Here, we utilized genome-wide expression analysis to study the association of MMP12 and HDAC9 expression in atherosclerotic plaques with plaque stability and with macrophage and smooth muscle cell markers. We found an association of HDAC9 and MMP12 expression in carotid artery plaques and identified M4 macrophages as a possible source of the increased MMP12 and HDAC9 expression in these plaques. Immunohistochemistry of tissue sections from artery plaques and healthy arteries confirmed colocalization of HDAC9 and MMP12 signals with each other and with the macrophage markers. These results suggest that M4 macrophages may play an important role in the development and progression of atherosclerotic plaques in arteries.

Oksala et al.
Synergistic Expression of Histone Deacetylase 9 and Matrix Metalloproteinase 12 in M4 Macrophages in Advanced Carotid Plaques.
Eur. J. Vasc. Endovasc. Surg. 2017, 53(5), 632-640

http://www.sciencedirect.com/science/article/pii/S1078588417301259

Talin stability influences cellular functions

Force-controlled unfolding of a central cell-matrix adhesion protein called talin has been suggested to act as a cellular mechanosensor, but so far the effects of talin destabilization have not been studied. In this study, we designed a panel of point mutations destabilizing a mechanosensitive subdomain in talin rod and analyzed the phenotypes induced by them in cultured fibroblast cells. Talin destabilization was found to affect adhesion protein dynamics, cell migration rate and ECM substrate sensing. These results provide evidence into how the controlled talin rod domain unfolding acts as a key regulator of adhesion structure and function in adherent animal cells.

Rahikainen et al.
Mechanical stability of talin rod controls cell migration and substrate sensing.
Scientific Reports 2017, 7, 3571

https://www.nature.com/articles/s41598-017-03335-2.epdf

Novel coxsackievirus vaccine

Vaccination would be powerful tool to prevent CVB associated diseases. We developed an efficient vaccine production protocol for CVB vaccines by optimizing virus production, purification and formulation steps. Administration of formalin-inactivated CVB1 induced a strong, virus-neutralizing antibody response in vaccinated mice, and protected mice against CVB1 infection. Altogether, these results provide valuable information for the development of new enterovirus vaccines for human use.

Hankaniemi et al.
Optimized production and purification of Coxsackievirus B1 vaccine and its preclinical evaluation in a mouse model Vaccine. 2017

Free access to full article: https://authors.elsevier.com/a/1VBag,60n7SQ~j

Article: www.sciencedirect.com

Stretching of talin rod

Using single-molecule atomic force microscopy (smAFM), we show that the entire talin rod can be unfolded by mechanical extension, over a physiological range of forces between 10 and 40 pN. We also demonstrate, through a combination of smAFM and steered molecular dynamics, that the different bundles within the talin rod exhibit a distinct hierarchy of mechanical stability. These results provide a mechanism by which different force conditions within the cell control a graduated unfolding of the talin rod. Mechanical unfolding of the rod subdomains, and the subsequent effect on talin’s binding interactions, would allow for a finely tuned cellular response to internally or externally applied forces.

Haining et al.

All Subdomains of the Talin Rod Are Mechanically Vulnerable and May Contribute To Cellular Mechanosensing.

ACS Nano. 2016, 10(7), 6648-58.
http://pubs.acs.org/doi/abs/10.1021/acsnano.6b01658

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