Recent results

Scientific articles (co)authored by our group members are summarized briefly here. Please also find links to the original articles below.

Talin variant P229S compromises integrin activation

We studied a de novo heterozygous c.685C>T (p.Pro229Ser) variant in the TLN1 gene from a patient with a complex phenotype. The mutation, identified by Prof. Joseph Church (Children’s Hospital Los Angeles), is located in the talin head region at the interface between the F2 and F3 domains. Our lab studied the characteristics of the mutated talin in talin-knockout cells and using computational modelling, and Prof. Ben Goult lab (University of Kent) examined the influence of the mutation on biochemical characteristics of talin head. We found that p.P229S talin variant influences adhesion dynamics that result from disturbance of the F2-F3 domain interface in the talin head. This causes defects in integrin activation, adhesion and cell migration.

Talin variant P229S compromises integrin activation and associates with multifaceted clinical symptoms

Latifeh Azizi, Lorena Varela, Paula Turkk, Vasyl V Mykuliak, Sanna Korpela, Teemu O Ihalainen, Joseph Church, Vesa P Hytönen, Benjamin T Goult

Human Molecular Genetics 2022, ddac163

https://doi.org/10.1093/hmg/ddac163

Functionalization of the phosphate-based bioactive glass enhanced cell compatibility

In this article, by a unique and simple basic buffer treatment of the phosphate-base bioactive glass followed by the silanization step, we were able to improve protein grafting on the glass surface. This treatment also allowed efficient early cell adhesion, and the formation of cell-material adhesion structures of mouse fibroblasts on the surface to a similar extent as with materials commonly used in cell culture.

Surface Modification of Bioactive Glass Promotes Cell Attachment and Spreading

Latifeh Azizi, Paula Turkki, Ngoc Huynh, Jonathan M. Massera, and Vesa P. Hytönen

ACS Omega 2021, 6, 35, 22635–22642

https://doi.org/10.1021/acsomega.1c02669

Antigenicity and immunogenicity of HA2 and M2e influenza virus antigens conjugated to norovirus-like, VP1 capsid-based particles by the SpyTag/SpyCatcher technology

We recently developed two influenza vaccine candidates based on a novel norovirus-like particle (noro-VLP) vaccine platform. This study examined the immunological properties of the produced influenza vaccines further. We found that decorating the noro-VLP had no effect on the vaccine-induced immune response against the corresponding norovirus, which demonstrates that the decorated noro-VLPs can still function as a norovirus vaccine. Although a high antibody response was induced by influenza HA2-decorated VLPs, the HA2-directed antibodies did not neutralize influenza virus in vitro.

Suvi Heinimäki, Vili Lampinen, Kirsi Tamminen, Minna M. Hankaniemi, Maria Malm, Vesa P. Hytönen, Vesna Blazevic

Virology 2022, 566:89-97

doi: 10.1016/j.virol.2021.12.001

https://www.sciencedirect.com/science/article/pii/S0042682221002415

Avidin-conjugated nanofibrillar cellulose hydrogel for 3D cell culturing

Avidin-conjugated nanofibrillar cellulose enables the attachment of biotinylated molecules on nanocellulose fibers. Fibroblasts were found to proliferate quicker in the hydrogel functionalized with biotinylated proteins originating from extracellular matrix compared to bare nanocellulose, and the cell viability remained high during the experiment. The cells also showed signs of efficient integrin signaling indicating that they have the capacity to attach tightly to functionalized nanocellulose. Avidin-conjugated nanocellulose offers promising possibilities for applications requiring tailored hydrogels, such as cell differentiation and tissue engineering.

Schematic presentation showing how avidin-conjugated nanocellulose fibers enable functionalization with biotinylated molecules, providing good environment for adherent cells. Reprinted with permission from Leppiniemi et al. Biomacromolecules https://doi.org/10.1021/acs.biomac.1c00579, Copyright 2021 American Chemical Society.

Avidin-Conjugated Nanofibrillar Cellulose Hydrogel Functionalized with Biotinylated Fibronectin and Vitronectin Promotes 3D Culture of Fibroblasts

Jenni Leppiniemi, Zeeshan Mutahir, Alexander Dulebo, Piia Mikkonen, Markus Nuopponen, Paula Turkki, and Vesa P. Hytönen

Biomacromolecules 2021, https://doi.org/10.1021/acs.biomac.1c00579

News in English: https://www.tuni.fi/en/news/nanocellulose-decorated-proteins-suitable-3d-cell-culturing

News in Finnish: https://www.tuni.fi/fi/ajankohtaista/proteiineilla-paallystetty-nanoselluloosa-sopii-solujen-3d-viljelyyn

Bacteriophytochromes DrBphP and Agp1 have opposite signaling functionalities

Phytochromes are photoreceptors, which transmit environmental stimuli to a response regulator through a histidine kinase domain. Phytochromes switch between red light-absorbing and far-red light-absorbing states. As a member of international team led by Dr. Heikki Takala, we analyzed the interactions of bacteriophytochromes from Deinococcus radiodurans (DrBphP) and Agrobacterium fabrum (Agp1). While these proteins share structural similarity, Agp1 acts as a conventional histidine kinase, but DrBphP functions as a light-sensitive phosphatase. Moreover, Agp1 was found to bind its cognate response regulator only transiently, while DrBphP showed tighter binding, which is rationalized at the structural level. Two key residues were identified affecting the balance between kinase and phosphatase activities. Light-controllable histidine kinases and phosphatases may open possibilities for applications in biotechnology.

Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling

Multamäki et al.

Nature Communications 2021, 12, 4394

https://www.nature.com/articles/s41467-021-24676-7

Insight into bacterial avidins

We catalogued avidin encoding genes among bacteria classified potential avidins according to taxonomy and the ecological niches utilized by host bacteria. The diversity of putative avidin sequences was high. The living strategies of bacteria hosting avidin encoding genes fall mainly into two categories: 1) human and animal pathogens 2) bacteria that either fix nitrogen or live in root nodules/rhizospheres of plants hosting nitrogen-fixing bacteria. Avidin encoding genes in plasmids hint that avidins may be horizontally transferred. The survey may be used as a basis in attempts to understand the ecological significance of biotin-binding capacity.

Bacterial avidins are a widely distributed protein family in Actinobacteria, Proteobacteria and Bacteroidetes

Olli H. Laitinen, Tanja P. Kuusela, Sampo Kukkurainen, Anssi Nurminen, Aki Sinkkonen, Vesa P. Hytönen

BMC Ecology and Evolution 2021; 21, 53
https://doi.org/10.1186/s12862-021-01784-y

Paxillin LIM domains are important for cell adhesion

Paxillin recruitment to β3 integrins and LIM domain-specific functions were assessed using a wide array of methods. Our findings suggest that LIM1, LIM2 and LIM3 are mostly responsible for focal adhesion interactions. Especially LIM2 was found to have the major role in docking paxillin to FAs. Using biosensor analysis, we found that both LIM1 deletion (LIM 234) and LIM2 (LIM 1334) replacement by LIM3 deprived talin head binding while LIM3 replacement by LIM2 (LIM 1224) potentially increased the interaction. Furthermore, we found that LIM4 has a unique feature with high positive charge and it represents a potential membrane binding domain.

Structural and functional analysis of LIM domain-dependent recruitment of paxillin to αvβ3 integrin-positive focal adhesions

Marta Ripamonti , Nicolas Liaudet, Latifeh Azizi, Daniel Bouvard, Vesa P Hytönen, Bernhard Wehrle-Haller
Commun. Biol. 2021; 4(1):380.
doi: 10.1038/s42003-021-01886-9

News in English:
https://www.eurekalert.org/pub_releases/2021-03/udg-cro032621.php

News in Finnish:
https://www.tuni.fi/fi/ajankohtaista/solujen-tartuntaelimet-estavat-niiden-liukumisen

Vaccine platform based on Norovirus-like particles

We developed a novel molecular platform that allows convenient protein presentation on the norovirus-like particle with the help of the recently developed SpyCatcher/SpyTag conjugation technology. The norovirus-like particles were decorated with two conserved influenza antigens and the conjugated particles were tested as vaccines in mice. Large proteins presented on the surface of the norovirus-like particle proved immunogenic, and most notably, we obtained high titers of antibodies against the conserved stem of influenza hemagglutinin without adjuvants.

Modular vaccine platform based on the norovirus-like particle

Vili Lampinen, Suvi Heinimäki, Olli H. Laitinen, Marko Pesu, Minna M. Hankaniemi*, Vesna Blazevic* & Vesa P. Hytönen*

Journal of Nanobiotechnology 2021, 19:25

doi: 10.1186/s12951-021-00772-0

https://rdcu.be/cdSyu

Cancer-associated talin mutations

Analysis of talin-1 point mutations screened from COSMIC database revealed potential contribution of talin for cancer progression. We explored the impact of mutations on protein characteristics, cell migration, invasion and proliferation. Mutation I392N in the F3 subdomain destabilized the F3 fold and increased the migration rate and invasiveness of the cells. Notably, cells expressing talin with a point mutation L2509P in the dimerization domain showed drastic interference in cellular functions.

Cancer associated talin point mutations disorganise cell adhesion and migration

Latifeh Azizi, Alana R. Cowell, Vasyl V. Mykuliak, Benjamin T. Goult, Paula Turkki & Vesa P. Hytönen

Scientific Reports 2021 11, 347

doi: 10.1038/s41598-020-77911-4

https://www.tuni.fi/en/news/structural-biology-and-computational-biology-open-opportunities-understand-molecular

Talin F1-loop contributes for integrin activation and clustering

Cells use integrin proteins on their surfaces to adhere. Talin, an intracellular protein, activates and clusters integrins and links them to the cytoskeleton. We utilized computational structural biology, biophysical characterization and cell biology methods to study the mechanisms of talin-integrin interaction. Previous research had showed that a flexible loop in the talin head binds to cell membrane lipids at adhesion sites. We showed here that the loop not only anchors talin to the cell membrane, but also interacts directly with integrin, and it may thereby facilitate integrin activation and clustering.

The F1 loop of the talin head domain acts as a gatekeeper in integrin activation and clustering

Sampo Kukkurainen, Latifeh Azizi, Pingfeng Zhang, Marie-Claude Jacquier, Mo Baikoghli, Magdaléna von Essen, Anne Tuukkanen, Mikko Laitaoja, Xiaonan Liu, Rolle Rahikainen, Adam Orłowski, Janne Jänis, Juha A. E. Määttä, Markku Varjosalo, Ilpo Vattulainen, Tomasz Róg, Dmitri Svergun, R. Holland Cheng, Jinhua Wu, Vesa P. Hytönen, Bernhard Wehrle-Haller

Journal of Cell Science 2020 133: jcs239202
doi: 10.1242/jcs.239202

JCS239202 (pdf) – Notes: Journal of Cell Science – Open Access (rights and permissions)

First person – Sampo Kukkurainen

Journal of Cell Science 2020 133: jcs254615
doi: 10.1242/jcs.254615

A hexavalent vaccine against Coxsackie B group enteroviruses

We produced a novel hexavalent vaccine targeting the Coxsackie B group enteroviruses (CVB1-6). This study documents the excellent immunogenicity of a traditional formalin-inactivated CVB1-6 vaccine in several mouse strains and a nonhuman primate model. We also report that this vaccine has the ability, in relevant preclinical models, to protect against acute CVB infections, block CVB infection of the heart, and prevent CVB-induced pancreatitis and diabetes. The vaccine we describe here provides a viable option for tackling CVB infections and associated diseases.

A hexavalent Coxsackievirus B vaccine is highly immunogenic and has a strong protective capacity in mice and nonhuman primates

V. M. Stone*, M. M. Hankaniemi*, O. H. Laitinen, A. B. Sioofy-Khojine, A. Lin, I. Diaz Lozano, M. A. Mazur, V. Marjomäki, K. Loré, H. Hyöty, V. P. Hytönen*, M. Flodström-Tullberg*
* These authors contributed equally to this work
Science Advances 6, eaaz2433
doi: 10.1126/sciadv.aaz2433
https://advances.sciencemag.org/content/6/19/eaaz2433

Review article: Rapid Diagnostics of Antimicrobial Resistance

We describe the currently available technologies for antibiotic resistance detection, introduce several future technologies, and evaluate how well the technologies serve the needs in healthcare.

Antti Vasala, Vesa P. Hytönen and Olli H. Laitinen
Modern Tools for Rapid Diagnostics of Antimicrobial Resistance

Front. Cell. Infect. Microbiol. 10: 308
https://doi.org/10.3389/fcimb.2020.00308
https://www.frontiersin.org/articles/10.3389/fcimb.2020.00308/full

Mechanoregulation on integrin interactions

The cell-adhesion molecule integrin αVβ3 has many potential binding partners. How αVβ3 integrin chooses between these possible binding partners was so far not analysed. This study demonstrated that mechanical force on the integrin switches between conformations of the integrins. At the same time, these conformations have different binding abilities. Thus, mechanical pulling by cells is a possibility for αVβ3 integrin to choose between different ligands.

Induction of ligand promiscuity of αVβ3 integrin by mechanical force

Bachmann M, Schäfer M, Mykuliak VV, Ripamonti M, Heiser L, Weißenbruch K, Krübel S, Franz CM, Hytönen VP, Wehrle-Haller B, Bastmeyer M.

Multiplexed assay for enteroviruses

We produced a panel of antigens from representatives of all human infecting enterovirus and rhinovirus species. We then set up a multiplexed serological immunoassay using the antigens and tested it with sera from 88 children and 42 adults. We found that adults have stronger responses for enteroviruses and rhinoviruses, but that children have more specific ones.

Multiplexed High-Throughput Serological Assay for Human Enteroviruses

Saarinen NVV, Lehtonen J, Veijola R, Lempainen J, Knip M, Hyöty H, Laitinen OH and Hytönen VP
Microorganisms 8(6), 963
https://doi.org/10.3390/microorganisms8060963

Syndecan-4 is an important mechanotransducer

A mechanism whereby syndecan–4 tunes cell mechanics in response to localized tension was revealed by using experimental and computational methods. Syndecan–4 changes conformation under force, tilting the cytoplasmic domain towards membrane. The results suggest that syndecan–4 is a key cellular mechanotransducer that regulates cell mechanics.

Chronopoulos et al.
Syndecan-4 tunes cell mechanics by activating the kindlin-integrin-RhoA pathway

Nature Materials, 2020
https://doi.org/10.1038/s41563-019-0567-1
https://www.imperial.ac.uk/news/194586/cell-hands-unlock-doors-health-research/
https://www.tuni.fi/fi/ajankohtaista/solukalvon-proteiinit-tekevat-yhteistyota-mekaanisten-viestien-valittamisessa
https://www.youtube.com/watch?v=XPVdx7_V-nU

A promising vaccine candidate against the most common enteric viruses

Enteroviruses are the most common human viruses, causing severe childhood infections, both acute and chronic diseases and major impact on the public health. Norovirus causes diarrhoea-vomiting at all age groups and rotavirus is the most common cause of this disease in children. To prevent many common enteric childhood infections with the same vaccine, we produced a trivalent virus-like particle (VLP) vaccine. VLPs are safe and economical options for traditional vaccines and by combining several VLPs in same vaccine the number of required injections can be reduced. A cocktail of VLPs corresponding to entero-, noro- and rotaviruses was highly immunogenic in mice and induced protective immune responses. The developed combination vaccine is a promising candidate for human clinical trials.

Heinimäki et al.
Combination of three virus-derived nanoparticles as a vaccine against enteric pathogens; enterovirus, norovirus and rotavirus

Vaccine. 2019, 37:7509-7518.
https://doi.org/10.1016/j.vaccine.2019.09.072

Antibodies against virus proteases as markers for an acute infection

Diagnosing acute enterovirus infections from single patient samples can be difficult. Viral RNA is detectable for only a few days using qPCR and antibody responses against structural proteins are very long-lived making it easy to confuse old infections for on-going ones. In this study we show that the antibody response against enteroviral proteases is more short-lived and thus a potential marker for an acute infection.

Antibody responses against enterovirus proteases are potential markers for an acute infection

Saarinen NVV, Stone VM, Hankaniemi MM, Mazur MA, Vuorinen T, Flodström-Tullberg M, Hyöty H, Hytönen VP, Laitinen OH
Viruses. 2020 12:E78.
https://www.mdpi.com/1999-4915/12/1/78

Novel insights into norovirus interaction with cellular receptors

Multivalent interactions between norovirus-like particle and its cellular receptors were studied using quartz crystal microbalance with dissipation monitoring. Norovirus-like particle was found to harvest its receptors into the attachment site from the surrounding membrane, enhancing avidity and thus enabling tight interaction with the membrane.

Nagma Parveen, Gustaf E. Rydell, Göran Larson, Vesa P. Hytönen, Vladimir P. Zhdanov, Fredrik Höök, Stephan Block
Competition for Membrane Receptors: Norovirus Detachment via Lectin Attachment

J Am Chem Soc. 2019, 141:16303-16311.
https://pubs.acs.org/doi/10.1021/jacs.9b06036

Genetically encoded protein superglue

A genetically encoded peptide that reacts with its genetically encoded protein partner with a speed close to the limit set by diffusion was described here. Extensive biophysical characterization revealed molecular details behind the enhanced functionality. The developed peptide–protein pair enabled reconstitution of split talin protein, restoring cell adhesion and migration.

Anthony H. Keeble, Paula Turkki, Samuel Stokes, Irsyad N. A. Khairil Anuar, Rolle Rahikainen, Vesa P. Hytönen, Mark Howarth
Approaching infinite affinity through engineering of peptide-protein interaction

PNAS 2019, 116:26523-26533.
https://www.pnas.org/content/116/52/26523
https://www.tuni.fi/en/news/researchers-develop-intracellular-molecular-super-glue

Berry pigment may enhance talin-integrin interaction

Cyanidin-3-glucoside (C3G) is a natural pigment, found in many colorful fruits and vegetables. It has known health benefits, including anti-inflammation, cancer prevention, and anti-diabetes. Here, we showed that C3G binds talin and supports the interaction of talin with β1A-integrin. Molecular docking analysis suggests that C3G binds to the interface of the talin-integrin complex.

Zbigniew Baster, Liqing Li, Sampo Kukkurainen, Olli Pentikäinen, Balázs Győrffy, Vesa P. Hytönen, Zenon Rajfur, Cai Huang
Cyanidin 3-Glucoside binds to talin and modulates colon cancer cell adhesions and 3D growth

FASEB J. 2020.
https://onlinelibrary.wiley.com/doi/full/10.1096/fj.201900945R

Formalin treatment is advantageous for coxsackievirus VLP

The six coxsackievirus B serotypes (CVB1-6) are common human pathogens. Particularly CVB1 causes serious infections in neonates. However, there are no vaccines or treatments available against CVBs. Virus-like particles (VLPs) lack the virus genome and are therefore safer to manufacture and administer than the traditional inactivated whole-virus vaccines. This study demonstrates that formalin treatment is advantageous for CVB1-VLP vaccine and may offer a universal tool for the stabilisation of VLPs in the production of more efficient vaccines.

Hankaniemi et al.
Formalin treatment increases the stability and immunogenicity of coxsackievirus B1 VLP vaccine

Antiviral Res.
https://doi.org/10.1016/j.antiviral.2019.104595

Review article: Cell Adhesion by Integrins

In this review, we provide some historical, structural, and physiological notes so that the diverse functions of integrin receptors can be appreciated and put into the context of the emerging field of mechanobiology.

Michael Bachmann, Sampo Kukkurainen, Vesa P. Hytönen and Bernhard Wehrle-Haller
Cell Adhesion by Integrins

Physiological Reviews 2019, 99:1655-1699
https://doi.org/10.1152/physrev.00036.2018

Intelectin 3 is dispensable for resistance against a mycobacterial infection in zebrafish (Danio rerio)

Tuberculosis is an epidemic infectious disease that is difficult to cure with the current antibiotic treatments. Since genetic background affects our susceptibility to tuberculosis, studying the impact of individual genes in a genetically tractable model organism can unravel novel possibilities in treating the disease. We used the zebrafish (Danio rerio) tuberculosis model, and identified intelectin 3 (itln3) among the most up-regulated genes associated with mycobacterial infection. In order to understand the role of itln3 in the mycobacterial immune response, we created itln3 knockout zebrafish and studied the survival and mycobacterial burden in both the mutant and wild type fish upon infection. The lack of itln3 did not affect the outcome of M. marinum infection in either the larvae or adult fish. Nevertheless, this study describes new possibilities for studying the zebrafish innate immune response and provides invaluable data about the genetic influence in mycobacterial infection.

Ojanen et al.
Intelectin 3 is dispensable for resistance against a mycobacterial infection in zebrafish (Danio rerio)

Scientific Reports 2019, Jan 30;9(1):995.
https://www.nature.com/articles/s41598-018-37678-1

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.2005599Editor’s pick: https://collections.plos.org/collection/cell-biology-picks/

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.
Press release: In English – Suomeksi

Tapio et al.
DNA-nanoparticle actuator enabling optical monitoring of nanoscale movements induced by electric field

Nanoscale 2018, 10:19297-19309
http://dx.doi.org/10.1039/C8NR05535A

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.

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.

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

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 (PDF)

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