Marko

Welcome to new lab members Emma, Gwen, Aleks and Miha!
Welcome to new members
Posted by Marko in News

Improved RAD51 binders through motif shuffling based on the modularity of BRC repeats

Laurens H. Lindenburg, Teodors Pantelejevs, Fabrice Gielen, Pedro Zuazua-Villar, Maren Butz, Eric Rees, Clemens F. Kaminski, Jessica A. Downs, Marko Hyvönen, and Florian Hollfelder

Proceedings of the National Academy of Sciences of the USA 118:e2017708118 (2021)
DOI: 10.1073/pnas.2017708118
Pubmed: 34772801
PDB coordinates: 6HQU (3D view)

Abstract

Exchanges of protein sequence modules support leaps in function unavailable through point mutations during evolution. Here we study the role of the two RAD51-interacting modules within the eight binding BRC repeats of BRCA2. We created 64 chimeric repeats by shuffling these modules and measured their binding to RAD51. We found that certain shuffled module combinations were stronger binders than any of the module combinations in the natural repeats. Surprisingly, the contribution from the two modules was poorly correlated with affinities of natural repeats, with a weak BRC8 repeat containing the most effective N-terminal module. Continue reading →

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The role of pro-domains in human growth factors and cytokines

Matthew Ratcliff, Richard Xu Zhou, Lutz Jermutus and Marko Hyvönen

Biochemical Society Transactions, BST20200663 (2021)
DOI: 10.1042/BST20200663
Pubmed: 34495310

Abstract

Many growth factors and cytokines are produced as larger precursors, containing prodomains, that require proteolytic processing to release the bioactive ligand. These prodomains can be significantly larger than the mature domains and can play an active role in the regulation of the ligands. Mining the UniProt database, we identified almost one hundred human growth factors and cytokines with pro-domains. These are spread across several unrelated protein families and vary in both their size and composition. Continue reading →

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Pathogenic ACVR1R206H activation by Activin A-induced receptor clustering and autophosphorylation

Anassuya Ramachandran, Merima Mehić, Laabiah Wasim, Dessislava Malinova, Ilaria Gori, Beata K Blaszczyk, Diana M Carvalho, Eileen M Shore, Chris Jones, Marko Hyvönen, Pavel Tolar, Caroline S Hill

EMBO Journal e106317 (2021)
DOI: 10.15252/embj.2020106317
Pubmed: 34003511

Abstract

Fibrodysplasia ossificans progressiva (FOP) and diffuse intrinsic pontine glioma (DIPG) are debilitating diseases that share causal mutations in ACVR1, a TGF-β family type I receptor. ACVR1R206H is a frequent mutation in both diseases. Pathogenic signaling via the SMAD1/5 pathway is mediated by Activin A, but how the mutation triggers aberrant signaling is not known. We show that ACVR1 is essential for Activin A-mediated SMAD1/5 phosphorylation and is activated by two distinct mechanisms. Wild-type ACVR1 is activated by the Activin type I receptors, ACVR1B/C. Continue reading →

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Downfalls of Chemical Probes Acting at the Kinase ATP-Site: CK2 as a Case Study

Eleanor L. Atkinson, Jessica Iegre, Paul D. Brear, Elizabeth A. Zhabina, Marko Hyvönen and David R. Spring

Molecules 26(7):1977(2021)
DOI: 10.3390/molecules26071977
Pubmed: 33807474

Abstract

Protein kinases are a large class of enzymes with numerous biological roles and many have been implicated in a vast array of diseases, including cancer and the novel coronavirus infection COVID-19. Thus, the development of chemical probes to selectively target each kinase is of great interest. Inhibition of protein kinases with ATP-competitive inhibitors has historically been the most widely used method. However, due to the highly conserved structures of ATP-sites, the identification of truly selective chemical probes is challenging. In this review, we use the Ser/Thr kinase CK2 as an example to highlight the historical challenges in effective and selective chemical probe development, alongside recent advances in the field and alternative strategies aiming to overcome these problems. Continue reading →

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Chemical probes targeting the kinase CK2: a journey outside the catalytic box

Jessica Iegre, Eleanor L. Atkinson, Paul D. Brear, Bethany M. Cooper, Marko Hyvönen and David R. Spring

Organic & Biomolecular Chemistry, in press, (2021)
DOI: 10.1039/D1OB00257K

Abstract

CK2 is a protein kinase that plays important roles in many physio-pathological cellular processes. As such, the development of chemical probes for CK2 has received increasing attention in the past decade with more than 40 lead compounds developed. In this review, we aim to provide the reader with a comprehensive overview of the chemical probes acting outside the highly-conserved ATP-site developed to date. Continue reading →

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A small-molecule inhibitor of the BRCA2-RAD51 interaction modulates RAD51 assembly and potentiates DNA damage-induced cell death

Duncan E. Scott, Nicola J. Francis-Newton, May E. Marsh, Anthony G. Coyne, Gerhard Fischer, Tommaso Moschetti, Andrew R. Bayly, Timothy D. Sharpe, Kalina T. Haas, Lorraine Barber, Chiara R. Valenzano, Rajavel Srinivasan, David J. Huggins, Miyoung Lee, Amy Emery, Bryn Hardwick, Matthias Ehebauer, Claudio Dagostin, Alessandro Esposito, Luca Pellegrini, Trevor Perrior, Grahame McKenzie, Tom L. Blundell, Marko Hyvönen, John Skidmore, Ashok R. Venkitaraman, Chris Abell

Cell Chemical Biology, Online now , (2021)
DOI: j.chembiol.2021.02.006
Pubmed: 33662256
PDB coordinates:
6TV3 (3D view), 6TWR (3D view), 6TW4 (3D view), 6XTW (3D view), 6TW9 (3D view)

Abstract

BRCA2 controls RAD51 recombinase during homologous DNA recombination (HDR) through eight evolutionarily conserved BRC repeats, which individually engage RAD51 via the motif Phe-x-x-Ala. Using structure-guided molecular design, templated on a monomeric thermostable chimera between human RAD51 and archaeal RadA, we identify CAM833, a 529 Da orthosteric inhibitor of RAD51:BRC with a Kd of 366 nM. The quinoline of CAM833 occupies a hotspot, the Phe-binding pocket on RAD51 and the methyl of the substituted α-methylbenzyl group occupies the Ala-binding pocket. Continue reading →

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Combined transcriptomic and phosphoproteomic analysis of BMP4 signaling in human embryonic stem cells

Angelos Papadopoulos, Varvara Chalmantzi, Olga Mikhaylichenko, Marko Hyvönen, Dimitris Stellas, Aditi Kanhere, John Heath, Debbie L Cunningham, Theodore Fotsis, Carol Murphy

Stem Cell Research 50:102133 (2021)
DOI: j.scr.2020.102133
Pubmed: 33383406

Abstract

Human embryonic stem cells (hESCs) are an invaluable tool in the fields of embryology and regenerative medicine. Activin A and BMP4 are well-characterised growth factors implicated in pluripotency and differentiation. In the current study, hESCs are cultured in a modified version of mTeSR1, where low concentrations of Activin A substitute for TGFβ. This culture system is further used to investigate the changes induced by BMP4 on hESCs by employing a combination of transcriptomic and phosphoproteomic approaches. Results indicate that in a pluripotent state, hESCs maintain WNT signaling under negative regulation by expressing pathway inhibitors. Continue reading →

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Proposed allosteric inhibitors bind to the ATP site of CK2α

Paul Brear, Darby Ball, Katherine Stott, Sheena D’Arcy and Marko Hyvönen

Journal of Medicinal Chemistry: 63, 21, 12786–12798 (2020)
DOI: 0.1021/acs.jmedchem.0c01173

PDB coordinates:
6YPH (3D view),6YPK (3D view),6YPJ (3D view),6YPN (3D view)


Abstract

CK2α is a ubiquitous, well-studied kinase that is a target for small-molecule inhibition, for treatment of cancers. While many different classes of ATP-competitive inhibitors have been described for CK2α, they tend to suffer from significant off-target activity and new approaches are needed. A series of inhibitors of CK2α has recently been described as allosteric, acting at a previously unidentified binding site. Given the similarity of these inhibitors to known ATP-competitive inhibitors, we have investigated these further. In our thorough structural and biophysical analyses, we have found no evidence that these inhibitors bind to the proposed allosteric site. Continue reading →

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Human BDNF/TrkB Variants Impair Hippocampal Synaptogenesis and Associate With Neurobehavioural Abnormalities

Takuhiro Sonoyama, Lukas K J Stadler, Mingyan Zhu, Julia M Keogh, Elana Henning, Fuki Hisama, Peter Kirwan, Magdalena Jura, Beata K Blaszczyk, David C DeWitt, Bas Brouwers, Marko Hyvönen, Inês Barroso, Florian T Merkle, Suzanne M Appleyard, Gary A Wayman, I Sadaf Farooqi

Scientific Reports, 2020 Jun 3;10(1):9028.
DOI: 10.1038/s41598-020-65531-x
Pubmed: 32493978

Abstract

Brain-derived neurotrophic factor (BDNF) signals through its high affinity receptor Tropomyosin receptor kinase-B (TrkB) to regulate neuronal development, synapse formation and plasticity. In rodents, genetic disruption of Bdnf and TrkB leads to weight gain and a spectrum of neurobehavioural phenotypes. Here, we functionally characterised a de novo missense variant in BDNF and seven rare variants in TrkB identified in a large cohort of people with severe, childhood-onset obesity. Continue reading →

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