Marko

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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Secreted BMP Antagonists and Their Role in Cancer and Bone Metastases

Grace M Todd, Zhichun Gao, Marko Hyvönen, Derek P Brazil, Peter Ten Dijke

Bone 137:115455 (2020)
DOI: 10.1016/j.bone.2020.115455
Pubmed: 32473315

Abstract

Bone morphogenetic proteins (BMPs) are multifunctional secreted cytokines that act in a highly context-dependent manner. BMP action extends beyond the induction of cartilage and bone formation, to encompass pivotal roles in controlling tissue and organ homeostasis during development and adulthood. BMPs signal via plasma membrane type I and type II serine/threonine kinase receptors and intracellular SMAD transcriptional effectors. Exquisite temporospatial control of BMP/SMAD signalling and crosstalk with other cellular cues is achieved by a series of positive and negative regulators at each step in the BMP/SMAD pathway. Continue reading →

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Demonstration of the utility of DOS-derived fragment libraries for rapid hit derivatisation in a multidirectional fashion

Sarah L. Kidd, Elaine Fowler, Till Reinhardt, Thomas Compton, Natalia Mateu, Hector Newman, Dom Bellini, Romain Talon, Joseph McLoughlin, Tobias Krojer, Anthony Aimon, Anthony Bradley, Michael Fairhead, Paul Brear, Laura Díaz-Sáez, Katherine McAuley, Hannah F. Sore, Andrew Madin, Daniel H. O’Donovan, Kilian V. M. Huber, Marko Hyvönen, Frank von Delft, Christopher G. Dowson and David R. Spring

Chemical Science 11, 10792-10801 (2020)
DOI: 10.1039/D0SC01232G

PDB coordinates: 6Y6O (3D view),6Y6N (3D view)

Abstract

Organic synthesis underpins the evolution of weak fragment hits into potent lead compounds. Deficiencies within current screening collections often result in the requirement of significant synthetic investment to enable multidirectional fragment growth, limiting the efficiency of the hit evolution process. Diversity-oriented synthesis (DOS)-derived fragment libraries are constructed in an efficient and modular fashion and thus are well-suited to address this challenge. To demonstrate the effective nature of such libraries within fragment-based drug discovery, we herein describe the screening of a 40-member DOS library against three functionally distinct biological targets using X-Ray crystallography. Continue reading →

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Diarylethene Moiety as an Enthalpy-Entropy Switch: Photoisomerizable Stapled Peptides for Modulating p53/MDM2 Interaction

Alexander V Strizhak, Oleg Babii, Sergii Afonin, Iuliia Bakanovic, Teodors Pantelejevs, Wenshu Xu, Elaine Fowler, Rohan Eapen, Krishna Sharma, Maxim O Platonov, Vasyl V Hurmach, Laura Itzhaki, Marko Hyvönen, Anne S Ulrich, David R Spring, Igor V Komarov

Organic and Biomolecular Chemistry, 2020 May 11, Advance article in press
DOI: 10.1039/d0ob00831a
Pubmed: 32390036

PDB coordinates: 6y4q (3D view)

Abstract

Analogs of the known inhibitor (peptide pDI) of the p53/MDM2 protein-protein interaction are reported, which are stapled by linkers bearing a photoisomerizable diarylethene moiety. The corresponding photoisomers possess significantly different affinities to the p53-interacting domain of the human MDM2. Apparent dissociation constants are in the picomolar-to-low nanomolar range for those isomers with diarylethene in the “open” configuration, but up to eight times larger for the corresponding “closed” isomers. Spectroscopic, structural, and computational studies showed that the stapling linkers of the peptides contribute to their binding. Continue reading →

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Genomic Structure and Transcript Analysis of the Rapid Alkalinization Factor (RALF) Gene Family During Host-Pathogen Crosstalk in Fragaria Vesca and Fragaria X Ananassa Strawberry

Francesca Negrini , Kevin O’Grady, Marko Hyvönen, Kevin M Folta, Elena Baraldi

PLoS One 15(3):e0226448
DOI: 10.1371/journal.pone.0226448
Pubmed: 32214345

Abstract

Rapid Alkalinization Factors (RALFs) are cysteine-rich peptides ubiquitous within plant kingdom. They play multiple roles as hormonal signals in diverse processes, including root elongation, cell growth, pollen tube development, and fertilization. Their involvement in host-pathogen crosstalk as negative regulators of immunity in Arabidopsis has also been recognized. In addition, peptides homologous to RALF are secreted by different fungal pathogens as effectors during early stages of infection. Previous studies have identified nine RALF genes in the diploid strawberry (Fragaria vesca) genome. This work describes the genomic organization of the RALF gene families in commercial octoploid strawberry (Fragaria × ananassa) and the re-annotated genome of F. vesca, and then compares findings with orthologs in Arabidopsis thaliana. Continue reading →

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The thrombospondin module 1 domain of the matricellular protein CCN3 shows an atypical disulfide pattern and incomplete CWR layers

Emma-Ruoqi Xu, Aleix Lafita, Alex Bateman, Marko Hyvönen

Acta Crystallographica Section D Structural Biology D76:124-134 (2020)
DOI: 10.1107/S2059798319016747
Pubmed: 32038043

PDB coordinates:

6RK1 (3D view)

Abstract

The members of the CCN (Cyr61/CTGF/Nov) family are a group of matricellular regulatory proteins that are essential to a wide range of functional pathways in cell signalling. Through interacting with extracellular matrix components and growth factors via one of their four domains, the CCN proteins are involved in critical biological processes such as angiogenesis, cell proliferation, bone development, fibrogenesis and tumorigenesis. Here, the crystal structure of the thrombospondin module 1 (TSP1) domain of CCN3 (previously known as Nov) is presented, which shares a similar three-stranded fold with the thrombo­spondin type 1 repeats of thrombospondin-1 and spondin-1, but with variations in the disulfide connectivity. Continue reading →

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A cryptic hydrophobic pocket in the polo-box domain of the polo-like kinase PLK1 regulates substrate recognition and mitotic chromosome segregation

Pooja Sharma, Robert Mahen, Maxim Rossmann, Jamie E. Stokes, Bryn Hardwick, David J. Huggins, Amy Emery, Dominique L. Kunciw, Marko Hyvönen, David R. Spring, Grahame J. McKenzie & Ashok R. Venkitaraman

Scientific Reports, 9:15930 (2019)
DOI: s41598-019-50702-2
Pubmed: tbd
PDB coordinates: 5NMM (3D view), 5NEI (3D view)

Abstract

The human polo-like kinase PLK1 coordinates mitotic chromosome segregation by phosphorylating multiple chromatin- and kinetochore-binding proteins. How PLK1 activity is directed to specific substrates via phosphopeptide recognition by its carboxyl-terminal polo-box domain (PBD) is poorly understood. Here, we combine molecular, structural and chemical biology to identify a determinant for PLK1 substrate recognition that is essential for proper chromosome segregation. We show that mutations ablating an evolutionarily conserved, Tyr-lined pocket in human PLK1 PBD trigger cellular anomalies in mitotic progression and timing. Continue reading →

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Organoid culture media formulated with growth factors of defined cellular activity

Manuela Urbischek, Helena Rannikmae, Thomas Foets, Katharina Ravn, Marko Hyvönen & Marc de la Roche

Scientific Reports 6193 (2019)
DOI: 0.1038/s41598-019-42604-0
Pubmed: 30996238

Abstract


The media formulations necessary for deriving and sustaining organoids from epithelial tissues such as prostate, colon, gastric, liver, pancreas, and others have been established. Critical components of organoid media are a set of growth factors that include R-spondins and BMP signalling antagonists such as Noggin or Gremlin 1. Currently, the practical limitations for formulating organoid media of reproducible potency and larger-scale media production that have hampered further technological applications of organoid technology include: the cost of growth factors such as R-spondins and Gremlin 1/Noggin and their production as defined specific activities free of contaminants that may affect organoid growth. Continue reading →

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Efficient development of stable and highly functionalised peptides targeting the CK2α/CK2β protein–protein interaction

Jessica Iegre, Paul Brear, David J. Baker, Yaw Sing Tan, Eleanor L. Atkinson, Hannah F. Sore, Daniel H. O’ Donovan, Chandra S. Verma, Marko Hyvönen and David R. Spring

Chem. Sci., advance publication (2019)

DOI: 10.1039/C9SC00798A
Pubmed: TBC

PDB coordinates:

6Q38 (3D view)
6Q4Q (3D view)

Abstract

The discovery of new Protein–Protein Interaction (PPI) modulators is currently limited by the difficulties associated with the design and synthesis of selective small molecule inhibitors. Peptides are a potential solution for disrupting PPIs; however, they typically suffer from poor stability in vivo and limited tissue penetration hampering their wide spread use as new chemical biology tools and potential therapeutics. In this work, a combination of CuAAC chemistry, molecular modelling, X-ray crystallography, and biological validation allowed us to develop highly functionalised peptide PPI inhibitors of the protein CK2. Continue reading →

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Balancing Specificity and Promiscuity in Enzyme Evolution: Multidimensional Activity Transitions in the Alkaline Phosphatase Superfamily

Bert van Loo, Christopher D. Bayer, Gerhard Fischer, Stefanie Jonas, Eugene Valkov, Mark F. Mohamed, Anastassia Vorobieva, Celine Dutruel, Marko Hyvönen and Florian Hollfelder

Journal of American Chemical Society 141:370-387 (2019)
DOI: 10.1021/jacs.8b10290
Pubmed: 30497259

PDB coordinates:
4UPH (3D view), 4UPI (3D view), 4UPL (3D view), 4UPK (3D view)

Abstract

Highly proficient, promiscuous enzymes can be springboards for functional evolution, able to avoid loss of function during adaptation by their capacity to promote multiple reactions. We employ a systematic comparative study of structure, sequence, and substrate specificity to track the evolution of specificity and reactivity between promiscuous members of clades of the alkaline phosphatase (AP) superfamily. Construction of a phylogenetic tree of protein sequences maps out the likely transition zone between arylsulfatases (ASs) and phosphonate monoester hydrolases (PMHs). Kinetic analysis shows that all enzymes characterized have four chemically distinct phospho- and sulfoesterase activities, with rate accelerations ranging from 1011- to 1017-fold for their primary and 109- to 1012-fold for their promiscuous reactions, suggesting that catalytic promiscuity is widespread in the AP-superfamily. Continue reading →

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