Ivarsson Group

Illustration of a cell that has a healthy part and a sick part. In the healthy part, there is a network of protein-protein interactions between different human proteins. In the diseased part, which has been infected by a virus, the network of human protein-protein interactions is destroyed because certain network proteins bind to viral proteins instead. This causes the cell to start producing virus particles that are released from the cell.

Molecular interactions in cell function and dysfunction

We focus on interactions between linear motifs and peptide binding domains and aim to contribute with novel insights into the human protein-protein interaction networks in health and diseases. In addition, we explore the interplay between protein-protein and protein-phospholipid interactions. Our research is interdisciplinary and combines biochemical and biophysical methods with bioinformatics and cell-based assays.

Read more about our research

Group members

Research leader: Ylva Ivarsson

Group members: Isabella Menart, Keziah Nomenyo, Leandro Simonetti, Vishakha Singh, Maximilian Vieler, Ana Zupancic

Publications

NUP98 regulates orthoflavivirus replication through interaction with vRNA and can be targeted for antiviral purposes

Peters, Marie B. A.; Lindqvist, Richard; Madhu, Priyanka; Lundmark, Richard et al.

Part of Nucleic Acids Research, 2026
- DOI for NUP98 regulates orthoflavivirus replication through interaction with vRNA and can be targeted for antiviral purposes
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A tryptophan-phenylalanine binding motif for the histone methyltransferases MLL4 and MLL3

Biswas, Soumi; Tavaf, Zohreh; Benz, Caroline; Khalil, Moustafa et al.

Part of Journal of Biological Chemistry, 2026
- DOI for A tryptophan-phenylalanine binding motif for the histone methyltransferases MLL4 and MLL3
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Proviral NUP153 binding to viral proteins and RNA regulates structural-nonstructural protein ratios in orthoflavivirus infection

Peters, Marie B. A.; Lindqvist, Richard; Kassa, Eszter; Yau, Wai-Lok et al.

Part of Nature Communications, 2026
- DOI for Proviral NUP153 binding to viral proteins and RNA regulates structural-nonstructural protein ratios in orthoflavivirus infection
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The evolving landscape of protein structure and molecular recognition

Ivarsson, Ylva; Petsko, Gregory A.

Part of Trends in Biochemical Sciences (TIBS), p. 525-528, 2026
- DOI for The evolving landscape of protein structure and molecular recognition
Systematic Discovery of Motif-based Interactions of the Auxiliary Domains of USP Family Deubiquitinases

Konstantinou, Aimiliani; Córdova-Pérez, Alicia; Varga, Julia K.; Madhu, Priyanka et al.

Part of Nature Communications, 2026
- DOI for Systematic Discovery of Motif-based Interactions of the Auxiliary Domains of USP Family Deubiquitinases
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Elucidation of short linear motif‑based interactions of the MIT and rhodanese domains of the ubiquitin‑specific protease 8

Konstantinou, Aimiliani; Varga, Julia K.; Córdova-Pérez, Alicia; Simonetti, Leandro et al.

Part of Biology Direct, 2025
- DOI for Elucidation of short linear motif‑based interactions of the MIT and rhodanese domains of the ubiquitin‑specific protease 8
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Defining short linear motif binding determinants by phage display-based deep mutational scanning

Benz, Caroline; Maasen, Lars; Simonetti, Leandro; Mihalič, Filip et al.

Part of Protein Science, 2025
- DOI for Defining short linear motif binding determinants by phage display-based deep mutational scanning
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Obituary-Per Jemth

Gianni, Stefano; Ivarsson, Ylva; Mgaard, Kristian Stromgaard

Part of Biochimica et Biophysica Acta - Proteins and Proteomics, 2025
- DOI for Obituary-Per Jemth
High-throughput investigation of cyclin docking interactions reveals the complexity of motif binding determinants

Örd, Mihkel; Winters, Matthew J.; Subbanna, Mythili S.; de Martin Garrido, Natalia et al.

Part of Nature Communications, 2025
- DOI for High-throughput investigation of cyclin docking interactions reveals the complexity of motif binding determinants
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Swapped domain orders in ZO-1 PDZ3 fusion proteins - implications for binding of established and novel targets

Hamsikova, Marie; Hurdalek, Jan; Simonetti, Leandro; Ptacek, Jakub et al.

Part of Archives of Biochemistry and Biophysics, 2025
- DOI for Swapped domain orders in ZO-1 PDZ3 fusion proteins - implications for binding of established and novel targets
MLL4 binds TET3

Becht, Dustin C.; Mohid, Sk Abdul; Lee, Ji-Eun; Zandian, Mohamad et al.

Part of Structure, 2024
- DOI for MLL4 binds TET3
Exploring the short linear motif-mediated protein-protein interactions of CrkL through ProP-PD

Pagano, L.; Simonetti, Leandro; Pennacchietti, V.; Toto, A. et al.

Part of Biochemical and Biophysical Research Communications - BBRC, 2024
- DOI for Exploring the short linear motif-mediated protein-protein interactions of CrkL through ProP-PD
Proteome-scale characterisation of motif-based interactome rewiring by disease mutations

Kliche, Johanna; Simonetti, Leandro; Krystkowiak, Izabella; Kuss, Hanna et al.

Part of Molecular Systems Biology, p. 1025-1048, 2024
- DOI for Proteome-scale characterisation of motif-based interactome rewiring by disease mutations
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ASXLs binding to the PHD2/3 fingers of MLL4 provides a mechanism for the recruitment of BAP1 to active enhancers

Zhang, Yi; Xie, Guojia; Lee, Ji-Eun; Zandian, Mohamad et al.

Part of Nature Communications, 2024
- DOI for ASXLs binding to the PHD2/3 fingers of MLL4 provides a mechanism for the recruitment of BAP1 to active enhancers
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Motif-dependent binding on the intervening domain regulates O-GlcNAc transferase

Blankenship, Connor M.; Xie, Jinshan; Benz, Caroline; Wang, Ao et al.

Part of Nature Chemical Biology, p. 1423-1431, 2023
- DOI for Motif-dependent binding on the intervening domain regulates O-GlcNAc transferase
Elucidation of Short Linear Motif-Based Interactions of the FERM Domains of Ezrin, Radixin, Moesin, and Merlin

Ali, Muhammad; Khramushin, Alisa; Yadav, Vikash K.; Schueler-Furman, Ora et al.

Part of Biochemistry, p. 1594-1607, 2023
- DOI for Elucidation of Short Linear Motif-Based Interactions of the FERM Domains of Ezrin, Radixin, Moesin, and Merlin
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SLiM-binding pockets: an attractive target for broad-spectrum antivirals

Simonetti, Leandro; Nilsson, Jakob; McInerney, Gerald; Ivarsson, Ylva et al.

Part of TIBS -Trends in Biochemical Sciences. Regular ed., p. 420-427, 2023
- DOI for SLiM-binding pockets: an attractive target for broad-spectrum antivirals
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Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets

Mihalic, Filip; Benz, Caroline; Kassa, Eszter; Lindqvist, Richard et al.

Part of Nature Communications, 2023
- DOI for Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets
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Evaluation of affinity-purification coupled to mass spectrometry approaches for capture of short linear motif-based interactions

Kassa, Eszter; Jamshidi, Sara; Mihalič, Filip; Simonetti, Leandro et al.

Part of Analytical Biochemistry, 2023
- DOI for Evaluation of affinity-purification coupled to mass spectrometry approaches for capture of short linear motif-based interactions
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Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions

Kliche, Johanna; Garvanska, Dimitriya Hristoforova; Simonetti, Leandro; Badgujar, Dilip et al.

Part of Molecular Systems Biology, 2023
- DOI for Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions
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The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome

Davey, Norman E.; Simonetti, Leandro; Ivarsson, Ylva

Part of Current opinion in structural biology, 2023
- DOI for The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome
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Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs

Mihalič, Filip; Simonetti, Leandro; Giudice, Girolamo; Rubin Sander, Marie et al.

Part of Nature Communications, 2023
- DOI for Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs
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Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition

Li, Yitong; Balakrishnan, Vijaya Kumar; Rowse, Michael; Wu, Cheng-Guo et al.

Part of eLIFE, 2022
- DOI for Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition
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A Syntenin Inhibitor Blocks Endosomal Entry of SARS-CoV-2 and a Panel of RNA Viruses

Lindqvist, Richard; Benz, Caroline; Sereikaite, Vita; Maassen, Lars et al.

Part of Viruses, 2022
- DOI for A Syntenin Inhibitor Blocks Endosomal Entry of SARS-CoV-2 and a Panel of RNA Viruses
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p Orchestrating serine/threonine phosphorylation and elucidating downstream effects by short linear motifs

Kliche, Johanna; Ivarsson, Ylva

Part of Biochemical Journal, p. 1-22, 2022
- DOI for p Orchestrating serine/threonine phosphorylation and elucidating downstream effects by short linear motifs
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Proteome-scale mapping of binding sites in the unstructured regions of the human proteome

Benz, Caroline; Ali, Muhammad; Krystkowiak, Izabella; Simonetti, Leandro et al.

Part of Molecular Systems Biology, 2022
- DOI for Proteome-scale mapping of binding sites in the unstructured regions of the human proteome
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ProP-PD for proteome-wide motif-mediated interaction discovery

Davey, Norman E.; Simonetti, Leandro; Ivarsson, Ylva

Part of TIBS -Trends in Biochemical Sciences. Regular ed., p. 547-548, 2022
- DOI for ProP-PD for proteome-wide motif-mediated interaction discovery
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How viral proteins bind short linear motifs and intrinsically disordered domains

Madhu, Priyanka; Davey, Norman E.; Ivarsson, Ylva

Part of Essays in Biochemistry, p. 935-944, 2022
- DOI for How viral proteins bind short linear motifs and intrinsically disordered domains
A High-Affinity Peptide Ligand Targeting Syntenin Inhibits Glioblastoma

Haugaard-Kedström, Linda M.; Clemmensen, Louise S.; Sereikaite, Vita; Jin, Zeyu et al.

Part of Journal of Medicinal Chemistry, p. 1423-1434, 2021
- DOI for A High-Affinity Peptide Ligand Targeting Syntenin Inhibits Glioblastoma
Integrated analysis of Shank1 PDZ interactions with C-terminal and internal binding motifs

Ali, Muhammad; McAuley, Mishal Mariam; Lüchow, Susanne; Knapp, Stefan et al.

Part of Current Research in Structural Biology, p. 41-50, 2021
- DOI for Integrated analysis of Shank1 PDZ interactions with C-terminal and internal binding motifs
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Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities

Kruse, Thomas; Benz, Caroline; Garvanska, Dimitriya H.; Lindqvist, Richard et al.

Part of Nature Communications, 2021
- DOI for Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities
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Cytoplasmic short linear motifs in ACE2 and integrin beta(3) link SARS-CoV-2 host cell receptors to mediators of endocytosis and autophagy

Kliche, Johanna; Kuss, Hanna; Ali, Muhammad; Ivarsson, Ylva

Part of Science Signaling, 2021
- DOI for Cytoplasmic short linear motifs in ACE2 and integrin beta(3) link SARS-CoV-2 host cell receptors to mediators of endocytosis and autophagy
Identification of Cellular Protein-Protein Interactions

Benz, Caroline; Kassa, Eszter; Tjärnhage, Elias; Bergström Lind, Sara et al.

Part of INHIBITORS OF PROTEIN-PROTEIN INTERACTIONS, p. 1-39, Royal Society of Chemistry, 2021
- DOI for Identification of Cellular Protein-Protein Interactions
Identification of PDZ Interactions by Proteomic Peptide Phage Display

Lüchow, Susanne; Sundell, Gustav; Ivarsson, Ylva

Part of PDZ Mediated Interactions, p. 41-60, Springer Nature, 2021
- DOI for Identification of PDZ Interactions by Proteomic Peptide Phage Display
Genetically Encoded Cyclic Peptide Phage Display Libraries

Simonetti, Leandro; Ivarsson, Ylva

Part of ACS CENTRAL SCIENCE, p. 336-338, 2020
- DOI for Genetically Encoded Cyclic Peptide Phage Display Libraries
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Deciphering the Unexpected Binding Capacity of the Third PDZ Domain of Whirlin to Various Cochlear Hair Cell Partners

Zhu, Yanlei; Delhommel, Florent; Cordier, Florence; Lüchow, Susanne et al.

Part of Journal of Molecular Biology, p. 5920-5937, 2020
- DOI for Deciphering the Unexpected Binding Capacity of the Third PDZ Domain of Whirlin to Various Cochlear Hair Cell Partners
Profiling calcium-dependent interactions between Sorcin and intrinsically disordered regions of human proteome

Genovese, Ilaria; Carotti, Andrea; Ilari, Andrea; Fiorillo, Annarita et al.

Part of Biochimica et Biophysica Acta - General Subjects, 2020
- DOI for Profiling calcium-dependent interactions between Sorcin and intrinsically disordered regions of human proteome
Systematic Discovery of Short Linear Motifs Decodes Calcineurin Phosphatase Signaling

Wigington, Callie P.; Roy, Jagoree; Damle, Nikhil P.; Yadav, Vikash K. et al.

Part of Molecular Cell, p. 342-+, 2020
- DOI for Systematic Discovery of Short Linear Motifs Decodes Calcineurin Phosphatase Signaling
A Consensus Binding Motif for the PP4 Protein Phosphatase

Ueki, Yumi; Kruse, Thomas; Weisser, Melanie Bianca; Sundell, Gustav N. et al.

Part of Molecular Cell, p. 953-964000000, 2019
- DOI for A Consensus Binding Motif for the PP4 Protein Phosphatase
Editorial overview: Folding and binding

Ivarsson, Ylva; Jemth, Per

Part of Current opinion in structural biology, p. 139-140, 2019
- DOI for Editorial overview: Folding and binding
Systematic identification of recognition motifs for the hub protein LC8

Jespersen, Nathan; Estelle, Aidan; Waugh, Nathan; Davey, Norman E. et al.

Part of Life Science Alliance, 2019
- DOI for Systematic identification of recognition motifs for the hub protein LC8
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Affinity and specificity of motif-based protein-protein interactions

Ivarsson, Ylva; Jemth, Per

Part of Current opinion in structural biology, p. 26-33, 2019
- DOI for Affinity and specificity of motif-based protein-protein interactions
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The Sign of Nuclear Magnetic Resonance Chemical Shift Difference as a Determinant of the Origin of Binding Selectivity: Elucidation of the Position Dependence of Phosphorylation in Ligands Binding to Scribble PDZ1

Sundell, Gustav; Vögeli, Beat; Ivarsson, Ylva; Chi, Celestine N.

Part of Biochemistry, p. 66-71, 2018
- DOI for The Sign of Nuclear Magnetic Resonance Chemical Shift Difference as a Determinant of the Origin of Binding Selectivity: Elucidation of the Position Dependence of Phosphorylation in Ligands Binding to Scribble PDZ1
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Proteome‐wide analysis of phospho‐regulated PDZ domain interactions

Sundell, Gustav; Arnold, Roland; Ali, Muhammad; Naksukpaiboon, Piangfan et al.

Part of Molecular Systems Biology, 2018
- DOI for Proteome‐wide analysis of phospho‐regulated PDZ domain interactions
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High-throughput discovery of functional disordered regions

Ali, Muhammad; Ivarsson, Ylva

Part of Molecular Systems Biology, 2018
- DOI for High-throughput discovery of functional disordered regions
Uncovering Novel Substrates and Functions for the Calcineurin Phosphatase in Human Cells

Wigington, Callie P.; Roy, Jagoree; Damle, Nikhil P.; El Cho, Shein et al.

Part of The FASEB Journal, 2017
Mapping the human calcineurin phosphatase signaling network through global identification of short linear motifs that mediate substrate recognition

Roy, J.; Wigington, C. P.; Damle, N. P.; Ulengin-Talkish, I. et al.

Part of Molecular Biology of the Cell, p. 3727-3727, 2017
- DOI for Mapping the human calcineurin phosphatase signaling network through global identification of short linear motifs that mediate substrate recognition
Investigating the phospho-regulation of ER shaping protein RTN1A (Reticulon-1A) by the Calcineurin phosphatase.

Cho, S. Ei; Roy, J.; Ivarsson, Ylva; Cyert, M. S.

Part of Molecular Biology of the Cell, p. 3727-3727, 2017
- DOI for Investigating the phospho-regulation of ER shaping protein RTN1A (Reticulon-1A) by the Calcineurin phosphatase.
A novel role for the Calcineurin phosphatase at the nuclear pore

Wigington, C. P.; Roy, J.; Damle, N. P.; Ulengin-Talkish, I. et al.

Part of Molecular Biology of the Cell, p. 3727-3727, 2017
- DOI for A novel role for the Calcineurin phosphatase at the nuclear pore
PP2A-B' holoenzyme substrate recognition, regulation and role in cytokinesis

Wu, Cheng-Guo; Chen, Hui; Guo, Feng; Yadav, Vikash K et al.

Part of Cell Discovery, 2017
- DOI for PP2A-B' holoenzyme substrate recognition, regulation and role in cytokinesis
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