Ivarssons grupp

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.

Ingår i Nucleic Acids Research, 2026

• DOI för 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.

Ingår i Journal of Biological Chemistry, 2026

• DOI för 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.

Ingår i Nature Communications, 2026

• DOI för 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.

Ingår i Trends in Biochemical Sciences (TIBS), s. 525-528, 2026

• DOI för 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.

Ingår i Nature Communications, 2026

• DOI för 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.

Ingår i Biology Direct, 2025

• DOI för 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.

Ingår i Protein Science, 2025

• DOI för 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

Ingår i Biochimica et Biophysica Acta - Proteins and Proteomics, 2025

• DOI för 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.

Ingår i Nature Communications, 2025

• DOI för 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.

Ingår i Archives of Biochemistry and Biophysics, 2025

• DOI för 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.

Ingår i Structure, 2024

• DOI för 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.

Ingår i Biochemical and Biophysical Research Communications - BBRC, 2024

• DOI för 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.

Ingår i Molecular Systems Biology, s. 1025-1048, 2024

• DOI för 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.

Ingår i Nature Communications, 2024

• DOI för 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.

Ingår i Nature Chemical Biology, s. 1423-1431, 2023

• DOI för 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.

Ingår i Biochemistry, s. 1594-1607, 2023

• DOI för 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.

Ingår i TIBS -Trends in Biochemical Sciences. Regular ed., s. 420-427, 2023

• DOI för 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.

Ingår i Nature Communications, 2023

• DOI för 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.

Ingår i Analytical Biochemistry, 2023

• DOI för 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.

Ingår i Molecular Systems Biology, 2023

• DOI för 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

Ingår i Current opinion in structural biology, 2023

• DOI för 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.

Ingår i Nature Communications, 2023

• DOI för 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.

Ingår i eLIFE, 2022

• DOI för 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.

Ingår i Viruses, 2022

• DOI för 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

Ingår i Biochemical Journal, s. 1-22, 2022

• DOI för 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.

Ingår i Molecular Systems Biology, 2022

• DOI för Proteome-scale mapping of binding sites in the unstructured regions of the human proteome
• Ladda ner fulltext (pdf) av Proteome-scale mapping of binding sites in the unstructured regions of the human proteome

ProP-PD for proteome-wide motif-mediated interaction discovery

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

Ingår i TIBS -Trends in Biochemical Sciences. Regular ed., s. 547-548, 2022

• DOI för 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

Ingår i Essays in Biochemistry, s. 935-944, 2022

• DOI för 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.

Ingår i Journal of Medicinal Chemistry, s. 1423-1434, 2021

• DOI för 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.

Ingår i Current Research in Structural Biology, s. 41-50, 2021

• DOI för 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.

Ingår i Nature Communications, 2021

• DOI för 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

Ingår i Science Signaling, 2021

• DOI för 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.

Ingår i INHIBITORS OF PROTEIN-PROTEIN INTERACTIONS, s. 1-39, Royal Society of Chemistry, 2021

• DOI för Identification of Cellular Protein-Protein Interactions

Identification of PDZ Interactions by Proteomic Peptide Phage Display

Lüchow, Susanne; Sundell, Gustav; Ivarsson, Ylva

Ingår i PDZ Mediated Interactions, s. 41-60, Springer Nature, 2021

• DOI för Identification of PDZ Interactions by Proteomic Peptide Phage Display

Genetically Encoded Cyclic Peptide Phage Display Libraries

Simonetti, Leandro; Ivarsson, Ylva

Ingår i ACS CENTRAL SCIENCE, s. 336-338, 2020

• DOI för Genetically Encoded Cyclic Peptide Phage Display Libraries
• Ladda ner fulltext (pdf) av Genetically Encoded Cyclic Peptide Phage Display Libraries

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.

Ingår i Journal of Molecular Biology, s. 5920-5937, 2020

• DOI för 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.

Ingår i Biochimica et Biophysica Acta - General Subjects, 2020

• DOI för 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.

Ingår i Molecular Cell, s. 342-+, 2020

• DOI för 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.

Ingår i Molecular Cell, s. 953-964000000, 2019

• DOI för A Consensus Binding Motif for the PP4 Protein Phosphatase

Editorial overview: Folding and binding

Ivarsson, Ylva; Jemth, Per

Ingår i Current opinion in structural biology, s. 139-140, 2019

• DOI för 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.

Ingår i Life Science Alliance, 2019

• DOI för Systematic identification of recognition motifs for the hub protein LC8
• Ladda ner fulltext (pdf) av Systematic identification of recognition motifs for the hub protein LC8

Affinity and specificity of motif-based protein-protein interactions

Ivarsson, Ylva; Jemth, Per

Ingår i Current opinion in structural biology, s. 26-33, 2019

• DOI för 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.

Ingår i Biochemistry, s. 66-71, 2018

• DOI för 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.

Ingår i Molecular Systems Biology, 2018

• DOI för Proteome‐wide analysis of phospho‐regulated PDZ domain interactions
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High-throughput discovery of functional disordered regions

Ali, Muhammad; Ivarsson, Ylva

Ingår i Molecular Systems Biology, 2018

• DOI för 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.

Ingår i 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.

Ingår i Molecular Biology of the Cell, s. 3727-3727, 2017

• DOI för 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.

Ingår i Molecular Biology of the Cell, s. 3727-3727, 2017

• DOI för 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.

Ingår i Molecular Biology of the Cell, s. 3727-3727, 2017

• DOI för 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.

Ingår i Cell Discovery, 2017

• DOI för PP2A-B' holoenzyme substrate recognition, regulation and role in cytokinesis
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