Ivarssons grupp

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

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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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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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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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
• Ladda ner fulltext (pdf) av Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets

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

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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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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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

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
• Ladda ner fulltext (pdf) av ProP-PD for proteome-wide motif-mediated interaction discovery

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

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
• Ladda ner fulltext (pdf) av A Syntenin Inhibitor Blocks Endosomal Entry of SARS-CoV-2 and a Panel of RNA Viruses

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

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
• Ladda ner fulltext (pdf) av Integrated analysis of Shank1 PDZ interactions with C-terminal and internal binding motifs

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
• Ladda ner fulltext (pdf) av Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities

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

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

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

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
• Ladda ner fulltext (pdf) av Affinity and specificity of motif-based protein-protein interactions

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

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
• Ladda ner fulltext (pdf) av Proteome‐wide analysis of phospho‐regulated PDZ domain interactions

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

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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Discovery of short linear motif-mediated interactions through phage display of intrinsically disordered regions of the human proteome

Davey, Norman E.; Seo, Moon-Hyeong; Yadav, Vikash Kumar; Jeon, Jouhyun et al.

Ingår i The FEBS Journal, s. 485-498, 2017

• DOI för Discovery of short linear motif-mediated interactions through phage display of intrinsically disordered regions of the human proteome
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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

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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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

Let There Be Light!

Raykova, Doroteya; Koos, Bjoern; Asplund, Anna; Gelleri, Marton et al.

Ingår i Proteomes, 2016

• DOI för Let There Be Light!
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Uncovering novel substrates and functions for the calcineurin phosphatase in human cells.

Wigington, C. P.; Damle, N. P.; Roy, J.; Cho, S. E. et al.

Ingår i Molecular Biology of the Cell, 2016

• DOI för Uncovering novel substrates and functions for the calcineurin phosphatase in human cells.

Proteomic peptide phage display uncovers novel interactions of the PDZ1-2 supramodule of syntenin

Garrido-Urbani, Sarah; Garg, Pankaj; Ghossoub, Rania; Arnold, Roland et al.

Ingår i FEBS Letters, s. 3-12, 2016

• DOI för Proteomic peptide phage display uncovers novel interactions of the PDZ1-2 supramodule of syntenin
• Ladda ner fulltext (pdf) av Proteomic peptide phage display uncovers novel interactions of the PDZ1-2 supramodule of syntenin

Pooled screening for antiproliferative inhibitors of protein-protein interactions.

Nim, Satra; Jeon, Jouhyun; Corbi-Verge, Carles; Seo, Moon-Hyeong et al.

Ingår i Nature Chemical Biology, s. 275-281, 2016

• DOI för Pooled screening for antiproliferative inhibitors of protein-protein interactions.

Improved affinity at the cost of decreased specificity: a recurring theme in PDZ-peptide interactions.

Karlsson, O Andreas; Sundell, Gustav N; Andersson, Eva; Ivarsson, Ylva et al.

Ingår i Scientific Reports, 2016

• DOI för Improved affinity at the cost of decreased specificity: a recurring theme in PDZ-peptide interactions.
• Ladda ner fulltext (pdf) av Improved affinity at the cost of decreased specificity: a recurring theme in PDZ-peptide interactions.

Frizzled 7 and PIP2 binding by syntenin PDZ2 domain supports Frizzled 7 trafficking and signalling

Egea-Jimenez, Antonio Luis; Gallardo, Rodrigo; Garcia-Pino, Abel; Ivarsson, Ylva et al.

Ingår i Nature Communications, 2016

• DOI för Frizzled 7 and PIP2 binding by syntenin PDZ2 domain supports Frizzled 7 trafficking and signalling
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Selectivity of Aggregation-Determining Interactions

Ganesan, Ashok; Debulpaep, Maja; Wilkinson, Hannah; Van Durme, Joost et al.

Ingår i Journal of Molecular Biology, s. 236-247, 2015

• DOI för Selectivity of Aggregation-Determining Interactions

Structural basis of Sorcin-mediated calcium-dependent signal transduction

Ilari, Andrea; Fiorillo, Annarita; Poser, Elena; Lalioti, Vasiliki S. et al.

Ingår i Scientific Reports, 2015

High-throughput methods for identification of protein-protein interactions involving short linear motifs

Blikstad, Cecilia; Ivarsson, Ylva

Ingår i Cell Communication and Signaling, 2015

• DOI för High-throughput methods for identification of protein-protein interactions involving short linear motifs
• Ladda ner fulltext (pdf) av High-throughput methods for identification of protein-protein interactions involving short linear motifs

Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes

Ivarsson, Ylva; Arnold, Roland; McLaughlin, Megan; Nim, Satra et al.

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 2542-2547, 2014

• DOI för Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes

Interaction Analysis through Proteomic Phage Display

Sundell, Gustav; Ivarsson, Ylva

Ingår i BioMed Research International, s. 176172, 2014

• DOI för Interaction Analysis through Proteomic Phage Display
• Ladda ner fulltext (pdf) av Interaction Analysis through Proteomic Phage Display

A Structural Portrait of the PDZ Domain Family

Ernst, Andreas; Appleton, Brent A; Ivarsson, Ylva; Zhang, Yingnan et al.

Ingår i Journal of Molecular Biology, s. 3509-3519, 2014

• DOI för A Structural Portrait of the PDZ Domain Family

The Development and Characterization of a Peptide-Based Syntenin Inhibitor: Implacations for Cancer Metastasis

Haugaard-Kedstrom, L. M.; Albertsen, L.; Gil, F. Abalde; Ivarsson, Ylva et al.

Ingår i Journal of Peptide Science, 2014

Prevalence, specificity and determinants of lipid-interacting PDZ domains from an in-cell screen and in vitro binding experiments

Ivarsson, Ylva; Wawrzyniak, Anna Maria; Kashyap, Rudra; Polanowska, Jolanta et al.

Ingår i PloS one, 2013

• DOI för Prevalence, specificity and determinants of lipid-interacting PDZ domains from an in-cell screen and in vitro binding experiments