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Ivarsson, Ylva
Publications (10 of 41) Show all publications
Sundell, G., Vögeli, B., Ivarsson, Y. & Chi, C. N. (2018). 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. Biochemistry, 57(1), 66-71
Open this publication in new window or tab >>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
2018 (English)In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 57, no 1, p. 66-71Article in journal (Refereed) Published
Abstract [en]

The use of nuclear magnetic resonance chemical shift perturbation to monitor changes taking place around the binding site of a ligand-protein interaction is a routine and widely applied methodology in the field of protein biochemistry. Shifts are often acquired by titrating various concentrations of ligand to a fixed concentration of the receptor and may serve the purpose, among others, of determining affinity constants, locating binding surfaces, or differentiating between binding mechanisms. Shifts are quantified by the so-called combined chemical shift difference. Although the directionality of shift changes is often used for detailed analysis of specific cases, the approach has not been adapted in standard chemical shift monitoring. This is surprising as it would not require additional effort. Here, we demonstrate the importance of the sign of the chemical shift difference induced by ligand-protein interaction. We analyze the sign of the 15N/1H shift changes of the PDZ1 domain of Scribble upon interaction with two pairs of phosphorylated and unphosphorylated peptides. We find that detailed differences in the molecular basis of this PDZ-ligand interaction can be obtained from our analysis to which the classical method of combined chemical shift perturbation analysis is insensitive. In addition, we find a correlation between affinity and millisecond motions. Application of the methodology to Cyclophilin a, a cis-trans isomerase, reveals molecular details of peptide recognition. We consider our directionality vector chemical shift analysis as a method of choice when distinguishing the molecular origin of binding specificities of a class of similar ligands, which is often done in drug discovery.

National Category
Medicinal Chemistry
Identifiers
urn:nbn:se:uu:diva-337645 (URN)10.1021/acs.biochem.7b00965 (DOI)000419999100011 ()29144123 (PubMedID)
Funder
Wenner-Gren Foundations, WG-17Swedish Research Council, 2012-05092
Available from: 2018-01-03 Created: 2018-01-03 Last updated: 2018-04-04Bibliographically approved
Davey, N. E., Seo, M.-H., Yadav, V. K., Jeon, J., Nim, S., Krystkowiak, I., . . . Ivarsson, Y. (2017). Discovery of short linear motif-mediated interactions through phage display of intrinsically disordered regions of the human proteome. The FEBS Journal, 284(3), 485-498
Open this publication in new window or tab >>Discovery of short linear motif-mediated interactions through phage display of intrinsically disordered regions of the human proteome
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2017 (English)In: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 284, no 3, p. 485-498Article in journal (Refereed) Published
Abstract [en]

The intrinsically disordered regions of eukaryotic proteomes are enriched in short linear motifs (SLiMs), which are of crucial relevance for cellular signaling and protein regulation; many mediate interactions by providing binding sites for peptide-binding domains. The vast majority of SLiMs remain to be discovered highlighting the need for experimental methods for their large-scale identification. We present a novel proteomic peptide phage display (ProP-PD) library that displays peptides representing the disordered regions of the human proteome, allowing direct large-scale interrogation of most potential binding SLiMs in the proteome. The performance of the ProP-PD library was validated through selections against SLiM-binding bait domains with distinct folds and binding preferences. The vast majority of identified binding peptides contained sequences that matched the known SLiM-binding specificities of the bait proteins. For SHANK1 PDZ, we establish a novel consensus TxF motif for its non-C-terminal ligands. The binding peptides mostly represented novel target proteins, however, several previously validated protein-protein interactions (PPIs) were also discovered. We determined the affinities between the VHS domain of GGA1 and three identified ligands to 40-130 mu M through isothermal titration calorimetry, and confirmed interactions through coimmunoprecipitation using full-length proteins. Taken together, we outline a general pipeline for the design and construction of ProP-PD libraries and the analysis of ProP-PD-derived, SLiM-based PPIs. We demonstrated the methods potential to identify low affinity motif-mediated interactions for modular domains with distinct binding preferences. The approach is a highly useful complement to the current toolbox of methods for PPI discovery.

Keyword
EVH1 domain, PDZ domain, Protein-protein interactions, short linear motifs, VHS domain
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-317956 (URN)10.1111/febs.13995 (DOI)000393601800011 ()28002650 (PubMedID)
Available from: 2017-03-31 Created: 2017-03-31 Last updated: 2017-11-29Bibliographically approved
Wu, C.-G., Chen, H., Guo, F., Yadav, V. K., Mcilwain, S. J., Rowse, M., . . . Xing, Y. (2017). PP2A-B' holoenzyme substrate recognition, regulation and role in cytokinesis. Cell Discovery, 3, Article ID 17027.
Open this publication in new window or tab >>PP2A-B' holoenzyme substrate recognition, regulation and role in cytokinesis
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2017 (English)In: Cell Discovery, ISSN 2056-5968, Vol. 3, article id 17027Article in journal (Refereed) Published
Abstract [en]

Protein phosphatase 2A (PP2A) is a major Ser/Thr phosphatase; it forms diverse heterotrimeric holoenzymes that counteract kinase actions. Using a peptidome that tiles the disordered regions of the human proteome, we identified proteins containing [LMFI]xx[ILV]xEx motifs that serve as interaction sites for B'-family PP2A regulatory subunits and holoenzymes. The B'-binding motifs have important roles in substrate recognition and in competitive inhibition of substrate binding. With more than 100 novel ligands identified, we confirmed that the recently identified LxxIxEx B'α-binding motifs serve as common binding sites for B' subunits with minor variations, and that S/T phosphorylation or D/E residues at positions 2, 7, 8 and 9 of the motifs reinforce interactions. Hundreds of proteins in the human proteome harbor intrinsic or phosphorylation-responsive B'-interaction motifs, and localize at distinct cellular organelles, such as midbody, predicting kinase-facilitated recruitment of PP2A-B' holoenzymes for tight spatiotemporal control of phosphorylation at mitosis and cytokinesis. Moroever, Polo-like kinase 1-mediated phosphorylation of Cyk4/RACGAP1, a centralspindlin component at the midbody, facilitates binding of both RhoA guanine nucleotide exchange factor (epithelial cell transforming sequence 2 (Ect2)) and PP2A-B' that in turn dephosphorylates Cyk4 and disrupts Ect2 binding. This feedback signaling loop precisely controls RhoA activation and specifies a restricted region for cleavage furrow ingression. Our results provide a framework for further investigation of diverse signaling circuits formed by PP2A-B' holoenzymes in various cellular processes.

Keyword
CIP2A, PP2A-B′ holoenzyme, SLiMs, centrosome, cytokinesis, midbody
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:uu:diva-337721 (URN)10.1038/celldisc.2017.27 (DOI)000414925200001 ()28884018 (PubMedID)
Funder
Swedish Research Council, 2012-05092 2016-04965Carl Tryggers foundation , CTS15:226
Available from: 2018-01-04 Created: 2018-01-04 Last updated: 2018-02-12Bibliographically approved
Wigington, C. P., Roy, J., Damle, N. P., El Cho, S., Davey, N., Ivarsson, Y., . . . Cyert, M. S. (2017). Uncovering Novel Substrates and Functions for the Calcineurin Phosphatase in Human Cells. Paper presented at Annual Meeting of the American-Society-for-Pharmacology-and-Experimental-Therapeutics (ASPET) at Experimental Biology Meeting, APR 22-26, 2017, Chicago, IL. The FASEB Journal, 31(1), Article ID 771.5.
Open this publication in new window or tab >>Uncovering Novel Substrates and Functions for the Calcineurin Phosphatase in Human Cells
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2017 (English)In: The FASEB Journal, ISSN 0892-6638, E-ISSN 1530-6860, Vol. 31, no 1, article id 771.5Article in journal, Meeting abstract (Other academic) Published
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-335024 (URN)000405461403004 ()
Conference
Annual Meeting of the American-Society-for-Pharmacology-and-Experimental-Therapeutics (ASPET) at Experimental Biology Meeting, APR 22-26, 2017, Chicago, IL
Available from: 2017-12-01 Created: 2017-12-01 Last updated: 2018-01-13Bibliographically approved
Raykova, D., Koos, B., Asplund, A., Gelleri, M., Ivarsson, Y., Danielson, U. H. & Söderberg, O. (2016). Let There Be Light!. Proteomes, 4(4), Article ID 36.
Open this publication in new window or tab >>Let There Be Light!
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2016 (English)In: Proteomes, ISSN 2227-7382, Vol. 4, no 4, article id 36Article, review/survey (Refereed) Published
Abstract [en]

The invention of the microscope has been fundamental for the understanding of tissue architecture and subcellular structures. With the advancement of higher magnification microscopes came the development of various molecular biology tools such as Forster resonance energy transfer (FRET) and in situ proximity ligation assay (in situ PLA) to monitor protein interactions. Microscopy has become a commonly used method for the investigation of molecular events within the cell, for the identification of key players in signaling networks, and the activation of these pathways. Multiple approaches are available for functional analyses in single cells. They provide information not only on the localization of proteins at a given time point, but also on their expression levels and activity states, allowing us to pinpoint hallmarks of different cellular identities within tissues in health and disease. Clever solutions to increase the sensitivity of molecular tools, the possibilities for multiplexing, as well as image resolution have recently been introduced; however, these methods have their pros and cons. Therefore, one needs to carefully consider the biological question of interest along with the nature of the sample before choosing the most suitable method or combination of methods. Herein, we review a few of the most exciting microscopy-based molecular techniques for proteomic analysis and cover the benefits as well as the disadvantages of their use.

Keyword
high resolution microscopy, protein-protein interactions, post-translational modifications, FRET, in situ PLA, proxHCR
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-316327 (URN)10.3390/proteomes4040036 (DOI)000392385500002 ()
Funder
EU, FP7, Seventh Framework Programme, 278568Swedish Research Council, 2014-02968, D0571301 , 2012-5092
Available from: 2017-05-16 Created: 2017-05-16 Last updated: 2017-05-16Bibliographically approved
Nim, S., Jeon, J., Corbi-Verge, C., Seo, M.-H., Ivarsson, Y., Moffat, J., . . . Kim, P. M. (2016). Pooled screening for antiproliferative inhibitors of protein-protein interactions.. Nature Chemical Biology, 12(4), 275-281
Open this publication in new window or tab >>Pooled screening for antiproliferative inhibitors of protein-protein interactions.
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2016 (English)In: Nature Chemical Biology, ISSN 1552-4450, E-ISSN 1552-4469, Vol. 12, no 4, p. 275-281Article in journal (Refereed) Published
Abstract [en]

Protein-protein interactions (PPIs) are emerging as a promising new class of drug targets. Here, we present a novel high-throughput approach to screen inhibitors of PPIs in cells. We designed a library of 50,000 human peptide-binding motifs and used a pooled lentiviral system to express them intracellularly and screen for their effects on cell proliferation. We thereby identified inhibitors that drastically reduced the viability of a pancreatic cancer line (RWP1) while leaving a control line virtually unaffected. We identified their target interactions computationally, and validated a subset in experiments. We also discovered their potential mechanisms of action, including apoptosis and cell cycle arrest. Finally, we confirmed that synthetic lipopeptide versions of our inhibitors have similarly specific and dosage-dependent effects on cancer cell growth. Our screen reveals new drug targets and peptide drug leads, and it provides a rich data set covering phenotypes for the inhibition of thousands of interactions.

National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
urn:nbn:se:uu:diva-278638 (URN)10.1038/nchembio.2026 (DOI)000372593200016 ()26900867 (PubMedID)
Available from: 2016-02-24 Created: 2016-02-24 Last updated: 2017-11-30Bibliographically approved
Garrido-Urbani, S., Garg, P., Ghossoub, R., Arnold, R., Lembo, F., Sundell, G. N., . . . Ivarsson, Y. (2016). Proteomic peptide phage display uncovers novel interactions of the PDZ1-2 supramodule of syntenin. FEBS Letters, 590(1), 3-12
Open this publication in new window or tab >>Proteomic peptide phage display uncovers novel interactions of the PDZ1-2 supramodule of syntenin
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2016 (English)In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 590, no 1, p. 3-12Article in journal (Refereed) Published
Abstract [en]

Syntenin has crucial roles in cell adhesion, cell migration and synaptic transmission. Its closely linked postsynaptic density-95, discs large 1, zonula occludens-1 (PDZ) domains typically interact with C-terminal ligands. We profile syntenin PDZ1-2 through proteomic peptide phage display (ProP-PD) using a library that displays C-terminal regions of the human proteome. The protein recognizes a broad range of peptides, with a preference for hydrophobic motifs and has a tendency to recognize cryptic internal ligands. We validate the interaction with nectin-1 through orthogonal assays. The study demonstrates the power of ProP-PD as a complementary approach to uncover interactions of potential biological relevance.

National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
urn:nbn:se:uu:diva-275039 (URN)10.1002/1873-3468.12037 (DOI)000368808900001 ()26787460 (PubMedID)
Funder
Åke Wiberg Foundation, 3773397Swedish Research Council, C0509201
Available from: 2016-01-28 Created: 2016-01-28 Last updated: 2017-11-30Bibliographically approved
Wigington, C. P., Damle, N. P., Roy, J., Cho, S. E., Davey, N. E., Ivarsson, Y. & Cyert, M. S. (2016). Uncovering novel substrates and functions for the calcineurin phosphatase in human cells.. Paper presented at ASCB Annual Meeting 2016. San Francisco California, dec 3-7.. Molecular Biology of the Cell, 27(25), Article ID 3947.
Open this publication in new window or tab >>Uncovering novel substrates and functions for the calcineurin phosphatase in human cells.
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2016 (English)In: Molecular Biology of the Cell, ISSN 1059-1524, E-ISSN 1939-4586, Vol. 27, no 25, article id 3947Article in journal, Meeting abstract (Refereed) Published
National Category
Cell Biology
Identifiers
urn:nbn:se:uu:diva-317516 (URN)10.1091/mbc.E16-10-0736 (DOI)000394259500302 ()
Conference
ASCB Annual Meeting 2016. San Francisco California, dec 3-7.
Available from: 2017-04-10 Created: 2017-04-10 Last updated: 2017-11-29
Blikstad, C. & Ivarsson, Y. (2015). High-throughput methods for identification of protein-protein interactions involving short linear motifs. Cell Communication and Signaling, 13, Article ID 38.
Open this publication in new window or tab >>High-throughput methods for identification of protein-protein interactions involving short linear motifs
2015 (English)In: Cell Communication and Signaling, ISSN 1478-811X, E-ISSN 1478-811X, Vol. 13, article id 38Article, review/survey (Refereed) Published
Abstract [en]

Interactions between modular domains and short linear motifs (3-10 amino acids peptide stretches) are crucial for cell signaling. The motifs typically reside in the disordered regions of the proteome and the interactions are often transient, allowing for rapid changes in response to changing stimuli. The properties that make domain-motif interactions suitable for cell signaling also make them difficult to capture experimentally and they are therefore largely underrepresented in the known protein-protein interaction networks. Most of the knowledge on domain-motif interactions is derived from low-throughput studies, although there exist dedicated high-throughput methods for the identification of domain-motif interactions. The methods include arrays of peptides or proteins, display of peptides on phage or yeast, and yeast-two-hybrid experiments. We here provide a survey of scalable methods for domain-motif interaction profiling. These methods have frequently been applied to a limited number of ubiquitous domain families. It is now time to apply them to a broader set of peptide binding proteins, to provide a comprehensive picture of the linear motifs in the human proteome and to link them to their potential binding partners. Despite the plethora of methods, it is still a challenge for most approaches to identify interactions that rely on post-translational modification or context dependent or conditional interactions, suggesting directions for further method development.

Keyword
Linear motif, Protein-protein interactions, Phage display, Yeast-surface display, Peptide arrays, Interaction profiling
National Category
Cell Biology Chemical Sciences
Identifiers
urn:nbn:se:uu:diva-262136 (URN)10.1186/s12964-015-0116-8 (DOI)000359837400001 ()26297553 (PubMedID)
Funder
Swedish Research Council, C0509201Åke Wiberg Foundation, 3773397Magnus Bergvall Foundation
Available from: 2015-09-09 Created: 2015-09-09 Last updated: 2017-12-04Bibliographically approved
Ganesan, A., Debulpaep, M., Wilkinson, H., Van Durme, J., De Baets, G., Jonckheere, W., . . . Rousseau, F. (2015). Selectivity of Aggregation-Determining Interactions. Journal of Molecular Biology, 427(2), 236-247
Open this publication in new window or tab >>Selectivity of Aggregation-Determining Interactions
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2015 (English)In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 427, no 2, p. 236-247Article in journal (Refereed) Published
Abstract [en]

Protein aggregation is sequence specific, favoring self-assembly over cross-seeding with non-homologous sequences. Still, as the majority of proteins in a proteome are aggregation prone, the high level of homogeneity of protein inclusions in vivo both during recombinant overexpression and in disease remains surprising. To investigate the selectivity of protein aggregation in a proteomic context, we here compared the selectivity of aggregation-determined interactions with antibody binding. To that purpose, we synthesized biotin-labeled peptides, corresponding to aggregation-determining sequences of the bacterial protein β-galactosidase and two human disease biomarkers: C-reactive protein and prostate-specific antigen. We analyzed the selectivity of their interactions in Escherichiacoli lysate, human serum and human seminal plasma, respectively, using a Western blot-like approach in which the aggregating peptides replace the conventional antibody. We observed specific peptide accumulation in the same bands detected by antibody staining. Combined spectroscopic and mutagenic studies confirmed accumulation resulted from binding of the peptide on the identical sequence of the immobilized target protein. Further, we analyzed the sequence redundancy of aggregating sequences and found that about 90% of them are unique within their proteome. As a result, the combined specificity and low sequence redundancy of aggregating sequences therefore contribute to the observed homogeneity of protein aggregation in vivo. This suggests that these intrinsic proteomic properties naturally compartmentalize aggregation events in sequence space. In the event of physiological stress, this might benefit the ability of cells to respond to proteostatic stress by allowing chaperones to focus on specific aggregation events rather than having to face systemic proteostatic failure.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-238885 (URN)10.1016/j.jmb.2014.09.027 (DOI)000348888200005 ()25451783 (PubMedID)
Available from: 2014-12-17 Created: 2014-12-17 Last updated: 2017-12-05Bibliographically approved
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