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Article ; Online: Orchestrating serine/threonine phosphorylation and elucidating downstream effects by short linear motifs.

Kliche, Johanna / Ivarsson, Ylva

2022 Volume 479, Issue 1, Page(s) 1–22

Abstract: Cellular function is based on protein-protein interactions. A large proportion of these interactions involves the binding of short linear motifs (SLiMs) by folded globular domains. These interactions are regulated by post-translational modifications, ... ...

Abstract	Cellular function is based on protein-protein interactions. A large proportion of these interactions involves the binding of short linear motifs (SLiMs) by folded globular domains. These interactions are regulated by post-translational modifications, such as phosphorylation, that create and break motif binding sites or tune the affinity of the interactions. In addition, motif-based interactions are involved in targeting serine/threonine kinases and phosphatases to their substrate and contribute to the specificity of the enzymatic actions regulating which sites are phosphorylated. Here, we review how SLiM-based interactions assist in determining the specificity of serine/threonine kinases and phosphatases, and how phosphorylation, in turn, affects motif-based interactions. We provide examples of SLiM-based interactions that are turned on/off, or are tuned by serine/threonine phosphorylation and exemplify how this affects SLiM-based protein complex formation.
MeSH term(s)	Binding Sites ; Humans ; Phosphoric Monoester Hydrolases/metabolism ; Phosphorylation ; Protein Interaction Domains and Motifs ; Protein Processing, Post-Translational ; Protein Serine-Threonine Kinases/metabolism ; Serine/chemistry ; Serine/metabolism ; Substrate Specificity ; Threonine/chemistry ; Threonine/metabolism
Chemical Substances	Threonine (2ZD004190S) ; Serine (452VLY9402) ; Protein Serine-Threonine Kinases (EC 2.7.11.1) ; Phosphoric Monoester Hydrolases (EC 3.1.3.2)
Language	English
Publishing date	2022-01-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2969-5
ISSN	1470-8728 ; 0006-2936 ; 0306-3275 ; 0264-6021
ISSN (online)	1470-8728
ISSN	0006-2936 ; 0306-3275 ; 0264-6021
DOI	10.1042/BCJ20200714
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Article ; Online: Cytoplasmic short linear motifs in ACE2 and integrin β

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

Science signaling

2021 Volume 14, Issue 665

Abstract: The spike protein of SARS-CoV-2 binds the angiotensin-converting enzyme 2 (ACE2) on the host cell surface and subsequently enters host cells through receptor-mediated endocytosis. Additional cell receptors may be directly or indirectly involved, ... ...

Abstract	The spike protein of SARS-CoV-2 binds the angiotensin-converting enzyme 2 (ACE2) on the host cell surface and subsequently enters host cells through receptor-mediated endocytosis. Additional cell receptors may be directly or indirectly involved, including integrins. The cytoplasmic tails of ACE2 and integrins contain several predicted short linear motifs (SLiMs) that may facilitate internalization of the virus as well as its subsequent propagation through processes such as autophagy. Here, we measured the binding affinity of predicted interactions between SLiMs in the cytoplasmic tails of ACE2 and integrin β
MeSH term(s)	Amino Acid Sequence ; Angiotensin-Converting Enzyme 2/chemistry ; Angiotensin-Converting Enzyme 2/genetics ; Angiotensin-Converting Enzyme 2/physiology ; Autophagy/physiology ; COVID-19/virology ; Endocytosis/physiology ; Host Microbial Interactions/genetics ; Host Microbial Interactions/physiology ; Humans ; Integrin beta3/chemistry ; Integrin beta3/genetics ; Integrin beta3/physiology ; Models, Molecular ; Pandemics ; Peptide Fragments/chemistry ; Peptide Fragments/genetics ; Peptide Fragments/physiology ; Phosphorylation ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Sorting Signals/genetics ; Protein Sorting Signals/physiology ; Receptors, Virus/chemistry ; Receptors, Virus/genetics ; Receptors, Virus/physiology ; SARS-CoV-2/genetics ; SARS-CoV-2/pathogenicity ; SARS-CoV-2/physiology ; Virus Internalization
Chemical Substances	Integrin beta3 ; Peptide Fragments ; Protein Sorting Signals ; Receptors, Virus ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2021-01-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2417226-1
ISSN	1937-9145 ; 1945-0877
ISSN (online)	1937-9145
ISSN	1945-0877
DOI	10.1126/scisignal.abf1117
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Supertertiary protein structure affects an allosteric network.

Laursen, Louise / Kliche, Johanna / Gianni, Stefano / Jemth, Per

Proceedings of the National Academy of Sciences of the United States of America

2020 Volume 117, Issue 39, Page(s) 24294–24304

Abstract: The notion that protein function is allosterically regulated by structural or dynamic changes in proteins has been extensively investigated in several protein domains in isolation. In particular, PDZ domains have represented a paradigm for these studies, ...

Abstract	The notion that protein function is allosterically regulated by structural or dynamic changes in proteins has been extensively investigated in several protein domains in isolation. In particular, PDZ domains have represented a paradigm for these studies, despite providing conflicting results. Furthermore, it is still unknown how the association between protein domains in supramodules, consitituting so-called supertertiary structures, affects allosteric networks. Here, we experimentally mapped the allosteric network in a PDZ:ligand complex, both in isolation and in the context of a supramodular structure, and show that allosteric networks in a PDZ domain are highly dependent on the supertertiary structure in which they are present. This striking sensitivity of allosteric networks to the presence of adjacent protein domains is likely a common property of supertertiary structures in proteins. Our findings have general implications for prediction of allosteric networks from primary and tertiary structures and for quantitative descriptions of allostery.
MeSH term(s)	Allosteric Regulation ; Kinetics ; Ligands ; Mutation ; PDZ Domains ; Protein Conformation ; Proteins/chemistry ; Proteins/genetics ; Proteins/metabolism
Chemical Substances	Ligands ; Proteins
Language	English
Publishing date	2020-09-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2007201117
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Article ; Online: Large-scale phosphomimetic screening identifies phospho-modulated motif-based protein interactions.

Kliche, Johanna / Garvanska, Dimitriya Hristoforova / Simonetti, Leandro / Badgujar, Dilip / Dobritzsch, Doreen / Nilsson, Jakob / Davey, Norman E / Ivarsson, Ylva

Molecular systems biology

2023 Volume 19, Issue 7, Page(s) e11164

Abstract: Phosphorylation is a ubiquitous post-translation modification that regulates protein function by promoting, inhibiting or modulating protein-protein interactions. Hundreds of thousands of phosphosites have been identified but the vast majority have not ... ...

Abstract	Phosphorylation is a ubiquitous post-translation modification that regulates protein function by promoting, inhibiting or modulating protein-protein interactions. Hundreds of thousands of phosphosites have been identified but the vast majority have not been functionally characterised and it remains a challenge to decipher phosphorylation events modulating interactions. We generated a phosphomimetic proteomic peptide-phage display library to screen for phosphosites that modulate short linear motif-based interactions. The peptidome covers ~13,500 phospho-serine/threonine sites found in the intrinsically disordered regions of the human proteome. Each phosphosite is represented as wild-type and phosphomimetic variant. We screened 71 protein domains to identify 248 phosphosites that modulate motif-mediated interactions. Affinity measurements confirmed the phospho-modulation of 14 out of 18 tested interactions. We performed a detailed follow-up on a phospho-dependent interaction between clathrin and the mitotic spindle protein hepatoma-upregulated protein (HURP), demonstrating the essentiality of the phospho-dependency to the mitotic function of HURP. Structural characterisation of the clathrin-HURP complex elucidated the molecular basis for the phospho-dependency. Our work showcases the power of phosphomimetic ProP-PD to discover novel phospho-modulated interactions required for cellular function.
MeSH term(s)	Humans ; Proteomics ; Peptide Library ; Phosphorylation ; Clathrin
Chemical Substances	Peptide Library ; Clathrin
Language	English
Publishing date	2023-05-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2193510-5
ISSN	1744-4292 ; 1744-4292
ISSN (online)	1744-4292
ISSN	1744-4292
DOI	10.15252/msb.202211164
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions

Johanna Kliche / Dimitriya Hristoforova Garvanska / Leandro Simonetti / Dilip Badgujar / Doreen Dobritzsch / Jakob Nilsson / Norman E Davey / Ylva Ivarsson

Molecular Systems Biology, Vol 19, Iss 7, Pp n/a-n/a (2023)

2023

Abstract: Abstract Phosphorylation is a ubiquitous post‐translation modification that regulates protein function by promoting, inhibiting or modulating protein–protein interactions. Hundreds of thousands of phosphosites have been identified but the vast majority ... ...

Abstract	Abstract Phosphorylation is a ubiquitous post‐translation modification that regulates protein function by promoting, inhibiting or modulating protein–protein interactions. Hundreds of thousands of phosphosites have been identified but the vast majority have not been functionally characterised and it remains a challenge to decipher phosphorylation events modulating interactions. We generated a phosphomimetic proteomic peptide‐phage display library to screen for phosphosites that modulate short linear motif‐based interactions. The peptidome covers ~13,500 phospho‐serine/threonine sites found in the intrinsically disordered regions of the human proteome. Each phosphosite is represented as wild‐type and phosphomimetic variant. We screened 71 protein domains to identify 248 phosphosites that modulate motif‐mediated interactions. Affinity measurements confirmed the phospho‐modulation of 14 out of 18 tested interactions. We performed a detailed follow‐up on a phospho‐dependent interaction between clathrin and the mitotic spindle protein hepatoma‐upregulated protein (HURP), demonstrating the essentiality of the phospho‐dependency to the mitotic function of HURP. Structural characterisation of the clathrin‐HURP complex elucidated the molecular basis for the phospho‐dependency. Our work showcases the power of phosphomimetic ProP‐PD to discover novel phospho‐modulated interactions required for cellular function.
Keywords	clathrin ; phage display ; phosphomimetic mutation ; phosphorylation ; protein–protein interactions ; Biology (General) ; QH301-705.5 ; Medicine (General) ; R5-920
Subject code	612 ; 500
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: 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 / Kliche, Johanna / Jemth, Per / Sara Bergström Lind / Ivarsson, Ylva

Analytical biochemistry

2022 Volume 663, Page(s) 115017

Abstract: Low affinity and transient protein-protein interactions, such as short linear motif (SLiM)-based interactions, require dedicated experimental tools for discovery and validation. Here, we evaluated and compared biotinylated peptide pulldown and protein ... ...

Abstract	Low affinity and transient protein-protein interactions, such as short linear motif (SLiM)-based interactions, require dedicated experimental tools for discovery and validation. Here, we evaluated and compared biotinylated peptide pulldown and protein interaction screen on peptide matrix (PRISMA) coupled to mass-spectrometry (MS) using a set of peptides containing interaction motifs. Eight different peptide sequences that engage in interactions with three distinct protein domains (KEAP1 Kelch, MDM2 SWIB, and TSG101 UEV) with a wide range of affinities were tested. We found that peptide pulldown can be an effective approach for SLiM validation, however, parameters such as protein abundance and competitive interactions can prevent the capture of known interactors. The use of tandem peptide repeats improved the capture and preservation of some interactions. When testing PRISMA, it failed to provide comparable results for model peptides that successfully pulled down known interactors using biotinylated peptide pulldown. Overall, in our hands, we find that albeit more laborious, biotin-peptide pulldown was more successful in terms of validation of known interactions. Our results highlight that the tested affinity-capture MS-based methods for validation of SLiM-based interactions from cell lysates are suboptimal, and we identified parameters for consideration for method development.
MeSH term(s)	Kelch-Like ECH-Associated Protein 1/metabolism ; NF-E2-Related Factor 2/metabolism ; Peptides/chemistry ; Mass Spectrometry/methods ; Chromatography, Affinity
Chemical Substances	Kelch-Like ECH-Associated Protein 1 ; NF-E2-Related Factor 2 ; Peptides
Language	English
Publishing date	2022-12-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1110-1
ISSN	1096-0309 ; 0003-2697
ISSN (online)	1096-0309
ISSN	0003-2697
DOI	10.1016/j.ab.2022.115017
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Zs.A 389: Show issues

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Article ; Online: Cytoplasmic short linear motifs in ACE2 and integrin β3 link SARS-CoV-2 host cell receptors to endocytosis and autophagy

Kliche, Johanna / Ali, Muhammad / Ivarsson, Ylva

bioRxiv

Abstract: The spike protein of the SARS-CoV-2 interacts with angiotensin converting enzyme 2 (ACE2) and enters the host cell by receptor-mediated endocytosis. Concomitantly, evidence is pointing to the involvement of additional host cell receptors, such as ... ...

Abstract	The spike protein of the SARS-CoV-2 interacts with angiotensin converting enzyme 2 (ACE2) and enters the host cell by receptor-mediated endocytosis. Concomitantly, evidence is pointing to the involvement of additional host cell receptors, such as integrins. The cytoplasmic tails of ACE2 and integrin β3 contain a plethora of predicted binding motifs. Here, we confirm the functionality of some of these motifs through affinity measurements. The class I PDZ binding motif in the ACE2 cytoplasmic tail binds the first PDZ domain of the scaffold protein NHERF3. The clathrin-adaptor subunit AP2 μ2 interacts with an endocytic motif in the ACE2 with low affinity and the interaction is abolished by phosphorylation of Tyr781. Furthermore, the C-terminal region of integrin b3 contains a LC3-interacting region, and its interaction with ATG8 domains is enhanced by phosphorylation. Together, our data provides possible molecular links between host cell receptors and endocytosis and autophagy. One sentence summary Affinity measurements confirmed binding of short linear motifs in the cytoplasmic tails of ACE2 and integrin β3, thereby linking the receptors to endocytosis and autophagy.
Keywords	covid19
Publisher	BioRxiv; WHO
Document type	Article ; Online
DOI	10.1101/2020.10.06.327742
Database	COVID19

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Article ; Online: Proteome-scale mapping of binding sites in the unstructured regions of the human proteome.

Benz, Caroline / Ali, Muhammad / Krystkowiak, Izabella / Simonetti, Leandro / Sayadi, Ahmed / Mihalic, Filip / Kliche, Johanna / Andersson, Eva / Jemth, Per / Davey, Norman E / Ivarsson, Ylva

Molecular systems biology

2022 Volume 18, Issue 1, Page(s) e10584

Abstract: Specific protein-protein interactions are central to all processes that underlie cell physiology. Numerous studies have together identified hundreds of thousands of human protein-protein interactions. However, many interactions remain to be discovered, ... ...

Abstract	Specific protein-protein interactions are central to all processes that underlie cell physiology. Numerous studies have together identified hundreds of thousands of human protein-protein interactions. However, many interactions remain to be discovered, and low affinity, conditional, and cell type-specific interactions are likely to be disproportionately underrepresented. Here, we describe an optimized proteomic peptide-phage display library that tiles all disordered regions of the human proteome and allows the screening of ~ 1,000,000 overlapping peptides in a single binding assay. We define guidelines for processing, filtering, and ranking the results and provide PepTools, a toolkit to annotate the identified hits. We uncovered >2,000 interaction pairs for 35 known short linear motif (SLiM)-binding domains and confirmed the quality of the produced data by complementary biophysical or cell-based assays. Finally, we show how the amino acid resolution-binding site information can be used to pinpoint functionally important disease mutations and phosphorylation events in intrinsically disordered regions of the proteome. The optimized human disorderome library paired with PepTools represents a powerful pipeline for unbiased proteome-wide discovery of SLiM-based interactions.
MeSH term(s)	Binding Sites ; Humans ; Peptide Library ; Peptides/genetics ; Peptides/metabolism ; Protein Binding ; Proteome/genetics ; Proteome/metabolism ; Proteomics
Chemical Substances	Peptide Library ; Peptides ; Proteome
Language	English
Publishing date	2022-01-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2193510-5
ISSN	1744-4292 ; 1744-4292
ISSN (online)	1744-4292
ISSN	1744-4292
DOI	10.15252/msb.202110584
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Article ; Online: Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome

Caroline Benz / Muhammad Ali / Izabella Krystkowiak / Leandro Simonetti / Ahmed Sayadi / Filip Mihalic / Johanna Kliche / Eva Andersson / Per Jemth / Norman E Davey / Ylva Ivarsson

Molecular Systems Biology, Vol 18, Iss 1, Pp n/a-n/a (2022)

2022

Abstract: Abstract Specific protein–protein interactions are central to all processes that underlie cell physiology. Numerous studies have together identified hundreds of thousands of human protein–protein interactions. However, many interactions remain to be ... ...

Abstract	Abstract Specific protein–protein interactions are central to all processes that underlie cell physiology. Numerous studies have together identified hundreds of thousands of human protein–protein interactions. However, many interactions remain to be discovered, and low affinity, conditional, and cell type‐specific interactions are likely to be disproportionately underrepresented. Here, we describe an optimized proteomic peptide‐phage display library that tiles all disordered regions of the human proteome and allows the screening of ~ 1,000,000 overlapping peptides in a single binding assay. We define guidelines for processing, filtering, and ranking the results and provide PepTools, a toolkit to annotate the identified hits. We uncovered >2,000 interaction pairs for 35 known short linear motif (SLiM)‐binding domains and confirmed the quality of the produced data by complementary biophysical or cell‐based assays. Finally, we show how the amino acid resolution‐binding site information can be used to pinpoint functionally important disease mutations and phosphorylation events in intrinsically disordered regions of the proteome. The optimized human disorderome library paired with PepTools represents a powerful pipeline for unbiased proteome‐wide discovery of SLiM‐based interactions.
Keywords	intrinsically disordered regions ; peptides ; phage display ; protein–protein interactions ; short linear motifs ; Biology (General) ; QH301-705.5 ; Medicine (General) ; R5-920
Subject code	500
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities.

Nature communications

2021 Volume 12, Issue 1, Page(s) 6761

Abstract: Viral proteins make extensive use of short peptide interaction motifs to hijack cellular host factors. However, most current large-scale methods do not identify this important class of protein-protein interactions. Uncovering peptide mediated ... ...

Abstract	Viral proteins make extensive use of short peptide interaction motifs to hijack cellular host factors. However, most current large-scale methods do not identify this important class of protein-protein interactions. Uncovering peptide mediated interactions provides both a molecular understanding of viral interactions with their host and the foundation for developing novel antiviral reagents. Here we describe a viral peptide discovery approach covering 23 coronavirus strains that provides high resolution information on direct virus-host interactions. We identify 269 peptide-based interactions for 18 coronaviruses including a specific interaction between the human G3BP1/2 proteins and an ΦxFG peptide motif in the SARS-CoV-2 nucleocapsid (N) protein. This interaction supports viral replication and through its ΦxFG motif N rewires the G3BP1/2 interactome to disrupt stress granules. A peptide-based inhibitor disrupting the G3BP1/2-N interaction dampened SARS-CoV-2 infection showing that our results can be directly translated into novel specific antiviral reagents.
MeSH term(s)	Adaptor Proteins, Signal Transducing/metabolism ; DNA Helicases/metabolism ; Humans ; Integration Host Factors/metabolism ; Poly-ADP-Ribose Binding Proteins/metabolism ; RNA Helicases/metabolism ; RNA Recognition Motif Proteins/metabolism ; RNA-Binding Proteins/metabolism ; SARS-CoV-2/metabolism ; Virus Replication/physiology
Chemical Substances	Adaptor Proteins, Signal Transducing ; G3BP2 protein, human ; Integration Host Factors ; Poly-ADP-Ribose Binding Proteins ; RNA Recognition Motif Proteins ; RNA-Binding Proteins ; DNA Helicases (EC 3.6.4.-) ; G3BP1 protein, human (EC 3.6.4.12) ; RNA Helicases (EC 3.6.4.13)
Language	English
Publishing date	2021-11-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-26498-z
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