Leandro Simonetti
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View article: Systematic Discovery of Motif-based Interactions of the Auxiliary Domains of USP Family Deubiquitinases
Systematic Discovery of Motif-based Interactions of the Auxiliary Domains of USP Family Deubiquitinases Open
The ubiquitin-specific proteases (USPs) family is the largest family of human deubiquitinating enzymes (DUBs). While most USPs are agnostic to polyubiquitin linkage-type, their substrate specificity is thought to be mediated by the recogni…
View article: Defining short linear motif binding determinants by phage display‐based deep mutational scanning
Defining short linear motif binding determinants by phage display‐based deep mutational scanning Open
Deep mutational scanning (DMS) has emerged as a powerful approach for evaluating the effects of mutations on binding or function. Here, we developed a DMS by phage display protocol to define the specificity determinants of short linear mot…
View article: Elucidation of short linear motif-based interactions of the MIT and rhodanese domains of the ubiquitin-specific protease 8
Elucidation of short linear motif-based interactions of the MIT and rhodanese domains of the ubiquitin-specific protease 8 Open
View article: Swapped Domain Orders in Zo-1 Pdz3 Fusion Proteins – Implications for Binding of Established and Novel Targets
Swapped Domain Orders in Zo-1 Pdz3 Fusion Proteins – Implications for Binding of Established and Novel Targets Open
View article: Defining short linear motif binding determinants by phage-based multiplexed deep mutational scanning
Defining short linear motif binding determinants by phage-based multiplexed deep mutational scanning Open
Deep mutational scanning (DMS) has emerged as a powerful approach for evaluating the effects of mutations on binding or function. Here, we developed a multiplexed DMS by phage display protocol to define the binding determinants of short li…
View article: Proteome-scale characterisation of motif-based interactome rewiring by disease mutations
Proteome-scale characterisation of motif-based interactome rewiring by disease mutations Open
Whole genome and exome sequencing are reporting on hundreds of thousands of missense mutations. Taking a pan-disease approach, we explored how mutations in intrinsically disordered regions (IDRs) break or generate protein interactions medi…
View article: ASXLs binding to the PHD2/3 fingers of MLL4 provides a mechanism for the recruitment of BAP1 to active enhancers
ASXLs binding to the PHD2/3 fingers of MLL4 provides a mechanism for the recruitment of BAP1 to active enhancers Open
The human methyltransferase and transcriptional coactivator MLL4 and its paralog MLL3 are frequently mutated in cancer. MLL4 and MLL3 monomethylate histone H3K4 and contain a set of uncharacterized PHD fingers. Here, we report a novel func…
View article: Benchmarking computational tools for de novo motif discovery
Benchmarking computational tools for de novo motif discovery Open
Background: Over the past twenty years, numerous motif discovery bioinformatic tools have been developed for discovering short linear motifs (SLiMs) from high-throughput experimental data on domain-peptide interactions. However, these tool…
View article: Benchmarking computational tools for de novo motif discovery (MEP-Bench datasets)
Benchmarking computational tools for de novo motif discovery (MEP-Bench datasets) Open
Supplementary material for the publication. Includes 3 files: Supplementary Table S2 [TAR.GZ]: Is a compilation of all results obtained from the benchmarking of 5 motif discovery tools and 7 alignment tools run over MEP-Bench, a set of ove…
View article: Benchmarking computational tools for de novo motif discovery (MEP-Bench datasets)
Benchmarking computational tools for de novo motif discovery (MEP-Bench datasets) Open
<p>Supplementary material for the publication. Includes 3 files:</p>\n<ol>\n<li><strong>Supplementary Table S2 [TAR.GZ]:</strong> Is a compilation of all results obtained from the benchmarking of 5 motif…
View article: Proteome-scale characterisation of motif-based interactome rewiring by disease mutations
Proteome-scale characterisation of motif-based interactome rewiring by disease mutations Open
Whole genome and exome sequencing are reporting on hundreds of thousands of missense mutations. Taking a pan-disease approach, we explored how mutations in the intrinsically disordered regions (IDRs) break or generate protein interactions …
View article: Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets
Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets Open
View article: AS ALTERAÇÕES HORMONAIS E O SEU IMPACTO NA IMPLANTODONTIA
AS ALTERAÇÕES HORMONAIS E O SEU IMPACTO NA IMPLANTODONTIA Open
<p>O tecido ósseo apresenta características como porosidade, anisotropia e heterogeneidade. Existem dois tipos principais de tecido ósseo: cortical e trabecular, sendo a porosidade do primeiro de 5 a 15% e a do s…
View article: Presenting technological workflows
Presenting technological workflows Open
View article: Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions
Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions Open
View article: Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs
Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs Open
View article: The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome
The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome Open
Short linear motifs (SLiMs) are a unique and ubiquitous class of protein interaction modules that perform key regulatory functions and drive dynamic complex formation. For decades, interactions mediated by SLiMs have accumulated through de…
View article: SLiM-binding pockets: an attractive target for broad-spectrum antivirals
SLiM-binding pockets: an attractive target for broad-spectrum antivirals Open
Short linear motif (SLiM)-mediated interactions offer a unique strategy for viral intervention due to their compact interfaces, ease of convergent evolution, and key functional roles. Consequently, many viruses extensively mimic host SLiMs…
View article: Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs
Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs Open
Library design of a the RIboVD phage library
View article: Evaluation of affinity-purification coupled to mass spectrometry approaches for capture of short linear motif-based interactions
Evaluation of affinity-purification coupled to mass spectrometry approaches for capture of short linear motif-based interactions Open
View article: Evaluation of affinity-purification coupled to mass spectrometry approaches for capture of short linear motif-based interactions
Evaluation of affinity-purification coupled to mass spectrometry approaches for capture of short linear motif-based interactions Open
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…
View article: Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets
Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets Open
The infection and replication cycle of all viruses depend on interactions between viral and host proteins. Each of these protein-protein interactions is therefore a potential drug target. These host-virus interactions often involve a disor…
View article: Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs
Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs Open
SUMMARY Viruses mimic host short linear motifs (SLiMs) to hijack and deregulate cellular functions. Studies of motif-mediated interactions therefore provide insight into virus-host dependencies, and reveal targets for therapeutic intervent…
View article: Large-scale identification of phospho-modulated motif-based protein-protein interactions
Large-scale identification of phospho-modulated motif-based protein-protein interactions Open
Phosphorylation is an extensively studied post-translation modification that regulates protein function by promoting, inhibiting or modulating protein-protein interactions. Deciphering which of the hundreds of thousands of phosphosites in …
View article: Extensive pan-viral mimicry of host short linear motifs hijack of the human interactome
Extensive pan-viral mimicry of host short linear motifs hijack of the human interactome Open
Code used for generating Figure 2D,E,F and supp Figure 2,3,4
View article: ProP-PD for proteome-wide motif-mediated interaction discovery
ProP-PD for proteome-wide motif-mediated interaction discovery Open
View article: Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome
Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome Open
View article: Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities
Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities Open
View article: Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities
Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities Open
Viral proteins make extensive use of short peptide interaction motifs to hijack cellular host factors. However, current methods do not identify this important class of protein-protein interactions. Uncovering peptide mediated interactions …
View article: Proteome-scale amino-acid resolution footprinting of protein-binding sites in the intrinsically disordered regions of the human proteome
Proteome-scale amino-acid resolution footprinting of protein-binding sites in the intrinsically disordered regions of the human proteome Open
Specific protein-protein interactions are central to all processes that underlie cell physiology. Numerous studies using a wide range of experimental approaches have identified tens of thousands of human protein-protein interactions. Howev…