A5038145734- Ubiquitin and proteasome pathways
- RNA and protein synthesis mechanisms
- Trypanosoma species research and implications
- Monoclonal and Polyclonal Antibodies Research
- Advanced Proteomics Techniques and Applications
- Bioinformatics and Genomic Networks
- interferon and immune responses
- Bacteriophages and microbial interactions
- vaccines and immunoinformatics approaches
- RNA modifications and cancer
- Chemical Synthesis and Analysis
- Glycosylation and Glycoproteins Research
- RNA Research and Splicing
- Cellular transport and secretion
- Distributed and Parallel Computing Systems
- Model-Driven Software Engineering Techniques
- Biochemical and Molecular Research
- HIV/AIDS drug development and treatment
- Synthesis and Biological Evaluation
- Gene expression and cancer classification
- SARS-CoV-2 and COVID-19 Research
- Toxin Mechanisms and Immunotoxins
- Protein Structure and Dynamics
- Microbial Natural Products and Biosynthesis
- Genomic variations and chromosomal abnormalities
Uppsala University
2020-2025
BMC Software (United States)
2024
Administración Nacional de Laboratorios e Institutos de Salud
2017
Consejo Nacional de Investigaciones Científicas y Técnicas
2010-2015
Experimental Medicine and Biology Institute
2010
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 protein-protein interactions. Uncovering mediated interactions provides both a molecular understanding viral with their and the foundation for developing novel antiviral reagents. Here we describe discovery approach covering 23 coronavirus strains that high resolution information on direct virus-host We 269...
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, reveal targets for therapeutic intervention. Here, we describe the pan-viral discovery 1712 SLiM-based using a phage peptidome tiling intrinsically disordered protein regions 229 RNA viruses. We find mimicry SLiMs be ubiquitous viral strategy, novel proteins hijacked by viruses, identify pathways frequently...
The rise in the world demand for food poses a challenge to our ability sustain soil fertility and sustainability. increasing use of no-till agriculture, adopted many areas as an alternative conventional farming, may contribute reduce erosion soils increase carbon pool. However, advantages agriculture are jeopardized when its is linked expansion crop monoculture. aim this study was survey bacterial communities find indicators quality related contrasting management under farming. Four sites...
Abstract Phosphorylation is a ubiquitous post‐translation modification that regulates protein function by promoting, inhibiting or modulating protein–protein interactions. Hundreds of thousands phosphosites have been identified but the vast majority not functionally characterised and it remains challenge to decipher phosphorylation events We generated phosphomimetic proteomic peptide‐phage display library screen for modulate short linear motif‐based The peptidome covers ~13,500...
The virus life cycle depends on host-virus protein-protein interactions, which often involve a disordered protein region binding to folded domain. Here, we used proteomic peptide phage display (ProP-PD) identify peptides from the intrinsically regions of human proteome that bind domains encoded by SARS-CoV-2 genome. Eleven proteins were found 281 proteins, and affinities 31 interactions involving eight determined (K
Many protein–protein interactions are mediated by short linear motifs (SLiMs; 3–10 amino acid stretches; typically found in intrinsically disordered regions; low-to-mid micromolar affinities). The human proteome is expected to contain tens of thousands SLiMs. However, date only ~3000 SLiM instances have been discovered. field required a scalable and accurate experimental approach tackle discovery. Proteomic peptide-phage display (ProP-PD) based on classical phage updated with combination...
ADVERTISEMENT RETURN TO ISSUEPREVFirst ReactionsNEXTGenetically Encoded Cyclic Peptide Phage Display LibrariesPhage display of self-cycling peptides as an efficient and scalable approach to discover macrocyclic inhibitors protein−protein interactions.Leandro SimonettiLeandro SimonettiDepartment Chemistry—BMC, Uppsala University, 751 23, SwedenMore by Leandro Simonettihttp://orcid.org/0000-0003-1283-9770 Ylva IvarssonYlva IvarssonDepartment SwedenE-mail: [email protected]More IvarssonCite...
Low affinity and transient protein-protein interactions, such as short linear motif (SLiM)-based require dedicated experimental tools for discovery validation. Here, we evaluated compared biotinylated peptide pulldown protein interaction screen on matrix (PRISMA) coupled to mass-spectrometry (MS) using a set of peptides containing motifs. Eight different sequences that engage in interactions with three distinct domains (KEAP1 Kelch, MDM2 SWIB, TSG101 UEV) wide range affinities were tested....
NKX2-5 is a homeodomain transcription factor that plays crucial role in heart development. It the first gene where single genetic variant (GV) was found to be associated with congenital diseases humans. In this study, we carried out comprehensive survey of GVs build unified, curated, and updated compilation all available GVs. We retrieved total 1,380 unique From these, 970 had information on their frequency general population 143 have been linked pathogenic phenotypes vitro effect...
The human methyltransferase and transcriptional coactivator MLL4 its paralog MLL3 are frequently mutated in cancer. monomethylate histone H3K4 contain a set of uncharacterized PHD fingers. Here, we report novel function the PHD2 PHD3 (PHD2/3) fingers that bind to ASXL2, component Polycomb repressive H2AK119 deubiquitinase (PR-DUB) complex. structure PHD2/3 complex with MLL-binding helix (MBH) ASXL2 mutational analyses reveal molecular mechanism which is conserved homologous ASXL1 ASXL3....
Abstract The large subunit of the eukaryotic ribosome possesses a long and protruding stalk formed by ribosomal P proteins. This structure is involved in translation step protein synthesis through interaction with elongation factor 2 (EF‐2). Trypanosoma cruzi complex composed four proteins about 11 kDa, TcP1α, TcP1β, TcP2α, TcP2β fifth TcP0 34 kDa. In previous work, yeast two‐hybrid (Y2H) protein–protein map T. was generated. order to gain new insight into assembly stalk, complete generated...
Abstract 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 thousands human interactions. However, many remain be discovered, and low affinity, conditional type-specific likely disproportionately under-represented. Moreover, for most known the binding regions uncharacterized. We previously developed proteomic peptide phage display (ProP-PD), method simultaneous...
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, reveal targets for therapeutic intervention. Here, we describe the pan-viral discovery 1,712 SLiM-based using a phage peptidome tiling intrinsically disordered protein regions 229 RNA viruses. We find mimicry SLiMs be ubiquitous viral strategy, novel proteins hijacked by viruses, identify pathways...
To deeply understand the role of antibodies in context Trypanosoma cruzi infection, we decided to characterize A2R1, a parasite antibody selected from single-chain variable fragment (scFv) phage display libraries constructed B cells chronic Chagas heart disease patients. Immunoblot, ELISA, cytometry, immunofluorescence and immunohistochemical assays were used A2R1 reactivity. identify target, performed an immunoprecipitation two-dimensional electrophoresis coupled mass spectrometry confirmed...
The ribosomal P proteins are located on the stalk of large subunit and play a critical role during elongation step protein synthesis. single chain recombinant antibody C5 (scFv C5) directed against C-terminal region Trypanosoma cruzi P2β (TcP2β) recognizes conserved end all T. proteins. Although this is highly among different species, surface plasmon resonance analysis showed that scFv possesses very low affinity for corresponding mammalian epitope, despite having only one amino-acid change....
Abstract Viral proteins make extensive use of short peptide interaction motifs to hijack cellular host factors. However, current methods do not identify this important class protein-protein interactions. Uncovering mediated interactions provides both a molecular understanding viral with their and the foundation for developing novel antiviral reagents. Here we describe scalable discovery approach covering 229 RNA viruses that high resolution information on direct virus-host We 269...
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 are generally evaluated individually and mostly using synthetic that do not accurately capture context observed within proteomic data. Consequently, it is unclear how perform in real-world use cases they compared to each other. Results: Here, we benchmarked...