A5090005259- Genomics and Phylogenetic Studies
- Mitochondrial Function and Pathology
- RNA and protein synthesis mechanisms
- Biochemical and Structural Characterization
- Metabolomics and Mass Spectrometry Studies
- Protein Structure and Dynamics
- Bacterial biofilms and quorum sensing
- Nicotinic Acetylcholine Receptors Study
- Photosynthetic Processes and Mechanisms
- Microbial Fuel Cells and Bioremediation
- bioluminescence and chemiluminescence research
- Malaria Research and Control
- Advanced Proteomics Techniques and Applications
- Bacterial Genetics and Biotechnology
- Machine Learning in Bioinformatics
- DNA Repair Mechanisms
- Coenzyme Q10 studies and effects
- Adipose Tissue and Metabolism
- Aquaculture disease management and microbiota
- vaccines and immunoinformatics approaches
- Mass Spectrometry Techniques and Applications
- Genetics, Bioinformatics, and Biomedical Research
- Cancer therapeutics and mechanisms
- Computational Drug Discovery Methods
- Scientific Computing and Data Management
Radboud University Nijmegen
2018-2024
Radboud University Medical Center
2018-2024
University Medical Center
2023
Radboud Institute for Molecular Life Sciences
2018-2021
Abstract Motivation Complexome profiling combines native gel electrophoresis with mass spectrometry to obtain the inventory, composition and abundance of multiprotein assemblies in an organelle. Applying complexome determine effect a mutation on protein complexes requires separating technical biological variations from caused by that mutation. Results We have developed COmplexome Profiling ALignment (COPAL) tool aligns multiple profiles each other. It includes all proteins two gels, using...
Protein complexes from the oxidative phosphorylation (OXPHOS) system are assembled with help of proteins called assembly factors. We here delineate function inner mitochondrial membrane protein TMEM70, in which mutations have been linked to OXPHOS deficiencies, using a combination BioID, complexome profiling and coevolution analyses. TMEM70 interacts complex I V for both loss results accumulation an intermediate followed by reduction next pathway. This indicates that has role stability...
Complexome profiling is an emerging 'omics' approach that systematically interrogates the composition of protein complexes (the complexome) a sample, by combining biochemical separation native with mass-spectrometry based quantitation proteomics. The resulting fractionation profiles hold comprehensive information on abundance and complexome, have high potential for reuse experimental computational researchers. However, lack central resource provides access to these data, reported adequate...
So-called ρ0 cells lack mitochondrial DNA and are therefore incapable of aerobic ATP synthesis. How adapt to survive ablation oxidative phosphorylation remains poorly understood. Complexome profiling analysis covered 1,002 proteins revealed changes in abundance organization numerous multiprotein complexes including previously not described assemblies. Beyond multiple subassemblies that would normally contain components encoded by DNA, we observed widespread reorganization the complexome....
Plasmodium species have a single mitochondrion that is essential for their survival and has been successfully targeted by antimalarial drugs. Most mitochondrial proteins are imported into this organelle, our picture of the proteome remains incomplete. Many data sources contain information about localization, including gene expression profiles, orthology to from other species, coevolutionary relationships, amino acid sequences, each with different coverage reliability. To obtain...
Knowledge of mutational patterns has expanded significantly, but a persistent challenge is to link these complex the underlying molecular mechanism or source DNA damage, especially when that damage endogenous and not driven by environmental mutagens. Technological advances now allow us catalogue mutation across tissues even closely related cell types, results are largely descriptive until we identify sources how they differ tissues. Here, combine mouse genetics, advanced sequencing,...
The 2020 European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) Developers' meeting was held from January 13th to 17th in Nyborg, Denmark. Among the participants were scientists as well developers working field of computational mass spectrometry (MS) and proteomics. 4-day program split between introductory keynote lectures parallel hackathon sessions. During latter, developed bioinformatics tools resources addressing outstanding needs community. hackathons allowed less...
Abstract Complexome profiling is an emerging ‘omics approach that systematically interrogates the composition of protein complexes (the complexome) a sample, by combining biochemical separation native with mass-spectrometry based quantitation proteomics. The resulting fractionation profiles hold comprehensive information on abundance and complexome, have high potential for reuse experimental computational researchers. However, lack central resource provides access to these data, reported...
Complexome profiling allows large-scale, untargeted, and comprehensive characterization of protein complexes in a biological sample using combined approach separating intact e.g., by native gel electrophoresis, followed mass spectrometric analysis the proteins resulting fractions. Over last decade, its application has resulted large collection complexome datasets. While computational methods have been developed for individual datasets, large-scale comparative complexomes from multiple...
Quorum sensing (QS) serves as a vital means of intercellular signalling in variety prokaryotes, which enables single cells to act multicellular configurations. The potential control community-wide responses has also sparked numerous recent biotechnological innovations. However, our capacity utilize communication is hindered due scarcity complementary systems and restricted comprehension interconnections between these caused by variations their dynamic range. In this study, we uniform...
Abstract Quorum sensing (QS) serves as a vital means of intercellular signalling in variety prokaryotes, which enables single cells to act multicellular configurations. The potential control community‐wide responses has also sparked numerous recent biotechnological innovations. However, our capacity utilize communication is hindered due scarcity complementary systems and restricted comprehension interconnections between these caused by variations their dynamic range. In this study, we...
Complexome profiling is an experimental approach to identify interactions by integrating native separation of protein complexes and quantitative mass spectrometry. In a typical complexome profile, thousands proteins are detected across typically ≤100 fractions. This relatively low resolution leads similar abundance profiles between that not necessarily interaction partners. To address this challenge, we introduce the Gaussian Interaction Profiler (GIP), mixture modeling-based clustering...
ABSTRACT Motivation Complexome profiling combines native gel electrophoresis with mass spectrometry to obtain the inventory, composition and abundance of multiprotein assemblies in an organelle. Applying complexome determine effect a mutation on protein complexes requires separating technical biological variations from caused by that mutation. Results We have developed COmplexome Profiling ALignment (COPAL) tool aligns multiple profiles each other. It includes all proteins two gels, using...
Abstract Plasmodium species have a single mitochondrion that is essential for their survival and has been successfully targeted by anti-malarial drugs. Most mitochondrial proteins are imported into this organelle our picture of the proteome remains incomplete. Many data sources contain information about localization, including gene expression profiles, orthology to from other species, co-evolutionary relationships, amino acid sequences, each with different coverage reliability. To obtain...
Abstract Complexome profiling allows large-scale, untargeted, and comprehensive characterization of protein complexes in a biological sample using combined approach separating intact e.g., by native gel electrophoresis, followed mass spectrometric analysis the proteins resulting fractions. Over last decade, its application has resulted large collection complexome datasets. While computational methods have been developed for individual datasets, large-scale comparative complexomes from...
Graphical Abstract The wide chemical diversity in bacterial languages is explored the Research Article by Markus B. Linder et al. (e202314469). structural similarities were mapped theoretically and sets of both closely related widely diverging ligand structures experimentally investigated. results suggest that quorum sensing ligands can be used as a starting point to predict non-cognate binding intercellular signalling systems. Orthogonal systems could significantly advance our engineering...
Abstract Protein complexes from the oxidative phosphorylation (OXPHOS) system are assembled with help of proteins called assembly factors. We here delineate function inner mitochondrial membrane protein TMEM70, in which mutations have been linked to OXPHOS deficiencies, using a combination BioID, complexome profiling and coevolution analyses. TMEM70 interacts complex I V for both loss results accumulation an intermediate followed by reduction next pathway. This indicates that has role...