A5074629805- Mass Spectrometry Techniques and Applications
- Advanced Proteomics Techniques and Applications
- Protease and Inhibitor Mechanisms
- Enzyme Structure and Function
- Liver Disease Diagnosis and Treatment
- Protein Structure and Dynamics
- Epigenetics and DNA Methylation
- Metabolomics and Mass Spectrometry Studies
- Genomics and Chromatin Dynamics
- Bacterial Genetics and Biotechnology
- HIV Research and Treatment
- RNA and protein synthesis mechanisms
- Blood Coagulation and Thrombosis Mechanisms
- Advanced biosensing and bioanalysis techniques
- vaccines and immunoinformatics approaches
- Glycosylation and Glycoproteins Research
- Liver Disease and Transplantation
- Analytical Chemistry and Chromatography
- DNA Repair Mechanisms
- Cell Adhesion Molecules Research
- interferon and immune responses
- Pharmaceutical industry and healthcare
- Sesquiterpenes and Asteraceae Studies
- NF-κB Signaling Pathways
- Calpain Protease Function and Regulation
University of Southern Denmark
2012-2024
Svendborg Sygehus
2020-2024
Odense University Hospital
2022-2024
University of California, San Diego
2016
Norwegian Institute of Bioeconomy Research
2011-2014
Ontario Institute for Cancer Research
2009
Hospital for Sick Children
2009
Radboud University Nijmegen
2009
University of Toronto
2009
Chromatin structure and function is influenced by histone posttranslational modifications. SET8 (also known as PR-Set7 SETD8) a methyltransferase that monomethylates histonfe H4-K20. However, for in mammalian cell proliferation has not been determined. We show small interfering RNA inhibition of expression leads to decreased accumulation cells S phase. This accompanied DNA double-strand break (DSB) induction recruitment the repair proteins replication protein A, Rad51, 53BP1 damaged regions....
Epigenome profiling has led to the paradigm that promoters of active genes are decorated with H3K4me3 and H3K9ac marks. To explore epigenome Plasmodium falciparum asexual stages, we performed MS analysis histone modifications found a general preponderance H3/H4 acetylation H3K4me3. ChIP-on-chip H3, H3K4me3, H3K9me3, from asynchronous parasites revealed an extensively euchromatic heterochromatin restricted variant surface antigen gene families (VSA) number hitherto unlinked VSA. Remarkably,...
Post-translational modifications (PTMs) of histone tails play a key role in epigenetic regulation gene expression range organisms from yeast to human; however, little is known about proteins the parasite that causes malaria humans, Plasmodium falciparum. We characterized P. falciparum PTMs using advanced mass spectrometry driven proteomics. Acid-extracted were resolved SDS-PAGE, in-gel trypsin digested, and analyzed by reversed-phase LC-MS/MS. Through combination Q-TOF LTQ-FT we obtained...
The eukaryotic cell cycle is regulated by multiple ubiquitin-mediated events, such as the timely destruction of cyclins and replication licensing factors. histone H4 methyltransferase SET8 (Pr-Set7) required for chromosome compaction in mitosis maintenance genome integrity. In this study, we show that targeted degradation during S phase CRL4(CDT2) ubiquitin ligase a proliferating nuclear antigen (PCNA)–dependent manner. requires conserved degron responsible its interaction with PCNA...
Protein and peptide mass analysis amino acid sequencing by spectrometry is widely used for identification annotation of post-translational modifications (PTMs) in proteins. Modification-specific increments, neutral losses or diagnostic fragment ions spectra provide direct evidence the presence modifications, such as phosphorylation, acetylation, methylation glycosylation. However, commonly database search engines are not always practical exhaustive searches multiple concomitant missed...
Given the complexity of mammalian proteome, high-resolution separation technologies are required to achieve comprehensive proteome coverage and enhance detection low-abundance proteins. Among several technologies, Multidimensional Protein Identification Technology (MudPIT) enables on-line highly complex peptide mixtures directly coupled with mass spectrometry-based identification. Here, we present a variation traditional MudPIT protocol, combining sensitive chromatography using nanoflow...
Mass spectrometry has become a valuable method for studying structural dynamics of proteins in solution by measuring their backbone amide hydrogen/deuterium exchange (HDX) kinetics. In typical experiment one or more are incubated deuterated buffer at physiological conditions. After given period deuteration, the reaction is quenched acidification (pH 2.5) and cooling (0 °C) protein (or digest thereof) analyzed mass spectrometry. The unavoidable loss deuterium (back-exchange) that occurs under...
Protein glycosylation is the most frequent post-translational modification and present on more than 50% of eukaryotic proteins. Glycosylation covers a wide subset modifications involving many types complex oligosaccharide structures, making structural analysis glycoproteins their glycans challenging for analytical techniques. Hydrogen/deuterium exchange monitored by mass spectrometry sensitive technique investigation protein conformational dynamics heterogeneous proteins in solution....
Tandem mass spectrometry (MS/MS) is a powerful tool for characterization of post-translationally modified proteins, including ε-N-acetyllysine-containing species. Previous reports indicate that ε-N-acetyllysine immonium ions are useful marker peptides containing ε-N-acetyllysine, but the specificity and sensitivity these assignment lysine acetylation by MS/MS have not been studied in detail. We investigated data sets 172 tryptic 268 nonacetylated to establish utility reliability...
RNA aptamers, selected from large synthetic libraries, are attracting increasing interest as protein ligands, with potential uses prototype pharmaceuticals, conformational probes, and reagents for specific quantification of levels in biological samples. Very little is known, however, about their effects on conformation dynamics. We have employed hydrogen/deuterium exchange (HDX) mass spectrometry to study the effect aptamers structural flexibility serpin plasminogen activator inhibitor-1...
The native fold of plasminogen activator inhibitor 1 (PAI-1) represents an active metastable conformation that spontaneously converts to inactive latent form. Binding the somatomedin B domain (SMB) endogenous cofactor vitronectin PAI-1 delays transition state and increases thermal stability protein dramatically. We have used hydrogen/deuterium exchange mass spectrometry assess inherent structural flexibility monitor changes induced by SMB binding. Our data show core consisting β-sheet is...
Abstract The metastability of the native fold makes serpin (serine protease inhibitor) proteins prone to pathological conformational change, often by insertion an extra β‐strand into central β‐sheet A. How this is made possible a hitherto unresolved question. By use advanced hydrogen/deuterium‐exchange mass spectrometry (HDX‐MS) it shown that plasminogen activator inhibitor 1 (PAI‐1) transiently unfolds under condition, on second‐to‐minute time scale. unfolding regions comprise 5A as well...
Hydrogen/deuterium exchange monitored by mass spectrometry (HDX-MS) has become an important method to study the structural dynamics of proteins. However, glycoproteins represent a challenge traditional HDX-MS workflow for determining deuterium uptake protein segments that contain glycan. We have recently demonstrated utility glycosidase PNGase A enable analysis N-glycosylated regions. Here, we investigated use acidic H+, which pH optimum at 2.6, efficiently deglycosylate N-linked...
Ultraviolet photodissociation (UVPD) has recently been introduced as an ion activation method for the determination of single-residue deuterium levels in H/D exchange tandem mass spectrometry experiments. In this regard, it is crucial to know which fragment types can be utilized purpose. UVPD yields rich product spectra where all possible backbone (a/x, b/y, and c/z) are typically observed. Here we provide a detailed investigation level scrambling upon peptide probe P1 (HHHHHHIIKIIK) using...
Plasminogen activator inhibitor type 1 (PAI-1) regulates the fibrinolysis pathway by inhibiting protease activity of plasminogen activators. PAI-1 works in concert with vitronectin (VN), an extracellular protein that aids localization active to tissues. The Peterson laboratory demonstrated Cu(II) and other transition metals modulate stability PAI-1, exhibiting effects are dependent on presence or absence somatomedin B (SMB) domain VN. study presented here dissects changes molecular dynamics...
Abstract Both function and dysfunction of serine protease inhibitors (serpins) involve massive conformational change in their tertiary structure but the dynamics facilitating these events remain poorly understood. We have studied dynamic preludes to serpin plasminogen activator inhibitor 1 (PAI-1). report first multi-microsecond atomistic molecular simulations PAI-1 compare data with experimental hydrogen/deuterium-exchange (HDXMS). The reveal notable flexibility helices D, E F major...
Antithrombin deficiency is associated with increased risk of venous thrombosis. In certain families, this condition caused by pathogenic polymerization mutated antithrombin in the blood. To facilitate future development pharmaceuticals against polymerization, an improved understanding polymerogenic intermediates crucial. However, X-ray crystallography these severely hampered difficulty obtaining well-diffracting crystals transient and heterogeneous noncovalent protein assemblies....