A5084495294- Mass Spectrometry Techniques and Applications
- Analytical Chemistry and Chromatography
- Enzyme-mediated dye degradation
- 14-3-3 protein interactions
- Enzyme Production and Characterization
- Advanced Proteomics Techniques and Applications
- Biofuel production and bioconversion
- DNA Repair Mechanisms
- RNA regulation and disease
- Photosynthetic Processes and Mechanisms
- RNA modifications and cancer
- Chemical and Physical Studies
- Enzyme Catalysis and Immobilization
- Electrochemical sensors and biosensors
- Fungal Biology and Applications
- Ubiquitin and proteasome pathways
- Radioactive Decay and Measurement Techniques
- Light effects on plants
- Fungal and yeast genetics research
- bioluminescence and chemiluminescence research
- Glycosylation and Glycoproteins Research
- RNA and protein synthesis mechanisms
- Genetic factors in colorectal cancer
- Microtubule and mitosis dynamics
- Photodynamic Therapy Research Studies
University of Calgary
2023-2024
Czech Academy of Sciences, Institute of Microbiology
2020-2022
Czech Academy of Sciences
2020-2022
Charles University
2020-2022
Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent redox enzymes that cleave recalcitrant biopolymers such as cellulose, chitin, starch and hemicelluloses. Although LPMOs receive ample interest in industry academia, their reaction mechanism is not yet fully understood. Recent studies showed H2O2 a more efficient cosubstrate for the enzyme than O2, which could greatly affect utilization of industrial settings.We probe reactivity LPMO9C from cellulose-degrading fungus Neurospora...
Abstract Polymerase theta (Polθ) acts in DNA replication and repair, its inhibition is synthetic lethal BRCA1 BRCA2-deficient tumor cells. Novobiocin (NVB) a first-in-class inhibitor of the Polθ ATPase activity, it currently being tested clinical trials as an anti-cancer drug. Here, we investigated molecular mechanism NVB-mediated inhibition. Using hydrogen deuterium exchange-mass spectrometry (HX-MS), biophysical, biochemical, computational cellular assays, found NVB non-competitive ATP...
Abstract We present a hydrogen/deuterium exchange workflow coupled to tandem mass spectrometry (HX-MS 2 ) that supports the acquisition of peptide fragment ions alongside their precursors. The approach enables true auto-curation HX data by mining rich set deuterated fragments, generated collisional-induced dissociation (CID), simultaneously confirm ID and authenticate MS 1 -based deuteration calculations. high redundancy provided fragments confidence assessment deuterium calculations using...
Hydrogen/deuterium exchange mass spectrometry (HX-MS) is a method used to study solution-phase protein structure and dynamics. Despite its many applications, HX-MS limited in throughput because manual data analysis still the norm. We previously developed HX-MS2 technology add second dimension of deuteration promote automated processing. Data-independent acquisition (DIA) techniques enable this approach, but we require optimized methods for best performance. Using an Orbitrap Eclipse...
Hydrogen/deuterium exchange mass spectrometry (HX-MS) is a method used to study solution-phase protein structure and dynamics. Despite its many applications, HX-MS limited in throughput because manual data analysis still the norm. We previously developed HX-MS2 technology add second dimension of deuteration promote automated processing. Data-independent acquisition (DIA) techniques enable this approach, but we require optimized methods for best performance. Using an Orbitrap Eclipse...
A combination of covalent labeling techniques and mass spectrometry (MS) is currently a progressive approach for deriving insights related to the mapping protein surfaces or protein–ligand interactions. In this study, we mapped an interaction interface between DNA binding domain (DBD) FOXO4 element (DAF16) using fast photochemical oxidation proteins (FPOP). Residues involved in protein–DNA were identified bottom-up approach. To confirm findings avoid misinterpretation obtained data, caused...
The natural function of cellobiose dehydrogenase (CDH) to donate electrons from its catalytic flavodehydrogenase (DH) domain via cytochrome (CYT) lytic polysaccharide monooxygenase (LPMO) is an example a highly efficient extracellular electron transfer chain. To investigate the CYT movement in two occurring steps, CDHs ascomycete Neurospora crassa (NcCDHIIA and NcCDHIIB) five chimeric CDH enzymes created by swapping were studied combination with fungus' own LPMOs (NcLPMO9C NcLPMO9F). Kinetic...
Abstract Flavin mononucleotide (FMN) belongs to the group of very efficient endogenous photosensitizers producing singlet oxygen, 1 O 2 , but with limited ability be targeted. On other hand, in genetically-encoded photosensitizers, which can targeted by means various tags, efficiency FMN produce is significantly diminished due its interactions surrounding amino acid residues. Recently, an increase production yield buried a protein matrix was achieved decrease quenching cofactor excited...
Among all species, caspase‐2 (C2) is the most evolutionarily conserved caspase required for effective initiation of apoptosis following death stimuli. C2 activated through dimerization and autoproteolytic cleavage inhibited phosphorylation at Ser 139 164 , within linker between recruitment p19 domains zymogen, followed by association with adaptor protein 14‐3‐3, which maintains in its immature form procaspase (proC2). However, mechanism 14‐3‐3‐dependent inhibition activation remains unclear....
Lytic polysaccharide monooxygenases (LPMOs) are industrially important oxidoreductases employed in lignocellulose saccharification. Using advanced time-resolved mass spectrometric techniques, we elucidated the structural determinants for substrate-mediated stabilization of fungal LPMO9C from Neurospora crassa during catalysis. LPMOs require a reduction active-site copper catalytic activity. We show that NcLPMO9C leads to rearrangements and compaction around active site. However, longer...
Abstract We developed a hydrogen/deuterium exchange workflow coupled to tandem mass spectrometry (HX-MS 2 ) that supports the acquisition of peptide fragment ions alongside their precursors. The approach enables true auto-validation HX data by mining rich set deuterated fragments, generated collisional-induced dissociation (CID), simultaneously confirm ID and authenticate MS 1 -based deuteration calculations. high redundancy provided fragments confidence assessment deuterium calculations...
Among all species, caspase‐2 (C2) is the most evolutionarily conserved caspase required for effective initiation of apoptosis following death stimuli. C2 activated through dimerization and autoproteolytic cleavage inhibited phosphorylation at Ser 139 164 , within linker between recruitment p19 domains zymogen, followed by association with adaptor protein 14‐3‐3, which maintains in its immature form procaspase (proC2). However, mechanism 14‐3‐3‐dependent inhibition activation remains unclear....