A5083099713- Glycosylation and Glycoproteins Research
- Carbohydrate Chemistry and Synthesis
- Protein Structure and Dynamics
- Enzyme Production and Characterization
- Microbial Metabolites in Food Biotechnology
- Biochemical and Molecular Research
- Enzyme Structure and Function
- Polysaccharides and Plant Cell Walls
- Biofuel production and bioconversion
- Monoclonal and Polyclonal Antibodies Research
- Galectins and Cancer Biology
- Enzyme Catalysis and Immobilization
- Lysosomal Storage Disorders Research
- Diet, Metabolism, and Disease
- Escherichia coli research studies
- Microbial Metabolic Engineering and Bioproduction
- Molecular spectroscopy and chirality
- Bacterial Genetics and Biotechnology
- Porphyrin and Phthalocyanine Chemistry
- Polyamine Metabolism and Applications
- Studies on Chitinases and Chitosanases
- Catalysis for Biomass Conversion
- Invertebrate Immune Response Mechanisms
- Advanced Physical and Chemical Molecular Interactions
- Cell Adhesion Molecules Research
Institute of Chemistry of the Slovak Academy of Sciences
2012-2024
Slovak Academy of Sciences
2015-2024
Slovak Medical University
2022-2023
Central European Institute of Technology
2011-2021
Central European Institute of Technology – Masaryk University
2011-2021
Masaryk University
2011-2017
Carbohydrate – receptor interactions are an integral part of biological events. They play important role in many cellular processes, such as cell-cell adhesion, cell differentiation and in-cell signaling. Carbohydrates can interact with a by using several types intermolecular interactions. One the most is interaction carbohydrate's apolar aromatic amino acid residues, known dispersion or CH/π interaction. In study presented here, we attempted for first time to quantify how contributes more...
Abstract The molecular recognition of carbohydrates by proteins plays a key role in many biological processes including immune response, pathogen entry into cell, and cell–cell adhesion (e.g., cancer metastasis). Carbohydrates interact with mainly through hydrogen bonding, metal‐ion‐mediated interaction, non‐polar dispersion interactions. dispersion‐driven CH–π interactions (stacking) protein–carbohydrate has been underestimated for long time considering the polar to be main forces...
In higher eukaryotes, a variety of proteins are post-translationally modified by adding O-linked N-acetylglucosamine (GlcNAc) residue to serine or threonine residues. Misregulation O-GlcNAcylation is linked wide diseases, such as diabetes, cancer, and neurodegenerative including Alzheimer's disease. GlcNAc transfer catalyzed an inverting glycosyltransferase O-GlcNAc transferase (uridine diphospho-N-acetylglucosamine:polypeptide β-N-acetylaminyltransferase, OGT) that belongs the GT-B...
The inverting O-GlcNAc glycosyltransferase (OGT) is an important post-translation enzyme, which catalyzes the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine (UDP-GlcNAc) to hydroxyl group Ser/Thr cytoplasmic, nuclear, and mitochondrial proteins. In past, three different catalytic bases were proposed for reaction: His498, α-phosphate, Asp554. this study, we used hybrid quantum mechanics/molecular mechanics (QM/MM) Car–Parrinello molecular dynamics investigate reaction paths...
Abstract In this study we present the first systematic computational three‐dimensional scan of carbohydrate hydrophobic patches for ability to interact through CH/π dispersion interactions. The carbohydrates β‐ d‐ glucopyranose, mannopyranose and α‐ l‐ fucopyranose were studied in a complex with benzene molecule, which served as model interaction carbohydrate/protein complexes. 3D relaxed scans performed at SCC‐DFTB‐D level 3 757 grid points both sides. energy all was recalculated DFT‐D...
In this article we present the first systematic study of additive properties (i.e. degree additivity) carbohydrate–aromatic moiety CH–π dispersion interaction. The were studied on β-D-glucopyranose, β-D-mannopyranose and α-L-fucopyranose complexes with naphthalene molecule by comparing monodentate (single CH–π) bidentate (two complexes. All model optimized using DFT-D approach, at BP/def2-TZVPP level theory. interaction energies refined single point calculations highly correlated ab initio...
Here, we present a comparative structure–function study of nematode and plant core α1,3-fucosyltransferase based on deletion point mutations the coding regions Caenorhabditis elegans FUT-1 Arabidopsis thaliana FucTA (FUT11). In particular, our results reveal novel "first cluster motif" shared by both Lewis-type α1,3-fucosyltransferases GT10 family. To evaluate role conserved serine within this motif, residue was replaced with alanine in (S218) (S243). The S218A replacement completely...
The glycosylation of cell surface proteins plays a crucial role in multitude biological processes, such as adhesion and recognition. To understand the process protein glycosylation, reaction mechanisms participating enzymes need to be known. However, mechanism retaining glycosyltransferases has not yet been sufficiently explained. Here we investigated catalytic human isoform 2 glycosyltransferase polypeptide UDP-GalNAc transferase by coupling two different QM/MM-based approaches, namely...
The Golgi glycosyltransferase, N-acetylglucosaminyltransferase I (GnT-I), catalyzes the transfer of a GlcNAc residue from donor UDP-GlcNAc to C2-hydroxyl group mannose in trimannosyl core Man5GlcNAc2-Asn-X oligosaccharide. catalytic mechanism GnT-I was investigated using hybrid quantum mechanical/molecular mechanical (QM/MM) method with QM part containing 88 atoms treated density functional theory (DFT) at BP/TZP level. remaining parts complex, altogether 5633 atoms, were modeled AMBER...
SUMMARY We report on the homo‐ and hetero‐transglycosylation activities of HvXET3 HvXET4 xyloglucan xyloglucosyl transferases (XET; EC 2.4.1.207) from barley ( Hordeum vulgare L.), visualisation these in young roots using Alexa Fluor 488‐labelled oligosaccharides. discover that isozymes catalyse transglycosylation reactions with chemically defined donor acceptor substrates, specifically penta‐galacturonide [α(1‐4)GalA p ] 5 – homogalacturonan (pectin) fragment. This activity is supported by...
Abstract Lectins display a variety of strategies for specific recognition carbohydrates. In several lectin families from different origin, one or two calcium ions are involved in the carbohydrate binding site with direct coordination sugar hydroxyl groups. Our work implied molecular docking study involving set bacterial and animal calcium-dependant lectins order to compare ability three programs reproduce key carbohydrate-metal interactions. Flexible was performed using AutoDock, DOCK...
Abstract β1,6‐GlcNAc‐transferase (C2GnT) is an important controlling factor of biological functions for many glycoproteins and its activity has been found to be altered in breast, colon, lung cancer cells, leukemia the lymhomonocytes multiple sclerosis patients, leukocytes from diabetes conditions causing immune deficiency. The result action C2GnT core 2 structure that essential further elongation carbohydrate chains O ‐glycans. catalytic mechanism this metal‐ion‐independent...
Hybrid QM/MM computational studies can provide invaluable insight into the mechanisms of enzymatic reactions that be exploited for rational drug design. Various approaches are available such studies. However, their strengths and weaknesses may not immediately apparent. Using retaining glycosyltransferase ppGalNAcT2 as a case study, we compare different methodologies used to obtain reaction paths transition state information. Ab Initio MD using CPMD coupled with String Method is derive...
Protein–carbohydrate interactions are very often mediated by the stacking CH–π involving side chains of aromatic amino acids such as tryptophan (Trp), tyrosine (Tyr) or phenylalanine (Phe). Especially suitable for is Trp residue. Analysis PDB database shows 265 carbohydrate like ligands in 5 208 containing motives. An appropriate model system to study an interaction AAL lectin family where play a crucial role and thought be driving force binding. In this we present data showing novel finding...
Abstract Mycobacterium tuberculosis features a unique cell wall that protects the bacterium from external environment. Disruption of assembly is promising direction for novel anti‐tuberculotic drugs. A key component galactan, polysaccharide chain composed galactofuranose (Galf) units connected by alternating β‐(1–5) and β‐(1–6) linkages. The majority galactan biosynthesized bifunctional enzyme—galactofuranosyl transferase 2 (GlfT2). GlfT2 catalyzes two reactions: formation It was suggested...
Mycobacterium tuberculosis, one of the deadliest pathogens in human history, is distinguished by a unique, multilayered cell wall, which offers bacterium high level protection from attacks host immune system. The primary structure wall core, composed covalently linked peptidoglycan, branched heteropolysaccharide arabinogalactan, and mycolic acids, well known, numerous enzymes involved biosynthesis its components are characterized. biogenesis takes place at both cytoplasmic periplasmic faces...