The laboratory focus on several topics for which there is a common interest in proteins with interesting synthetic, biotechnological or therapeutic potential. The first topic is the study of enzymes (glycosidases and transglycosidases) suitable for the synthesis of new glycoconjugates. Another group of proteins studied in our laboratory are plant and bacterial nucleases (DNases, RNases), which are further tested for anti-tumor effects. We also study proteins that stabilize lipid droplets in yeast, plants, or other model organisms (marine bacteria Alcanivorax borkumensis). Another topic is the study of enzymes from organisms living in permanently cold environments. We also use and work on developing molecular modeling methods to simulate slow and computationally demanding processes, such as protein folding or protein-ligand interactions.
Enzyme synthesis of glycoconjugates
Because of the unique and irreplaceable role of various glycosylated molecules in biologically important processes (both natural and pathological), it is of paramount interest to study their properties and the possibilities of their synthesis. Our laboratory is engaged in the use of enzymes for the synthesis of various oligosaccharides and glycoconjugates of potential importance for the food or pharmaceutical industry, using molecular genetics methods, recombinant protein expression and various chromatographic methods.
Nucleases and their anti-tumor effec
Nucleases have been studied for a long time because of their anti-tumor effects. So far, the main focus has been on animal nuclases. However, in our group we are focusing on enzymes from other sources, such as plants or bacteria. These enzymes are studied using molecular biology and protein engineering methods. Biological studies and crystallographic experiments are carried out in cooperation with the Institute of Plant Molecular Biology, the Institute of Physiology and Animal Genetics and the Biotechnology and Biomedical Center of the Academy of Sciences and Charles University in Vestec (BIOCEV).
Proteomics of lipid droplets
We are interested in lipid droplets and their life cycle, with special emphasis on the characterization of proteins associated with lipid droplets permanently or within a specific stage of the life cycle. Our goal is to contribute to the description of the life cycle of these specialized organelles and thus to the biotechnological use of both lipid droplets themselves (lipid and biofuel production, oil degradation, drug transport and immobilization systems) and their associated proteins (fusion anchors for industrial recombinant protein expression). As model organisms we use both prokaryotic (marine bacteria Alcanivorax borkumensis able to break down oil) and eukaryotic (plant Arabidopsis thaliana and yeast Saccharomyces cerevisiae) organisms.
We use and develop methods for molecular modeling of processes that are difficult to study using "conventional" methods. Conventionally, it is possible to simulate nano- to microseconds "from the life" of a protein, carbohydrate, or other biomolecule. However, many interesting processes take place in milliseconds or longer. We use metadynamics and other methods to simulate such slow processes. We have developed a new method called Flying Gaussians in our group (Šućur and Spiwok, 2016).
Enzymes from organisms living in permanently cold environments (e.g. mountain and polar regions) have significantly higher activity at low temperatures compared to enzymes from meso- and thermophilic sources. his property makes them interesting biocatalysts for low temperature applications. In our group we study cold-active enzymes (specifically β-galactosidase, cellulase, chitinase, amylase) using molecular biology, recombinant production, molecular modeling and (in collaboration with BIOCEV) protein crystallography.
Trapl D, Horvacanin I, Mareška V, Ozcelik F, Unal G, Spiwok V. Anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations. Front Mol Biosci 2019; 6
Kovaľová T, Koval' T, Benešová E, Vodičková P, Spiwok V, Lipovová P, Dohnálek J. Active site complementation and hexameric arrangement in the GH family 29; a structure–function study of α-l-fucosidase isoenzyme 1 from Paenibacillus thiaminolyticus. Glycobiology 2019; 29(1): 59-73.
Podzimek T, Přerovská T, Šantrůček J, Koval' T, Dohnálek J, Matoušek J, Lipovová P. N-glycosylation of tomato nuclease TBN1 produced in N. benthamiana and its effect on the enzyme activity. Plant Sci 2018; 276: 152-161.
Kříž P, Šućur Z, Spiwok V. Free-Energy Surface Prediction by Flying Gaussian Method: Multisystem Representation. J Phys Chem B 2017; 121(46): 10479-10483.
Hošek P, Toulcová D, Bortolato A ,Spiwok V. Altruistic Metadynamics: Multisystem Biased Simulation. J Phys Chem B 2016; 120(9): 2209-2215.
Hošek P, Spiwok V. Metadyn View: Fast web-based viewer of free energy surfaces calculated by metadynamics. Comput Phys Commun 2016; 198: 222-229.
Šućur Z, Spiwok V. Sampling Enhancement and Free Energy Prediction by Flying Gaussian Method. J Chem Theory Comput 2016; 12(9): 4644-4650.
Benešová E, Lipovová P, Krejzová J, Kovaľová T, Buchtová P, Spiwok V, Králová B. α-L-Fucosidase Isoenzyme iso2 from Paenibacillus thiaminolyticus. BMC Biotechnol 2015; 15: 36.
Spiwok V, Hošek P, Šućur Z. Enhanced Sampling Techniques in Biomolecular Simulations. Biotechnol Adv 2015; 6 pt 2: 1130-1140.
Purkrtová Z, Chardot T, Froissard M. N-terminus of Seed Caleosins is Essential for Lipid Droplet Sorting but not for Lipid Accumulation. Arch Biochem Biophys 2015; 579: 47-54.
Benešová E, Lipovová P, Dvořáková H, Králová B. α-L-fucosidase from Paenibacillus thiaminolyticus: Its Hydrolytic and Transglycosylation Abilities. Glycobiology 2013; 23(9): 1052-1065.
Koval' T, Lipovová P, Podzimek T, Matoušek J, Dušková J, Skálová T, Stěpánková A, Hašek J, Dohnálek J. Plant Multifunctional Nuclease TBN1 with Unexpected Phospholipase Activity: Structural Study and Reaction-Mechanism Analysis. Acta Crystallogr D Biol Crystallogr 2013; 69(Pt 2): 213-226.