A5023686894- Protein Structure and Dynamics
- Genomics and Phylogenetic Studies
- Microbial Metabolic Engineering and Bioproduction
- RNA and protein synthesis mechanisms
- Enzyme Catalysis and Immobilization
- Advanced Proteomics Techniques and Applications
- Enzyme Structure and Function
- Machine Learning in Bioinformatics
- Evolution and Genetic Dynamics
- Genomics and Rare Diseases
- Glycosylation and Glycoproteins Research
- Enzyme Production and Characterization
- Protein Hydrolysis and Bioactive Peptides
- Plant Pathogens and Fungal Diseases
- Transgenic Plants and Applications
- Bacteriophages and microbial interactions
- Plant pathogens and resistance mechanisms
- Advanced Nanomaterials in Catalysis
- Bacterial biofilms and quorum sensing
- Innovative Microfluidic and Catalytic Techniques Innovation
- Fungal and yeast genetics research
- Bioinformatics and Genomic Networks
- Enzyme-mediated dye degradation
- Protein purification and stability
- Mycorrhizal Fungi and Plant Interactions
Masaryk University
2016-2025
St. Anne's University Hospital Brno
2017-2025
University Hospital Brno
2017-2025
Brno University of Technology
2016-2024
RECETOX
2016-2018
An important message taken from human genome sequencing projects is that the population exhibits approximately 99.9% genetic similarity. Variations in remaining parts of determine our identity, trace history and reveal heritage. The precise delineation phenotypically causal variants plays a key role providing accurate personalized diagnosis, prognosis, treatment inherited diseases. Several computational methods for achieving such have been reported recently. However, their ability to...
There is a continuous interest in increasing proteins stability to enhance their usability numerous biomedical and biotechnological applications. A number of silico tools for the prediction effect mutations on protein have been developed recently. However, only single-point with small are typically predicted existing be followed by laborious expression, purification, characterization. Here, we present FireProt, web server automated design multiple-point thermostable mutant that combines...
Natural enzymes are delicate biomolecules possessing only marginal thermodynamic stability. Poorly stable, misfolded, and aggregated proteins lead to huge economic losses in the biotechnology biopharmaceutical industries. Consequently, there is a need design optimized protein sequences that maximize stability, solubility, activity over wide range of temperatures pH values buffers different composition presence organic cosolvents. This has created great interest using computational methods...
Abstract The majority of naturally occurring proteins have evolved to function under mild conditions inside the living organisms. One critical obstacles for use in biotechnological applications is their insufficient stability at elevated temperatures or presence salts. Since experimental screening stabilizing mutations typically laborious and expensive, silico predictors are often used narrowing down mutational landscape. recent advances machine learning artificial intelligence further...
HotSpot Wizard 2.0 is a web server for automated identification of hot spots and design smart libraries engineering proteins’ stability, catalytic activity, substrate specificity enantioselectivity. The integrates sequence, structural evolutionary information obtained from 3 databases 20 computational tools. Users are guided through the processes selecting using four different protein strategies optimizing resulting library's size by narrowing down set substitutions at individual randomized...
Abstract Thermostable proteins find their use in numerous biomedical and biotechnological applications. However, the computational design of stable often results single-point mutations with a limited effect on protein stability. construction multiple-point mutants can prove difficult due to possibility antagonistic effects between individual mutations. FireProt protocol enables automated highly mutants. 2.0 builds top previously published web, retaining original functionality expanding it...
Abstract There is a great interest in increasing proteins’ stability to widen their usability numerous biomedical and biotechnological applications. However, native proteins cannot usually withstand the harsh industrial environment, since they are evolved function under mild conditions. Ancestral sequence reconstruction well-established method for deducing evolutionary history of genes. Besides its applicability discover most probable ancestors modern proteins, ancestral has proven be useful...
Abstract The quest to predict and understand protein evolution has been hindered by limitations on both the theoretical experimental fronts. Most existing models of are descriptive, rather than predictive, leaving final modifications in hands researchers. Existing techniques help probe evolutionary sequence space proteins, such as directed evolution, resource-intensive require specialised skills. We present successor predictor (SSP) an innovative solution. Successor is silico design method...
Stability is one of the most important characteristics proteins employed as biocatalysts, biotherapeutics, and biomaterials, role computational approaches in modifying protein stability rapidly expanding. We have recently identified stabilizing mutations haloalkane dehalogenase DhaA using phylogenetic analysis but were not able to reproduce effects these force-field calculations. Here we tested four different hypotheses explain molecular basis stabilization structural, biochemical,...
Protein solubility is an attractive engineering target primarily due to its relation yields in protein production and manufacturing. Moreover, better knowledge of the mutational effects on could connect several serious human diseases with aggregation. However, we have limited understanding structural determinants solubility, available data mostly been scattered literature. Here, present SoluProtMutDB - first database containing changes upon mutations. Our accommodates 33 000 measurements 17...
Abstract Protein evolution and protein engineering techniques are of great interest in basic science industrial applications such as pharmacology, medicine, or biotechnology. Ancestral sequence reconstruction (ASR) is a powerful technique for probing evolutionary relationships robust proteins with good thermostability broad substrate specificity. The following protocol describes the setting up execution an automated FireProt ASR workflow using dedicated web site. service allows inference...
Catalase-peroxidases (KatGs) are unique bifunctional oxidoreductases that contain heme in their active centers allowing both the peroxidatic and catalatic reaction modes. These originally bacterial enzymes broadly distributed among various fungi them to cope with reactive oxygen species present environment or inside cells. We used biophysical, biochemical, bioinformatics methods investigate differences between catalase-peroxidases originating thermophilic mesophilic from different habitats....
In this study, we focus on a detailed bioinformatics analysis of hyBpox genes, mainly within the genomes Sclerotiniaceae (Ascomycota, Leotiomycetes), which is specifically evolved fungal family necrotrophic host generalists and saprophytic or biotrophic specialists. Members genus Sclerotium produce only sclerotia no fruiting bodies spores. Thus, their physiological role for peroxidases remains open. A representative species, S. cepivorum, dangerous plant pathogen causing white rot in Allium...
Protein tunnels are essential in transporting small molecules into the active sites of enzymes. Tunnels' geometrical and physico-chemical properties influence transport process. The attractive hot spots for protein engineering drug development. However, studying ligand binding unbinding using experimental techniques is challenging, while silico methods come with their limitations, especially case resource-demanding virtual screening pipelines. Caver Web 1.2 a new version web server combining...
Abstract The quest to predict and understand protein evolution has been hindered by limitations on both the theoretical experimental fronts. Most existing models of are descriptive, rather than predictive, leaving final modifications in hands researchers. Existing techniques help probe evolutionary sequence space proteins, such as directed evolution, resource-intensive require specialised skills. We present Successor Sequence Predictor (SSP) an innovative solution. is silico method that...
Abstract Summary Protein design requires information about how mutations affect protein stability. Many web-based predictors are available for this purpose, yet comparing them or using en masse is difficult. Here, we present BenchStab, a console tool/Python package easy and quick execution of 19 result collection on list mutants. Moreover, the tool easily extensible with additional predictors. We created an independent dataset derived from FireProtDB evaluated 24 different prediction...