A5068594064- Protein Structure and Dynamics
- Enzyme Structure and Function
- Microbial Metabolic Engineering and Bioproduction
- thermodynamics and calorimetric analyses
- Enzyme Catalysis and Immobilization
- Alzheimer's disease research and treatments
- Computational Drug Discovery Methods
- RNA and protein synthesis mechanisms
- Parkinson's Disease Mechanisms and Treatments
- Bacteriophages and microbial interactions
- Bacterial Genetics and Biotechnology
- Machine Learning in Bioinformatics
- Scientific Computing and Data Management
- Protein purification and stability
- Fibroblast Growth Factor Research
- Lipid Membrane Structure and Behavior
- Enzyme Production and Characterization
- Microbial bioremediation and biosurfactants
- Metabolomics and Mass Spectrometry Studies
- Pancreatic function and diabetes
- Analytical Chemistry and Chromatography
- Advanced Proteomics Techniques and Applications
- Pharmaceutical and Antibiotic Environmental Impacts
- Microbial Community Ecology and Physiology
- Microbial Metabolites in Food Biotechnology
Technical University of Denmark
2023-2024
Masaryk University
2016-2024
St. Anne's University Hospital Brno
2017-2024
University Hospital Brno
2018-2024
International Clinical Research Center, St. Anne's University Hospital Brno
2021
RECETOX
2016-2020
John Wiley & Sons (United States)
2018
Hudson Institute
2018
Poor protein solubility hinders the production of many therapeutic and industrially useful proteins. Experimental efforts to increase are plagued by low success rates often reduce biological activity. Computational prediction expressibility in Escherichia coli using only sequence information could cost experimental studies enabling prioritization highly soluble proteins.A new tool for sequence-based expression E.coli, SoluProt, was created gradient boosting machine technique with TargetTrack...
Thermostability is an essential requirement for the use of enzymes in bioindustry. Here, we compare different protein stabilization strategies using a challenging target, stable haloalkane dehalogenase DhaA115. We observe better performance automated platforms FireProt and PROSS designing multiple-point mutations over introduction disulfide bonds strengthening intra- inter-domain contacts by silico saturation mutagenesis. reveal that was still compromised due to some destabilizing mutations....
Amyloid fibrils of proteins such as α-synuclein are a hallmark neurodegenerative diseases and much research has focused on their kinetics mechanisms formation. The question to the thermodynamic stability structures received less attention. Here, we newly utilize principle transient incomplete separation species in laminar flow combination with chemical depolymerization for quantification amyloid fibril stability. relative concentrations monomer at equilibrium determined through an
Recombinant proteins play pivotal roles in numerous applications including industrial biocatalysts or therapeutics. Despite the recent progress computational protein structure prediction, solubility and reduced aggregation propensity remain challenging attributes to design. Identification of aggregation-prone regions is essential for understanding misfolding diseases designing efficient protein-based technologies, as such has a great socio-economic impact. Here, we introduce AggreProt,...
Fibroblast growth factors (FGFs) serve numerous regulatory functions in complex organisms, and their corresponding therapeutic potential is of growing interest to academics industrial researchers alike. However, applications these proteins are limited due low stability. Here we tackle this problem using a generalizable computer-assisted protein engineering strategy create unique modified FGF2 with nine mutations displaying unprecedented stability uncompromised biological function. The data...
Studies of protein unfolding mechanisms are critical for understanding functions inside cells, de novo design as well defining the role misfolding in neurodegenerative disorders. Calorimetry has proven indispensable this regard recording full energetic profiles and permitting data fitting based on pathway models. While both kinetic thermodynamic stability analysed by varying scan rates reheating, latter is rarely used curve-fitting, leading to a significant loss information from experiments....
Abstract Background Apolipoprotein E (ApoE) ε4 genotype is the most prevalent risk factor for late-onset Alzheimer’s Disease (AD). Although ApoE4 differs from its non-pathological ApoE3 isoform only by C112R mutation, molecular mechanism of proteinopathy unknown. Methods Here, we reveal aggregation using a combination experimental and computational techniques, including X-ray crystallography, site-directed mutagenesis, hydrogen-deuterium mass spectrometry (HDX-MS), static light scattering...
Computational study of the effect drug candidates on intrinsically disordered biomolecules is challenging due to their vast and complex conformational space. Here, we developed a comparative Markov state analysis (CoVAMPnet) framework quantify changes in distribution dynamics biomolecule presence absence small organic candidate molecules. First, molecular trajectories are generated using enhanced sampling, molecule candidates, ensembles soft models (MSMs) learned for each system unsupervised...
Despite significant advances in the understanding of protein structure-function relationships, revealing folding pathways still poses a challenge due to limited number relevant experimental tools. Widely-used techniques, such as calorimetry or spectroscopy, critically depend on proper data analysis. Currently, there are only separate analysis tools available for each type experiment with model selection. To address this problem, we have developed CalFitter web server be unified platform...
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,...
Abstract Protein aggregation is a hallmark of multiple neurodegenerative diseases and great hindrance in recombinant protein production, handling, storage. Identification prone residues or regions (APRs) proteins their suppression by mutations powerful straightforward strategy for improving solubility yield, which significantly increases application potential. Towards this, we developed deep neural network based predictor that generates residue level profile one several input sequences. The...
The functionality of an enzyme depends on its unique three-dimensional structure, which is a result the folding process when nascent polypeptide follows funnel-like energy landscape to reach global minimum. Computer-encoded algorithms are increasingly employed stabilize native proteins for use in research and biotechnology applications. Here, we reveal example where computational stabilization monomeric α/β-hydrolase (Tm = 73.5 °C; ΔTm > 23 °C) affected protein landscape. introduction eleven...
Seed amplification assays (SAAs) are a promising avenue for the early diagnosis of neurodegenerative diseases However, when amplifying fibrils from patient-derived samples in commonly used format multiwell plates, it is currently highly challenging to accurately quantify aggregates. It therefore desirable transfer such into digital microemulsion droplets enable direct quantification aggregate numbers. To achieve conventional plate-based microfluidic format, effective seed needs be achieved...
<p><b>Motivation:</b> Poor protein solubility hinders the production of many therapeutic and industrially useful proteins. Experimental efforts to increase are plagued by low success rates often reduce biological activity. Computational prediction expressibility in <i>Escherichia coli</i> using only sequence information could cost experimental studies enabling prioritisation highly soluble proteins.</p> <p><b>Results:</b> A new tool for...
Haloalkane dehalogenases (HLDs) have recently been discovered in a number of bacteria, including symbionts and pathogens both plants humans. However, the biological roles HLDs these organisms are unclear. The development efficient HLD inhibitors serving as molecular probes to explore their function would represent an important step toward better understanding interesting enzymes. Here we report identification for this enzyme family using two different approaches. first builds on structures...
Abstract The importance of the quantitative description protein unfolding and aggregation for rational design stability or understanding molecular basis misfolding diseases is well established. Protein thermostability typically assessed by calorimetric spectroscopic techniques that monitor different complementary signals during unfolding. CalFitter webserver has already proved integral to deriving invaluable energy parameters global data analysis. Here, we introduce 2.0, which newly...
Protein folding, unfolding, and aggregation are important in a variety of biological processes intimately linked to "protein misfolding diseases". The ability perform experiments at different temperatures allows the extraction information regarding kinetics thermodynamics such processes. Unfortunately, conventional stopped-flow methods difficult implement, generate limited information, involve complex sample handling. To address this issue, we present temperature-controlled droplet-based...
ABSTRACT Computational study of the effect drug candidates on intrinsically disordered biomolecules is challenging due to their vast and complex conformational space. Here we developed a Comparative Markov State Analysis (CoVAMPnet) framework quantify changes in distribution dynamics biomolecule presence absence small organic candidate molecules. First, molecular trajectories are generated using enhanced sampling, molecule candidates, ensembles soft state models (MSMs) learned for each...
Abstract Fibroblast growth factors (FGFs) play numerous regulatory functions in complex organisms, and their corresponding therapeutic potential is of growing interest to academics industrial researchers alike. However, applications these proteins are limited due low stability vivo vitro . Here we tackle this problem using a generalizable computer-assisted protein engineering strategy create unique modified FGF2 with nine mutations displaying unprecedented uncompromised biological function.
Phase separated condensates can accelerate α-synuclein (α-Syn) amyloid fibril formation implicated in Parkinson′s disease pathogenesis. The effects of pathological modifications, i.e., truncations and familial mutations on the thermodynamics, material properties, extent aggregation within α-Syn remain elusive. Here, we quantitatively demonstrate that terminal significantly alter phase separation, while impart minimal effects. Spontaneous sol-gel transitions truncated variants could give rise...