Research Topics

Loschmidt Laboratories consist of two experimental and two theoretical teams, which are collaborating tightly. Multiple rounds of computational protein design, experimental testing, and structural analyses are required for the development of novel strategies, software tools, artificial intelligence-based models, and lab-on-chips.

Zbynek Prokop’s Enzyme Kinetics and Microfluidics Team. We find answers to critical mechanistic questions related to enzyme catalysis and protein stability by comprehensive kinetic analysis based on advanced biophysical measurements and global data analysis using a combination of equation-based fitting and numerical integration methods. We apply these methods to a range of biological molecules (e.g., luciferases, haloalkane dehalogenases, fluorinases, fibroblast growth factors, thrombolytic enzymes, amyloid beta) and participate in the development of various biotechnologies for industrial, medical and environmental applications. We also develop modern microfluidics devices for high-throughput screening, combinatorial biophysical characterisation and deep kinetic and thermodynamic analysis of enzymes. The kinetic and thermodynamic data complement the structural and molecular modelling data to provide a detailed structure-function understanding essential for protein design and development of novel tools in protein engineering.

Martin Marek’s Structural Biology Team. We are an enthusiastic team of researchers who wish to understand the inner organisation and workings of biocatalysts. By combining molecular biology, biochemistry, X-ray crystallography and cryo-electron microscopy, we elucidate the molecular principles and evolution of biocatalytic processes that occur in living organisms. The obtained structural information is complemented with kinetic measurements, theoretical calculations, and further employed in protein engineering efforts. Such complex information will contribute to the development of future environmentally friendly technologies applicable in biomedicine, environmental protection, and agriculture. Our recent achievements include (i) delineation of the molecular basis underlying the hyperstabilization in haloalkane dehalogenases, (ii) unravelling mechanism of coelenterazine-powered bioluminescence at alpha/beta-hydrolase fold and (iii) visualisation of the bioluminescence resonance energy transfer.

David Bednar’s Molecular Modelling and Bioinformatics Team. Our team develops new concepts, methods, and software tools for computational protein design. We apply molecular docking, molecular mechanics, molecular dynamics, quantum mechanics, and structural bioinformatics to analyse structure-function relationships. We use bacterial haloalkane dehalogenases as the model enzymes for designing novel engineering strategies. The computational designs conducted on protein structures are materialised by site-directed mutagenesis or gene synthesis. We work in close partnership with the experimental teams, where the impact of mutations on protein structure and function are studied. We aim for rational and semi-rational engineering of biopharmaceutics for diagnostics and treatment of Alzheimer’s Disease and ischemic stroke.

Stanislav Mazurenko’s Artificial Intelligence Team. We broaden our knowledge of proteins by applying data-intensive machine learning methods to various types of protein data. We explore supervised, unsupervised, and semi-supervised approaches to decipher patterns in experimental measurements, protein sequences, structures, alignments, and computer simulations. Our goals are to gain insights into the underlying biophysical mechanisms and to create reliable and interpretable software tools for the design of improved protein variants. We leverage the data to provide all the teams with the support in making decisions, designing experiments, analysing data, and drawing conclusions.

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