Research Topics

 

MAIN RESEARCH TOPICS

  • Investigation of substrate spectrum of enzymes; analysis of reaction products.

  • Studies of kinetics and thermodynamics of enzyme's reduction and oxidation half-cycles.

  • Inhibition and deactivation study.

  • Enzyme immobilization.

  • Modeling reaction pathways with quantum chemical methods (QM and QM:MM).

  • Modeling enzyme-substrate complexes with molecular docking and molecular dynamics simulations.

  • Modeling enzymatic reactivity with Quantitative Structure Activity Relationship (QSAR) approach.

  • X-ray protein crystallography.

 

METHODS

  • Investigation of enzyme activities towards different substrates based on spectroscopic assay. Rapid mixing stopped flow kinetic measurements of half-cycle redox reaction in cooperation with the group of Prof. Grażyna Stochel from the Chemistry Department of the Jagiellonian University.

  • FPLC and electrophoresis techniques for enzyme purification.

  • LC-MS and GC-MS with RP and chiral columns for separation of reaction's products and identification of enzyme stereospecificity.

  • Liquid-liquid and solid phase extraction (SPE) of reaction mixtures for products purification.

  • Isothermal titration calorimetry for investigation of thermodynamics of enzyme reaction.

  • Quantum chemical modeling of enzyme active sites and reaction mechanisms

  • Molecular dynamics and docking simulations for enzyme-substrate complexes.

  • Prediction of biological activity with artificial neural networks and QSAR equations based on quantum chemical parameters.

  • X-ray crystallography.

 

 

SELECTED PROJECTS

EBDH

Ethylbenzene dehydrogenase (EBDH) is a key enzyme in mineralization of ethylbenzene by Aromatoleum aromaticum, i.e. a denitrifying bacterium related to the genera Azoarcus and Thauera. It is a molybdoenzyme belonging to the DMSO reductase family. Molybdenum enzymes feature a unique active site containing molybdenum atom, one or two pteridine cofactors and additional ligands (i.e. amino acid residues of Ser, Cys, SeCys or Asp and very often an oxo ligand).

Moco cofactor

Structure of EBDH

 

 

EBDH is a complex bacterial metalloenzyme (αβγ 164 kDa) containing monomolibdenum center (MoCo), iron-sulfur clusters and heme b559 prosthetic group. EBDH catalyses stereospecific hydroxylation of ethylbenzene to 1-(S)-phenylethanol.


HppE

(S)-2-hydroxypropylphosphonic acid epoxidase (HppE) is a bacterial enzyme catalyzing the ultimate step of biosynthesis of fosfomycin – a clinically useful antibiotic. HppE belongs to a group of nonheme iron enzymes, which means it binds in its active site iron ion without involvement of a porphyrin group. For the native HppE substrate – S-HPP, the catalytic reaction involves oxidative dehydrogenation coupled to formation of oxirane ring. Stereoisomer R-HPP undergoes simpler oxidation to a ketone product. Our studies aims to provide insights into the reaction mechanism of the enzymatic process of HppE.



 Reakcje katalizowane przez HppEStruktura miejsca aktywnego HppE 

       

Reactions catalyzed by HppE                                           Structure of the active site of HppE

 

Polyhydroxyalkanoates

Polyhydroxyalkanoates (PHAs) are biopolymers that represent one of the leading bioproduct sectors. PHAs represent a class of optically active biodegradable polyesters accumulated by numerous bacteria as isolated intracellular granules or as extracellular net-like structures. PHAs serve primarily as a reserve of carbon and energy. The chemical structure of PHA can be described as a linear formation of (R) -3-hydroxy acids, where the carboxyl group of one monomer forms an ester bond with the hydroxyl group of the adjacent monomer. PHA can be divided into several categories depending on the criterion used. Considering the size of the PHA monomer, it is divided into short (C3-C5; scl-PHA), medium (C6-C14; mcl-PHA) or long (> C14; lcl-PHA) chain polymers.

Chemical structure of PHA, where R1 and R2 are different side chains

Our research focuses on PHA polymers as well as their monomers. Ongoing work involves biocatalysis for the functionalization of PHA polymers and its monomers. We use enzymes from the group α / β-hydrolases - lipases, thanks to which we create new materials based on PHA. Bioplastic is subjected to enzymatic functionalization with selected drugs, on the other hand, monomers by biocatalysis are attached to sugar molecules. The research aims to create new materials for tissue regeneration, dressing materials, new anti-cancer drugs and surfactants.

Four research projects are carried out in a given topic:

  • NCN Sonata project "Biosynthesis of new lactose esters via lipases. Characteristics of their physicochemical and anti-cancer properties" No. 2015/17 / D / ST4 / 0051
  • Project Know "Biocatalytic synthesis of sugar esters"
  • NCBiR Leader project "New functionalized biopolymers for medical applications" No. 0090 / L-7/2015
  • TECHMATSTRATEG project "Technology for biorefining vegetable oils for the production of advanced composite materials" No. 407507/1 / NCBR / 2019