Home Institute: Politechnika Śląska, Poland
Main supervisor: Artur Góra 
Co-Supervisors: Marco Fraaije (RUG)
Nikola Loncar (GECCO)
Required academic background: Chemistry, Biochemistry, Structural Biology, Computational Chemistry, Biophysics, Bioinformatics and related areas. Strong coding skills are an advantage.

This project will primarily focus on discovering and optimizing oxidoreductases involved in monomer functionalization. It will include searching enzyme libraries to identify promising folds with strong surface affinity (adhesive proteins) and develop pipelines for i) supporting a rational binding design through the development of methods based on Brownian Dynamics simulations, capable of predicting the binding affinity of enzymes to non-natural surfaces and ii) grafting active sites into the protein binding surface. The design processes will rely on the analysis of molecular dynamics simulations, employing an in-house developed method called AQUA-DUCT, which combines solvent tracking and a local density approach. Also, docking, Rosetta, and evolutionary analysis will be used. Through these versatile approaches, the binding affinity of enzymes to crystals, amorphous surfaces, and long polymer chains will be optimized and tested through secondments on both functionalized monomers from lignin (RUG) and polyamide (GECCO), with collaboration from UdG and BASF SE for pipeline development.   

Objectives:

  • Development of tools for prediction of enzymes binding affinity to bulky polymer surfaces and screening of the existing fold library for promising folds with high surface affinity.
  • Evolutionary analysis of the adaptation of adhesive proteins.
  • Improvement of the binding affinity of proteins via hot-spots identification using mix solvent MD.
  • Grafting of the hydrolytic sites into the protein binding surface.

Expected results:

  • Identification of the most suitable folds for further optimization of catalytic properties.
  • Develop the pipeline to support the rational binding design.
  • Development of the pipeline for active site grafting.