Home Institute: Universitat de Girona, Spain
Main supervisor: Silvia Osuna
Co-Supervisors: Ulrich Schwaneberg (DWI) and
Valerio Ferrario (BASF) 
Required academic background: Chemistry, Biochemistry, Structural Biology, Computational Chemistry, Biophysics, Bioinformatics and related areas. Strong coding skills are an advantage.

This project will develop methods for simulating polymer peptide-based functionalized derivatives and polymer-enzyme interactions to understand polymer-degrading enzymes, particularly polyamides. It will involve creating models of polymer samples and polymer enzymes and evaluating their conformational dynamics and molecular interactions. Computational tools, including MD simulations and enhanced sampling techniques, will be employed to identify the potential polymer-enzyme interaction. The possible binding modes will be further characterized by GFN methods to better represent the polymer-enzyme interactions. Various analyses will be conducted at different conformational states, such as non-covalent interactions hydrogen-bond analysis, and the in-house SPM method will be used to identify key hot spots for generating a library of mutants to be screened experimentally. 

Objectives:

  • Develop computational approaches for the modeling of polymer substrates and peptide-based functionalized derivatives.

  • Develop computational pipelines for the evaluation of the potential polymer-enzyme binding modes and identify key positions for the design of polymer-degrading enzymes based on the evaluation of conformational dynamics, semi-empirical calculations, non-covalent interactions, and distal active site mutation prediction.
  • Develop new strategies to estimate the catalytic potential of the new computationally designed polymer-acting enzymes.

Expected results:

  • New computational approach for modeling polymer and peptide-based functionalized derivatives.

  • Computational pipeline based on Molecular Dynamics simulations, semiempirical calculations, non-covalent interaction analysis and correlation-based tools for identifying potential polymer-enzyme binding modes and identifying key positions for designing new enzymes acting on polymers.
  • New descriptors of catalytic potential of polymer-acting enzymes.