Protein engineering to improve plastic-degrading enzymes

The Project

Plastics are durable materials that have allowed humanity to reduce the packaging costs of many products. However, this same durability becomes a significant environmental problem since most living organisms are not able to degrade plastic materials and obtain nourishment from them. Therefore, plastic residues end up in our natural ecosystems. Some bacteria, however, have developed some specialized enzymes that can degrade some of the most popular plastics.

Studying and improving these bacterial enzymes can influence new ways to dispose and recycle plastic residues, which would, in turn, reduce dramatically the environmental consequences of plastic accumulation in our oceans. In this project, we aim to study the enzyme machinery that allow the bacteria to degrade plastic, and design improved variants that can do so more efficiently.

By joining this project, you will learn how enzymes can perform their functions, by manipulating and changing their building blocks, the amino acids. In this way, you will be introduced to the boundless world of protein engineering and the tools from computational modeling supplies to impact real-world scenarios. For example, you will use a database, the Protein Data Bank, to visualize and manipulate the 3D structure of a protein. Moreover, several bioinformatic tools will be provided ​​to​​ study different aspects of the problem of interest.

First, you will learn how to prepare a protein in such a way that the simulation will reproduce the specified reactive conditions. Then, a Monte Carlo-based technique known as Protein Energy Landscape Exploration (PELE) will be used to simulate the interaction between several variants and the substrate to differentiate between active and inactive enzymes. Moreover, you will learn to analyze the data obtained from your simulations and draw conclusions.

Finally, you will apply these techniques for a real case. You will simulate the mechanism of a bacterial plastic-eating enzyme. Then, you will propose your variants to improve the plastic cleaning process, considering the data obtained in the previous simulations.  At the end, you will check your hypothesis comparing the simulations between​​ the ​​natural enzyme and ​​your​​ variant, and find out if your variant could be a potential candidate for plastic degradation!

Besides the experience of being a computational researcher, you will have the opportunity of visiting MareNostrum, which consists of a guided tour through the infrastructures of one of ​​the ​​largest​​ supercomputers ​​in ​​the ​​world.

Join this project and be part of a real enzyme engineering investigation!

Matching profiles

This project is addressed to students interested in Chemistry, Biology, Biochemistry, Computer Science or Bioinformatics

Learning objectives
  • Understand the chemistry behind plastic degradation
  • Basics of rational design in enzyme engineering
  • Get introduced to the most used bioinformatics tools in enzyme engineering
Required materials
  • Laptop (minimum hardware requirements: x86_64 compatible processor; 4 GB memory per core; 10 GB free disk space for software installation).
  • Mouse
  • (don't forget your plug and adaptor)
Coordinators of the project
Albert Cañellas Solé

Albert Cañellas Solé

  • Junior Research Engineer at BSC
  • Degree in Biotechnology by Universitat Rovira i Virgili (URV).
  • Degree in Computer Engineering by Universitat Rovira i Virgili (URV).
  • Master in Bioinformatics and Biostatistics by Universitat Oberta de Catalunya (UOC).
Mireia Martínez Sugrañes

Mireia Martínez Sugrañes

  • Enzyme characterization and engineering modeler at BSC
  • Degree in Biochemistry and Molecular Biology by Universitat Rovira i Virgili (URV).
  • Master  in Bioinformatics by Universitat Autònoma de Barcelona (UAB).

Ignasi Puch Giner

  • First stage researcher at BSC; PhD student in Computational and Applied Physics
  • MSc in Computational Modeling for Physics, Chesmitry and Biochemistry at University of Barcelona and UPC
  • BSc in Physics at University of Barcelona
The center

The Barcelona Supercomputing Center (BSC) is one of the world's leading supercomputing centres, with more than 900 employees, most of whom are researchers in four scientific departments: Computer Science, Life Sciences, Earth Sciences and Computational Applications for Science and Engineering.