Proteins fold into a particular 3D shape which gives them a specific function in biological processes. Proteins misbehaving in these processes can lead to disease. By decoding the 3D shape of a protein, scientists can study how proteins function as well as design new molecules to control them when things go wrong. To study the structure of a protein you need to have a lot of it. Proteins are usually produced in the laboratory through bacterial expression, a process in which scientists can hijack the machinery of a bacterial cells and force them to make the protein they want. Some proteins, unfortunately, cannot be expressed easily due to tricky amino acid sequences within the protein.

Heparanase is a protein which cuts up heparin sulfate, an important component of the molecular “scaffolding” around cells. When heparanase slices up heparin sulfate, this scaffolding is degraded or remodelled. This process is known to be unregulated in diseases such as cancer, diabetes, and COVID-19, meaning that heparanase is an important target for new drugs. Heparanase has traditionally been hard to study, it does not express in bacterial cells easily and it is too large to produce by chemical synthesis.

Last year, PhD student Cassidy Whitefield with supervisor CI Colin Jackson, published their innovative research on the high-yielding production of a variant of heparanase. Their goal was to design a version of heparanase that would be easier to work with but would have the same properties as the natural protein. The research team used computational modelling to predict which amino acids would be important for the protein function and which could be swapped out. The program could also predict what overall effect swapping amino acids would likely have on the structure.

The version of heparanase that was designed by the computer, called HPSE P6, included 26 amino acid swaps. HPSE P6 could be expressed easily and showed virtually the same functional properties as the natural protein. The team also carefully studied the changes made to the protein, which provided insight into amino acid sequences important for protein folding and function.

This work by the Jackson lab will allow other researchers to produce and study heparanase to aid the design of new drugs to treat a range of diseases. The DNA of HPSE P6 has now been deposited into at addgene – a not-for-profit DNA repository, set up to accelerate science by freely sharing DNA worldwide, and has already been sent to over ten different laboratories around the world. Their work also contributes to the important field around the effect of amino acid sequence on protein structure and folding.  

Reference: https://pubs.rsc.org/en/content/articlelanding/2022/CB/D1CB00239B