Lasso peptides are natural products made by bacteria. Their unusual lasso shape endows them with remarkable stability, protecting them from extreme conditions. In a new study, published in Nature Chemical Biology, researchers have constructed and tested models for how these peptides are made and demonstrated how this information might be used to advance lasso peptide-based drugs into the clinic.
"Lasso peptides are interesting because they are basically linear molecules that have been tied into a slip knot-like shape," said Susanna Barrett, a graduate student in the Mitchell lab (MMG). "Due to their incredible stability and engineerability, they have a lot of potential as therapeutics. They have also been shown to have antibacterial, antiviral, and anti-cancer properties."
Lasso peptides are ribosomally synthesized and post-translationally modified molecules. The peptide chains are formed from joining amino acids together in the form of a string, which is done by the ribosome. Two enzymes, a peptidase and a cyclase, then collaborate to convert a linear precursor peptide into the distinctive knotted lasso structure. Since their discovery over three decades ago, scientists have been trying to understand how the cyclase folds the lasso peptide.
"One of the major challenges of solving this problem has been that the enzymes are difficult to work with. They are generally insoluble or inactive when you attempt to purify them," Barrett said.
One rare counterexample is fusilassin cyclase, or FusC, which the Mitchell lab characterized in 2019. Former group members were able to purify the enzyme, and since then, it has served as a model to understand the lasso knot-tying process. Yet, the structure of FusC remained unknown, making it impossible to understand how the cyclase interacts with the peptide to fold the knot.
In the current study, the group used the artificial intelligence program AlphaFold to predict the FusC protein structure. They used the structure and other artificial intelligence-based tools, like RODEO, to pinpoint which cyclase active site residues were important for interacting with the lasso peptide substrate.
"FusC is made up of approximately 600 amino acids and the active site contains 120. These programs were instrumental to our project because they allowed us to do 'structural studies' and whittle down which amino acids are important in the active site of the enzyme," Barrett said.
