A snapshot of ligand-free SETD8 in one of the twenty-four metastable states. Image credit: Rafal P Wiewiora (CC BY 4.0)
Our cells contain thousands of proteins that perform many different tasks. Such tasks often involve significant changes in the shape of a protein that allow it to interact with other proteins or ligands. Understanding these shape changes can be an essential step for predicting and manipulating how proteins work or designing new drugs. Some changes in protein shape happen quickly, whereas others take longer. Existing experimental approaches generally only capture some, but not all, of the different shapes an individual protein adopts.
A family of proteins known as protein lysine methyltransferases (PKMTs) help to regulate the activities of other proteins by adding small tags called methyl groups to specific positions on their target proteins. PKMTs play important roles in many life processes including in activating genes, maintaining stem cells and controlling how organs develop.
It is important for cells to properly control the activity of PKMTs because too much, or too little, activity can promote cancers and neurological diseases. For example, genetic mutations that increase the levels of a PKMT known as SETD8 appear to promote the progression of some breast cancers and childhood leukemia. There is a pressing need to develop new drugs that can inhibit SETD8 and other PKMTs in human patients. However, these efforts are hindered by the lack of understanding of exactly how the shape of PKMT proteins change as they operate in cells.
Chen, Wiewiora et al. used a technique called X-ray crystallography to generate structural models of the human SETD8 protein in the presence or absence of native or foreign ligands. These models were used to develop computer simulations of how the shape of SETD8 changes as it operates. Further computational analysis and laboratory experiments revealed how slow changes in the shape of SETD8 contribute to the ability of the protein to attach methyl groups to other proteins.
This work is a significant stepping-stone to developing a complete model of how the SETD8 protein works, as well as understanding how genetic mutations may affect the protein’s role in the body. The next step is to refine the model by integrating data from other approaches including biophysical models and mathematical calculations of the energy associated with the shape changes, with a long-term goal to better understand and then manipulate the function of SETD8.
