Characterization of intrinsically disordered proteins

Proteins have crucial functions in living cells and organisms. For many years, the function of proteins was thought to be tightly coupled to its three-dimensional structure. While this holds for many proteins, more and more proteins have been discovered that seem to be intrinsically disordered. Intrinsically disordered proteins (IDPs) or proteins with intrinsically disordered regions (IDRs) do still have very important roles, for instance in the regulation of cellular processes. However, such proteins are very difficult to study by methods that are currently available in the fields of structural biology or biophysics. They cannot be described by a single, representative, structure, but are best characterized by a very large number of different conformations, also referred to as an ensemble of conformations. In this project we will combine experimental measurements with computer simulations of IDPs and IDRs to generate realistic ensembles of their conformations and to learn about how they perform their function in cellular regulation. We have selected two sets of proteins to perform this research on: 1) the regulatory domain of the human tyrosine hydroxylase (TyrH), which has an intrinsically disordered region and 2) the microtubule associated protein 2c (Map2c), along with the similar tau protein. Strikingly, in spite of their similarity, the latter two proteins behave differently in their regulatory role, suggesting that there must be some structural difference between them. The challenges for this project lie in the size of the proteins and the size of the ensembles that are needed to describe their behavior correctly. We will first use new simulation techniques to generate collections of very many, and very different protein structures. Next, we will use experimental data that is generated by our project partners in the Czech Republic to adjust these collections, such that they represent the experimental data best. The resulting ensembles can then be analyzed in terms of their similarities and differences, in order to better understand how these intriguing proteins function.

Proteins have crucial functions in living cells and organisms. For many years, the function of proteins was thought to be tightly coupled to its three-dimensional structure. While this holds for many proteins, more and more proteins have been discovered that seem to be intrinsically disordered. Intrinsically disordered proteins (IDPs) or proteins with intrinsically disordered regions (IDRs) do still have important roles, for instance in the regulation of cellular processes. However, such proteins are very difficult to study by methods that are currently available in the fields of structural biology or biophysics. They cannot be described by a single, representative, structure, but are best characterized by a very large number of different conformations, also referred to as an ensemble of conformations. In this project we combined experimental measurements with computer simulations of IDPs and IDRs to generate realistic ensembles of their conformations and to learn about how they perform their function in cellular regulation. We have selected three proteins to perform this research on: 1) a fragment of the Tau protein,suggested to play a role in several neurodegenerative diseases 2) the regulatory domain of the human tyrosine hydroxylase (TyrH), which has an intrinsically disordered region and 3) the microtubule associated protein 2c (Map2c). The challenges for this project were in the size of the proteins and the size of the ensembles that are needed to describe their behavior correctly. We first generated collections of very many, and very different protein structures by splitting the proteins up into smaller fragments. We then explored the possibilities to use experimental data that was generated by our project partners in the Czech Republic to adjust these collections, such that they represent the experimental data best. The resulting ensembles can then be analyzed in terms of their similarities and differences, in order to better understand how these intriguing proteins function.