Grant: Discovery Grants Program - Individual

The natural "habitat" of proteins - the interior of cells - is a highly crowded space where various macromolecules, such as proteins and nucleic acids, frequently occupy 30-40% of the total volume. It has been firmly established that proteins can behave differently in cellular environments compared to the highly dilute solutions used in typical test tube experiments. However, detailed understanding of macromolecular crowding effects is currently lacking even for basic properties of proteins, such as stability. Computer simulations are uniquely positioned to solve this problem by providing insight at the molecular level, but are hampered by the size and complexity of crowded systems. In this research program we will develop an all-atom approach for simulating proteins in crowded environments, in which surrounding water molecules are implicitly represented. With this approach we will study large-scale conformational transitions in proteins, which have not been subject to computational crowding studies previously. Our approach will permit the use of various conformational sampling techniques, such as reptation-like moves, to speed up calculations. We will apply this approach to fold switching proteins, which undergo reversible transitions between entirely different structural states. In particular, we will study how crowding leads to shifts in the relative population between these states, which is important as it determines the biological activity in this class of proteins. In addition to crowding, this research program will address the related but different issue of spatial confinement of proteins. Confinement can occur in cells when proteins enter molecular pores that are of sizes similar to that of the protein itself. Here we will use explicit-water molecular dynamics simulations to test the hypothesis that confinement impacts proteins indirectly through changes in the water structure. One of our objectives is to study peptides and small proteins embedded in nanometer-sized water droplets and to characterize the impact on molecular interactions that are important for biomolecules, including the hydrophobic effect. In addition to insight into the structure and stability of proteins in crowded environments, we expect the outcomes of this research program to have implications for specific molecular complexes that use pore-like spaces to help proteins escape misfolded states by inducing unfolding. The graduate and undergraduate students who will carry out this research will receive training in state-of-the art computational methods, learn to communicate scientific results, and engage in interdisciplinary collaborations with experimental research groups.