Grant: Discovery Grants Program - Individual

Understanding and describing the dynamic properties underlying the design of macromolecular machines is a current frontier in biophysical research and biomolecular engineering. The proposed research focuses on the cellular components that are part of the cells machinery to decode genetic information and to synthesize functional proteins during a process called translation. Translation takes part at the ribosome, a large macromolecular complex that is essential to all living cells. The ribosome is composed of proteins and RNAs, the two major classes of functional biomolecules. Structural studies have revealed that the ribosome is a highly dynamic biomolecular assembly line in which the two key functions (peptide-bond formation and decoding) seem to be carried out solely by RNA. However, for the rapid and accurate translation observed in living cells, additional protein factors are required. Initiation (IF) and release factors (RF) are involved in initiation and termination of protein synthesis, whereas elongation factors (EF) are required for the cyclic process of peptide chain elongation. Many of these translation factors are nucleotide hydrolases that function as molecular switches, responding to a particular input signal with a specific output. The dynamics of these information processing and decision-making events are of great interest for our understanding of translation and the design principles underlying the performance of biomolecular machines. We are just beginning to understand how the design of highly dynamic networks relaying information at the molecular scale is involved in molecular process such as translation. Thus, the proposed research will target these communication networks and provide molecular tools enabling their detailed analysis. The proposed research program addresses this challenge by studying the structural dynamics and biochemical properties of translational (tr) GTPases. Translational GTPases constitute a diverse class of regulatory enzymes that although sharing a common structural design, have vastly different enzymatic properties and functions during ribosome-dependent protein synthesis. A particular focus will be the conserved bacterial trGTPases YchF and LepA. Structurally related to EF-Tu and EF-G, these non-canonical GTPase contain modifications to the common structural core that expand their functional repertoire. To identify at the atomic level how the enzymatic properties and mechanistic roles are rooted in the dynamic properties of the particular trGTPase and what the underlying design strategies are, we will use a combination of state-of-the-art biophysical techniques such as fluorescence spectroscopy, rapid kinetics and molecular dynamics (MD) simulations. The atom-level description of dynamic properties in macromolecular assemblies like the ribosome will be of great importance for our understanding of protein/RNA folding and function as well as rational engineering of novel biomolecular nano-machines.