In our lab, we are interested in the structural biology of cellular signaling. Cells are constantly sensing different stimuli both internal, e.g. nutrients, stresses, and external, e.g. growth factors, mechanic force, and fine-tuning various processes accordingly. This signal integration and transduction is performed by a vast machinery of molecules – proteins, lipids, nucleic acids – which must physically encode those various input to adjust their output.
We are interested in the modular nature of the molecules involved in this process. Specifically, we aim to use structural characterization of large signaling molecules by cryo-EM to understand the conformational landscape which governs their function within signaling.
We will focus our efforts on two classes of molecules embedded in growth factor signaling and cytoskeletal remodeling at the plasma membranes.
Small GTPase signaling at the plasma membrane
Small GTPases are a family of signaling proteins which alternate between an active and transducing GTP-bound state, and an inactive GDP-bound state. The interconversion of these two states relies on two classes of regulatory molecules: GTPase activating proteins (GAPs) and Guanidine exchange factors (GEFs), which promote their inhibition and activation respectively. The Rho GTPases are involved in cytoskeletal remodeling, and their hyperactivation has been associated with cancer progression and metastasis. More over there are remarkable cross-linking between Rho signaling with Ras signaling (growth factor) and Arf signaling (cellular trafficking). Several GEFs and GAPs of these GTPases either respond directly to activation of other GTPases, or are situated downstream of their signaling pathway. These include the RhoGEFs Prex1/2 and Tiam1, and the ArfGAP ARAP1-3.
Few structures of full-length versions of these proteins are available, even fewer show interactions with the tertiary factors proposed to regulate their activity. We will address the following questions: (1) how does the multi-modular architecture of GTPase regulating proteins enable fine regulation of Rho signaling; (2) what tertiary factors are involved in this process and (3) how can we leverage knowledge of these protein structures to develop new therapies for cancers?
Long non-coding RNAs and cellular signaling
Since their discovery at the beginning of the century, long non-coding RNAs have for the most part eluded efforts to understand their function. A growing body of work now shows that several lncRNAs have the capacity to modulate activation of the PI3K/Akt/mTOR axis and other phosphoinositide signaling pathways via a few different proposed mechanisms. With the emergence of a body of work suggesting their auxiliary role in cell signaling, and their clear association with a broad range of cancers, there is a clear need for a better molecular understanding of the role of lncRNAs within cells and in cancers. The object of our work is to address the dearth in molecular level information on the function of lncRNAs which have been shown to be involved in regulating the PI3K/Akt/mTOR axis. To tackle this problem, we will set out to better characterize the interactome of prominent lncRNAs proposed to regulate PI3K/Akt signaling and determine their tri-dimensional structure.
The Chaker-Margot Lab 