Molecular Mechanisms of Topological Rearrangements in Integral Membrane Proteins

University Of Wisconsin-Madison, Madison WI

Investigators

Abstract

This project investigates the mechanisms by which membrane proteins (i.e., proteins that reside within the cell membrane) obtain correct orientations with respect to the membrane after protein synthesis. Membrane proteins are critical for cellular functions including transport, signaling, and enzymatic activity. To function properly, a membrane protein must fold into its correct topology, which requires all structural elements of the protein to obtain specific orientations with respect to the membrane. Membrane proteins that fail to obtain a correct topology are rapidly degraded in the cell. This project uses molecular simulation techniques to address gaps in the knowledge of how membrane protein topology is established. This knowledge will inform engineering approaches to maximize correct protein production. The research team will incorporate undergraduate students, including students from underrepresented groups, to train the next generation of researchers in an interdisciplinary research environment. Learning modules based on this project will be developed for outreach initiatives targeted at middle-school students to inspire young students to pursue research careers. Results from this project will also be incorporated into graduate and advanced undergraduate courses. This project will use molecular dynamics simulations to study experimentally characterized topological rearrangements in a series of representative membrane proteins. Recent experimental results have indicated that certain membrane proteins undergo topological rearrangements in which hydrophilic protein elements directly cross the membrane, even though this process should face a large energy barrier. Atomistic and coarse-grained simulations, accelerated by enhanced sampling techniques, will be performed to characterize the pathways by which hydrophilic protein elements cross the membrane. These simulations will elucidate the interplay of protein, lipid, and water interactions that facilitate topological rearrangements on biologically relevant timescales. Based on simulation insight, sequence mutations will be tested for each of the model systems to generate experimentally verifiable predictions. The simulation methods developed and applied in this project will also be of value for studying similar bilayer translocation processes relevant to lipid flip-flop, membrane protein conformational changes, or the delivery of drug carriers to cells. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.