Structure and Function of YidC, an Insertase that Channels Newly Synthesized Proteins into the Cell Membrane

Abstract

Membrane proteins, comprising almost one-third of the human genome, play crucial roles in diverse cellular processes. A number of secretory and insertion mechanisms have evolved to guide these proteins from their point of synthesis in the ribosome to their destination inside the membrane. The universally conserved YidC protein mediates this integration process either individually, or in concert with the canonical protein-conducting channel, SecY. Combining cryo-EM, covariance, and biochemical complementarity data with homology modeling and molecular dynamics (MD) simulations our group has derived one of the first all-atom structures of YidC. Following three decades of intense community-wide effort to derive the YidC structure, only now has it become possible to seek functional insights into the SecY-independent pathway of protein translocation. The specific nascent protein to be translocated via YidC is FoC, the c-ring helix from the transmembrane domain of ATP synthase. Availability of the initial and final FoC translocation states would permit simulation of the transition path connecting these two states and consequently the calculation of the free energy difference between them, which in turn would help to determine the energy cost of nascent protein translocation via YidC. As groundwork for this simulation, a 3.9 M atom structure of YidC bound to the ribosome was constructed and equilibrated. Molecular Dynamics Flexible Fitting was used to model an initial state of the nascent protein insertion pathway, in which FoC is placed within the exit tunnel where it begins to interact with YidC. The final state of the complex is provided by EM data. Steered MD was used to find the most favorable path for the nascent protein insertase. In the current work modeling of the initial ribosome-bound YidC complex and the steering protocol are presented.