Pressure-based mapping of Arf1 switch transition.

Abstract

Biomolecular functions are often associated with complex conformational reorganization. These concerted, nontrivial rearrangements among various regions of proteins are essential for their biological functions. Although crystal structures of proteins can provide snapshots of end states essential for their function, a thorough understanding of the structural mechanics of conformational ensemble associated with protein function remains elusive for most proteins. A combination of experimental and computational techniques can assist in understanding these processes. ADP-ribosylation factor 1 (Arf1) is a small GTPase that is implicated in cellular trafficking from the endoplasmic reticulum to the Golgi complex. The transition of Arf1 from its GDP-bound inactive state to the GTP-bound, active state involves a series of conformational transitions resulting in GDP dissociation, a shift in the register of the β-strands in the inter-switch region, and reorganization of the N-terminal helix, and the switch 1 and switch 2 regions. Here we use a combination of molecular modelling, extensive molecular dynamic simulations, pressure perturbation NMR-constrained simulations and pressure perturbation SAXS guided ensemble optimization methods to obtain a comprehensive picture of the functional dynamics of Arf1. Our approach illuminates the events associated with the allosteric communication required for the activation of Arf1.