Relative Mechanical Flexibility of Ubiquitin Family Proteins: A Study using Elastic Network Model

Abstract

The conformational flexibility of biomolecules is essential for their function. Elastic Network Model (ENM) is a class of harmonic models used to computationally describe the flexibility of biomolecules. Despite the simplicity of the underlying potential, ENMs show intriguing abilities to capture functionally relevant conformational changes in proteins, as seen in their crystallographic structures, through their low-frequency normal-mode displacements. We present an ENM based study of the mechanical flexibility of proteins having high structural similarity but low sequence homology.Single-molecule atomic force microscopic (AFM) measurements reveal that ubiquitin requires a higher unfolding force when pulled along N-C termini than the SUMO proteins. The higher mechanical stability of ubiquitin relative to the SUMOs is presumably a sequence effect, as the proteins have identical secondary structures. Our calculations at the atomistic resolution show a strong imprint of the experimentally observed disparity in stabilities of the ubiquitin-like proteins in their flexibilities. Spring constants for normal modes of ubiquitin are higher than that of the SUMOs, implying larger stiffness of ubiquitin over the latter. The residues on the clamp (terminal β-sheets) region of these proteins that govern their stabilities show mobility that is implicated in their flexibilities. We discuss physical considerations for extracting a reduced dimensional basis from ENM for the description of equilibrium flexibility of proteins.The large-amplitude normal modes that represent concerted protein motions additionally reveal the conformational changes taking place when ubiquitin and SUMOs bind with substrates, as observed in the complex crystallographic structures. The flexible SUMO proteins tend to be as stiff as ubiquitin on substrate-binding whereas, there seems to be no considerable enhancement in the rigidity of apo-ubiquitin. We elucidate this feature in our study in the light of spring constants of the slowest normal modes.