Structural disorder and Molecular Recognition

During the last fifteen years, one of the key concepts of Structural Biology (the one according to which the function of proteins resides in the fact that they have a well defined three-dimensional structure) was challenged by the discovery of a new class of proteins called "intrinsically disordered proteins" as they are devoid of a precise three-dimensional structure. Nevertheless, they are functional and are extremely abundant in living world. Proteins can be seen as pearl necklaces where every pearl would correspond to an amino acid. Unlike classic proteins, in which all the pearls occupy fixed positions in time, within disordered proteins the position of each pearl varies in time. Consequently, a disordered protein is a very dynamic object that cannot be likened to a single necklace, but rather to an ensemble of necklaces.
During the last ten years, we discovered that the nucleoprotein and phosphoprotein of three human pathogenic viruses (namely, measles Nipah and Hendra viruses) possess disordered regions. This discovery opens numerous interesting perspectives from a fundamental point of view but also in terms of potential therapeutic applications. Indeed, the interaction between the nucleoprotein and the phosphoprotein, which is crucial for the replication of the virus, represents a potential target for a new class of drugs that could block this interaction. These drugs, unlike drugs blocking the activity of structured proteins according to the "lock and key" model, would thus have as targets disordered proteins, namely proteins whose shape continuously changes over time.

Figure 1 : Schematic representation of the complex molecular partnership established by MeV N_TAIL.

Cryo-electron microscopy reconstruction of MeV nucleocapsid according to (Bhella et al., J Mol Biol 2004) onto which only a few N_TAIL regions have been depicted for the sake of clarity. The ribbon representations of MeV XD (pdb code 1OKS) (Johansson et al., J Biol Chem 2003), of the regulatory domain of IRF-3 (pdb code 1QWT) (Qin et al., Nat Struct Biol 2003), and of the E. coli DnaK chaperone (the prokaryotic counterpart of hsp70) (pdb ode 2KHO) (Bertelsen et al., Proc Natl Acad Sci 2009) are shown. The question mark symbolizes the lack of structural data for both MeV M and NR. This latter is represented inserted in the membrane of B/T lymphocytes and of dendritic cells.

The team focuses on the identification, characterization and elucidation of the functional role of disordered regions within proteins relevant in terms of human health. In particular, we are interested in structural disorder within proteins of the replicative complex of three human pathogenic viruses: the measles virus and the recently emerged Nipah and Hendra viruses. These viruses belong to the Paramyxoviridae family (Mononegavirales order). Their genome consists in a non-segmented, single-stranded RNA molecule of negative polarity. The viral genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid (Figure 1). This latter is the substrate for both transcription and replication. These activities are carried out by the viral polymerase that consists in a complex between the L protein and the phosphoprotein (P). The P protein is an essential polymerase co-factor as it allows the recruitment of L onto the nucleocapsid template. The C-terminal region of N (NTAIL) is an intrinsically disordered domain exposed at the surface of the nucleocapsid. The plasticity of NTAIL and its exposure at the surface of the nucleocapsid allows the establishment of a broad and complex molecular partnership leading to multiple biological effects. Indeed NTAIL interacts with various cellular partners (including the major inducible heat shock protein hsp70, the Interferon Regulator Factor 3 (IRF 3), a yet uncharacterized nucleoprotein receptor, NR, expressed at the surface of lymphocytes and dendritic cells) and viral partners (including the P protein and the matrix, M, protein). During these last years, we have been studying the interaction that the measles and henipavirus NTAIL region establishes with its various viral and cellular partners.

The research activities of the team embrace four major axes, namely the identification of disordered regions and the elucidation of the functional role of structural disorder within the replicative machinery of paramyxoviruses and its relevance in virus-host cell interactions, the unraveling of the molecular mechanisms of folding coupled to binding events, the understanding of the molecular bases of specificity and affinity in partner recognition by intrinsically disordered proteins (IDPs), and the discovery of compounds capable of blocking crucial interactions involving intrinsically disordered regions (IDRs). The model system used in these studies is the interaction between the disordered C-terminal region of the nucleoprotein (N_TAIL) from three paramyxoviruses (namely, the Measles, Nipah and Hendra viruses) and various partner proteins.

• Molecular partnership of the intrinsically disorder C-terminal domain of the measles virus nucleoprotein (NTAIL)
• Structural disorder and molecular partnership of intrinsically disordered regions of the nucleoproteins and phosphoproteins of Henipaviruses
• Molecular bases of specificity and affinity in partner recognition by intrinsically disordered proteins (IDPs)
• Development of MeDor, a metaserver for the prediction of protein disorder
• SL’s Team