KCTD5 is endowed with large, functionally relevant, interdomain motions.
The KCTD family is an emerging class of proteins that are involved in important biological processes whose biochemical and structural properties are rather poorly characterized or even completely undefined. We here used KCTD5, the only member of the family with a known three-dimensional structure, to gain insights into the intrinsic structural stability of the C-terminal domain (CTD) and into the mutual dynamic interplay between the two domains of the protein. Molecular dynamics (MD) simulations indicate that in the simulation timescale (120 ns), the pentameric assembly of the CTD is endowed with a significant intrinsic stability. Moreover, MD analyses also led to the identification of exposed β-strand residues. Being these regions intrinsically sticky, they could be involved in the substrate recognition. More importantly, simulations conducted on the full-length protein provide interesting information of the relative motions between the BTB domain and the CTD of the protein. Indeed, the dissection of the overall motion of the protein is indicative of a large interdomain twisting associated with limited bending movements. Notably, MD data indicate that the entire interdomain motion is pivoted by a single residue (Ser150) of the hinge region that connects the domains. The functional relevance of these motions was evaluated in the context of the functional macromolecular machinery in which KCTD5 is involved. This analysis indicates that the interdomain twisting motion here characterized may be important for the correct positioning of the substrate to be ubiquitinated with respect to the other factors of the ubiquitination machinery.
a Institute of Biostructures and Bioimaging, C.N.R. , Via Mezzocannone 16, Naples I-80134 , Italy.|b Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche , Seconda Università di Napoli , Caserta 81100 , Italy.
Daniela
D
Barone
a Institute of Biostructures and Bioimaging, C.N.R. , Via Mezzocannone 16, Naples I-80134 , Italy.|b Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche , Seconda Università di Napoli , Caserta 81100 , Italy.
Nicole
N
Balasco
a Institute of Biostructures and Bioimaging, C.N.R. , Via Mezzocannone 16, Naples I-80134 , Italy.
Luigi
L
Vitagliano
D008958:Models, Molecular; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D015221:Potassium Channels / Q000737:chemistry* / Q000378:metabolism*; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D055550:Protein Stability; D013329:Structure-Activity Relationship
D015221:Potassium Channels
molecular dynamics; structure–function relationships; substrate recognition domain; twisting; ubiquitination