Binding of rabies virus polymerase cofactor to recombinant circular nucleoprotein-RNA complexes.
In rabies virus, the attachment of the L polymerase (L) to the viral nucleocapsids (NCs)-a nucleoprotein (N)-RNA complex that serves as template for RNA transcription and replication-is mediated by the polymerase cofactor, the phosphoprotein (P). P forms dimers (P(2)) that bind through their C-terminal domains (P(CTD)) to the C-terminal region of the N. Recombinant circular N(m)-RNA complexes containing 9 to 12 protomers of N (hereafter, the subscript m denotes the number of N protomers) served here as model systems for studying the binding of P to NC-like N(m)-RNA complexes. Titration experiments show that there are only two equivalent and independent binding sites for P dimers on the N(m)-RNA rings and that each P dimer binds through a single P(CTD). A dissociation constant in the nanomolar range (160+/-20 nM) was measured by surface plasmon resonance, indicating a strong interaction between the two partners. Small-angle X-ray scattering (SAXS) data and small-angle neutron scattering data showed that binding of two P(CTD) had almost no effect on the size and shape of the N(m)-RNA rings, whereas binding of two P(2) significantly increased the size of the complexes. SAXS data and molecular modeling were used to add flexible loops (N(NTD) loop, amino acids 105-118; N(CTD) loop, amino acids 376-397) missing in the recently solved crystal structure of the circular N(11)-RNA complex and to build a model for the N(10)-RNA complex. Structural models for the N(m)-RNA-(P(CTD))(2) complexes were then built by docking the known P(CTD) structure onto the completed structures of the circular N(10)-RNA and N(11)-RNA complexes. A multiple-stage flexible docking procedure was used to generate decoys, and SAXS and biochemical data were used for filtering the models. In the refined model, the P(CTD) is bound to the C-terminal top of one N protomer (N(i)), with the C-terminal helix (alpha(6)) of P(CTD) lying on helix alpha(14) of N(i). By an induced-fit mechanism, the N(CTD) loop of the same protomer (N(i)) and that of the adjacent one (N(i)(-1)) mold around the P(CTD), making extensive protein-protein contacts that could explain the strong affinity of P for its template. The structural model is in agreement with available biochemical data and provides new insights on the mechanism of attachment of the polymerase complex to the NC template.
Ribeiro
Euripedes de Almeida
Ede A
Unit of Virus Host Cell Interactions (UVHCI), UMI 3265 UJF-EMBL-CNRS, Grenoble Cedex 9, France.
Leyrat
Cédric
C
Gérard
Francine C A
FC
Albertini
Aurélie A V
AA
Falk
Caroline
C
Ruigrok
Rob W H
RW
Jamin
Marc
M
D001665:Binding Sites; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D019281:Dimerization; D046911:Macromolecular Substances; D008958:Models, Molecular; D033363:Neutron Diffraction; D019590:Nucleocapsid Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D010252:Paramyxoviridae / Q000235:genetics / Q000378:metabolism; D020836:Protein Structure, Quaternary; D017434:Protein Structure, Tertiary; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011820:Rabies virus / Q000235:genetics / Q000378:metabolism*; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012209:Rhabdoviridae / Q000235:genetics / Q000378:metabolism; D053838:Scattering, Small Angle; D013045:Species Specificity; D055672:Static Electricity; D020349:Surface Plasmon Resonance; D013816:Thermodynamics; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D014961:X-Ray Diffraction
D046911:Macromolecular Substances; D019590:Nucleocapsid Proteins; D012367:RNA, Viral; D011994:Recombinant Proteins; D014764:Viral Proteins; C099601:nucleocapsid protein, Rabies virus; C097625:L protein, Rabies virus; D012321:DNA-Directed RNA Polymerases