Plant viral movement proteins (MPs) participate actively in the intra- and intercellular movement of
RNA plant viruses to such an extent that MP dysfunction impairs
viral infection. However, the molecular mechanism(s) of their interaction with cognate
nucleic acids are not well understood, partly due to the lack of structural information. In this work, a
protein dissection approach was used to gain information on the structural and
RNA-binding properties of this class of
proteins, as exemplified by the 61-amino
acid residue p7 MP from carnation mottle virus (CarMV). Circular dichroism spectroscopy showed that CarMV p7 is an alpha/beta
RNA-binding soluble
protein. Using synthetic
peptides derived from the p7 sequence, we have identified three distinct putative domains within the
protein. EMSA showed that the central region, from residue 17 to 35 (represented by
peptide p7(17-35)), is responsible for the
RNA binding properties of CarMV p7. This binding
peptide populates a nascent alpha-helix in water
solution that is further stabilized in the presence of either secondary structure inducers, such as
trifluoroethanol and monomeric SDS, or
RNA (which also changes its conformation upon binding to the
peptide). Thus, the
RNA recognition appears to occur via an "adaptive binding" mechanism. Interestingly, the amino acid sequence and structural properties of the RNA-binding domain of p7 seem to be conserved among carmoviruses and some other
RNA-binding proteins and
peptides. The low conserved N terminus of p7 (peptide p7(1-16)) is unstructured in
solution. In contrast, the highly conserved C terminus motif (peptide p7(40-61)) adopts a beta-sheet conformation in aqueous
solution.
Alanine scanning mutagenesis of the RNA-binding motif showed how selected positive charged
amino acids are more relevant than others in the
RNA binding process and how hydrophobic
amino acid side chains would participate in the stabilization of the
protein-
RNA complex.