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essentially an RNA switch that promotes packaging of a dimeric genome
by making protein binding sites in the RNA that are sequestered in the
monomeric RNA available upon dimerization.
RNA-Protein Interaction in Viral RNA Packaging:
Present and Future
The examples discussed above illustrate that the molecular mecha-
nisms used by RNA viruses to ensure the incorporation of the correct
genomic material are both simple and diverse. Even though the same
molecular interactions — for example, stacking of bases with
hydrophobic protein surfaces, or electrostatic interactions between
charged amino acids and the RNA phosphate backbone — appear in
all three complexes, the details in which they contribute to specific
recognition differ significantly. Moreover, the same protein unit (and
perhaps also the RNA) can recognize different RNA binding partners
due to adaptive binding, indicating that the internal dynamics of both
binding partners is crucial for the control of the interaction. The
examples also demonstrate that one needs to be cautious when using
secondary structures as a basis for interpreting binding data: Even
though both the MS2 and the AMV packaging sites contain stem-
loop structures, the loop is only involved in the recognition process
during packaging of MS2. In AMV the stem-loop structures are sim-
ply providing a three-dimensional scaffold that ensures the presenta-
tion of the repeat sequences that are the key for specific recognition.
The increase in structural information about RNA packaging sig-
nals has greatly improved our understanding of the molecular details
that control this crucial process in the viral lifecycle. Due to its impor-
tance for the biogenesis of infectious virus particles, we can hope that
this research will in the near future provide us with a novel approach
to combat viral diseases, even in cases where immunization is difficult.
Acknowledgements
The molecular graphics in this chapter were produced using the Chimera
package from the Computer Graphics Laboratory, University of
