Biology Reference
In-Depth Information
5 is stacking with the side
chain of tyrosine 85, a type of interaction frequently seen in RNA pro-
tein interactions.
23
The hydroxyl group of the tyrosine is involved in
a hydrogen bond to the U-5 phosphate group. The specificity for a
pyrimidine in the position seems to be established by a hydrogen
bond between asparagines 87 and the O2 of the base (Fig. 4). The ade-
nine in position
The uridine in the loop at position
−
5.
A comparison between the RNA structure in its free and bound
form illustrates what has become a common theme in RNA-protein
interactions: Whereas the protein adjusts its structure only slightly in
the process of complex formation, the RNA undergoes a significant
structural transition often including the folding of previously unstruc-
tured elements. In the case of the MS2 packing signal hairpin, the
adenine in position
−
7 is stacked below the uridine base in position
−
10 — which is stacked inside the stem in the free
RNA — is bulged out of the helix and becomes one of the key play-
ers in conferring specificity. Furthermore, there is no evidence for the
stacking of the loop nucleotide at position
−
−
5 on top of the adenine
at position
7 as seen in the complex. The whole loop segment of the
free RNA is not well-structured and shows signs of internal dynamics.
−
Alfalfa Mosaic Virus
The alfalfa mosaic virus (AMV) is a positive-sense RNA plant virus.
Its genome consists of three genomic RNAs (RNAs 1, 2, and 3) and
one subgenomic RNA (RNA 4). Each of the RNAs are separately
recognized and packaged.
24
RNAs 1 and 2 encode proteins with
replicase functions,
25
the viral movement protein (required for cell-
to-cell virus movement) is encoded by RNA 3, and the subgenomic
RNA 4 (transcribed from the negative-sense of RNA 3) encodes the
AMV coat protein.
26
The encapsidation of the genomic RNAs is controlled by specific,
high-affinity signal sequences that comprise 39 nucleotides and are
located in the 3´-untranslated regions of all four RNAs (Fig. 1).
27-29
This
minimal sequence is competent for binding either full-length AMV coat
protein or 26-amino acid peptides that contain the N-terminal RNA
binding domain of the coat protein.
27
The Pro-Thr-x-Arg-Ser-x-x-Thy
