Biology Reference
In-Depth Information
bind the NC protein with high affinity and specificity. SL4 only exhibits
weak affinity for the NC protein and its likely function is in stabilizing
the structure of the
-site RNA.
72
A 19-nucleotide RNA based on the
sequence of SL2 binds NC protein with an affinity (K
d
=
Ψ
110 nM) sim-
ilar to that observed for the binding of SL3 to NC (K
d
170 nM).
73
The solution structure of this SL2-NC complex was determined by
NMR spectroscopy. In this structure the N- and C-terminal zinc knuck-
les of NC bind to the exposed guanine bases in the GGUG tetraloop
(Fig. 9).
73
The amino acids 3-11 of the NC protein form a 3
10
-helix
that packs against the closest zinc knuckle and interacts with the RNA
backbone in the stem mainly via electrostatic interactions (Fig. 9). The
N-terminal zinc knuckle interacts with the A:U:A base triple platform
in the minor groove of the RNA stem (Fig. 9).
Recognition of SL3 by the NC protein is achieved in a similar
manner as observed for SL2. However, there are important differ-
ences in the molecular details.
73
Again, both zinc knuckles are engaged
in binding to the stem-loop RNA. The N-terminal zinc knuckle binds
in the major of SL2, whereas in the case of SL2 the interaction takes
place with the A:U:A base triple in the minor groove. The relative ori-
entation the N- and C-terminal knuckles differs in both complexes
(Fig. 9). Sequence-specific recognition in the SL3-NC protein com-
plex involves the guanine nucleotide bases of the loop (G7 and G9 in
Fig. 9). The adenine in the loop (A8 in Fig. 9) packs against the
amino-terminal zinc knuckle and forms hydrogen bonds with a con-
served arginine (Arg 32). The residues 3-10 of the NC protein form
a 3
10
-helix that binds to the major groove of the SL3 stem and makes
specific hydrogen bond contacts with the RNA. In contrast, the N-ter-
minal helix in the SL2 complex is not involved in specific interactions.
These differences demonstrate that the NC protein binds in an adaptive
manner to SL2 and SL3 using different subsets of inter- and intra-
molecular interactions.
=
Packaging of the Dimeric Genome
Retroviruses like HIV-1 or MMLV package two copies of their genomes
during the viral assembly process. This is a requirement for strand-
transfer mediated recombination during reverse transcription.
74,75
The
