Biology Reference
In-Depth Information
of each stem and thus effectively caps the structure (Fig. 5). Proline 14
introduces a sharp turn into the peptide chain that forms an L-shape
and allows the N-terminal part of peptide 2 to follow the shape of the
RNA surface, and in the case of peptide 1 to provide additional con-
tacts with the RNA backbone. This conformation is stabilized by
hydrogen bonds from the side chain hydroxyl groups and main chain
amides of threonine 15 and serine 18.
The mode of recognition between RNA and AMV coat protein
again demonstrates the importance of a dynamic RNA that facili-
tates folding in the presence of the protein partner. However, in this
structure the dynamics go a step further and also include the protein
because both the RNA signal sequence and the RNA binding domain
of the coat protein undergo significant structural rearrangement during
co-folding. This system also illustrates that the proposed secondary
structure of the RNA signal sequence can be misleading. Even though
the sequence folds into two stem-loop structures, similar to the MS2
signal sequence, the interaction with the AMV coat protein ignores
the loops and takes place at the bottom of the stem with the AUGC
repeats playing a key role.
Retroviruses
All retroviruses encode a gag polyprotein, which is produced in the
host cell during the late stages of the infection cycle. This protein
directs the encapsidation of two copies of the unspliced viral genome
during viral assembly and budding. Gag is cleaved into the matrix
protein (MA), the capsid protein (CA), and the nucleocapsid protein
(NC) by the viral protease during viral maturation. The nucleocapsid
protein associates with the viral RNA molecules that are encapsidated
in the viral core particle.
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The Nucleocapsid Protein
The genome recognition in most retroviruses seems to be primarily
mediated by the NC domain of the gag precursor polyprotein.
Structures of several NC proteins have been determined in the past
