Determining Interdomain Structure and Dynamics of
a Retroviral Capsid Protein in the Presence of Oligomerization: Implication
for Structural Transition in Capsid Assembly
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Abstract
Capsid
(CA) proteins from all retroviruses, including HIV-1, are
structurally homologous dual-domain helical proteins. They form a
capsid lattice composed of unitary symmetric CA hexamers. X-ray crystallography
has shown that within each hexamer a monomeric CA adopts a single
conformation, where most helices are parallel to the symmetry axis.
In solution, large differences in averaged NMR spin relaxation rates
for the two domains were observed, suggesting they are dynamically
independent. One relevant question for the capsid assembly remains:
whether the interdomain conformer within a hexamer unit needs to be
induced or pre-exists within the conformational space of a monomeric
CA. The latter seems more consistent with the relaxation data. However,
possible CA protein oligomerization and the structure of each domain
will affect relaxation measurements and data interpretation. This
study, using CA proteins from equine infectious anemia virus (EIAV)
as an example, demonstrates a linear extrapolation approach to obtain
backbone <sup>15</sup>N spin relaxation time ratios <i>T</i><sub>1</sub>/<i>T</i><sub>2</sub> for a monomeric EIAV-CA
in the presence of oligomerization equilibrium. The interdomain motion
turns out to be limited. The large difference in the domain averaged
⟨<i>T</i><sub>1</sub>/<i>T</i><sub>2</sub>⟩ for a CA monomer is a consequence of the orthogonal distributions
of helices in the two domains. The new monomeric interdomain conformation
in solution is significantly different from that in CA hexamer. Therefore,
if capsid assembly follows a nucleation–propagation process,
the interdomain conformational change might be a key step during the
nucleation, as the configuration in hexagonal assembly is never formed
by diffusion of its two domains in solution