G'day Petr;
Sorry to not have replied sooner, but I have been doing some lit chasing
based on your last e-mail and considering what the micro-environment of a
virion may be.
Firstly, I have found nothing to suggest that a virion needs to be a
discreet "delivery bag". Contrary to this there is great evidence a
virus can exchange ions and solvent with its' surrounds, some possibly
having ion channels to aid this not unlike a dialysis bag I imagine. Under
such conditions the viral particle can still be a densely packed,
semi-solid body as you describe, or in the words of Tuma and Thomas
["Mechanisms of virus assembly probed by Raman spectroscopy: the
icosahedral bacteriophage P22." Biophys Chem 68: 17-31 (1997)] "A molten
globule". In this state the virion has all the properties that help it
survive in extreme conditions such as heat, acid/base, oxidation and even
time.
However, even with the ability to exchange I think it occurs relatively
slowly as shown by deuterium exchange in model SDS micelles, so your point
is still valid, but there may be a window of time for the protease to be
active before it is trapped in a "static" state (after reading the
literature I hypothesise the gelatenous state is a desired state that is
reached to enhance longivity of the viral core - perhaps even from
the protease as well as environmental factors).
The host-cell protein, cyclophilin A, is also incorporated into HIV-1
particles. Once the viral core gains entry to the cell, the protective
envelope about the core is degraded by the absconded cellular enzyme
cyclophilin A. This allows the release into the cytoplasm of the
pre-integration complex (PIC), which contains the machinery necessary for
reverse transcription of the RNA viral sequence and integration into the
host genome.
But what about the protease? If there is very little of the protease
present as you have suggested, what happens? I believe after, or at
budding the protease becomes active and starts its little work of chewing
up the gag and gag-pol precursors in and acidic and salty microenvironment
which is exchanging with the surround to move away from these conditions
and more towards a neutral pH (at the viral surface where the protease is
active). Proteins that carry out cysteine oxidation reduction can modify
the protease to enhance and later stop activity. The protease will also
chew itself to pieces, and at more neutral pH, the sequence element in p2
(a critical element for HIV-1 packaging between the NC and gp120 and is
close to the virion surface where the pH will be closest to the outside
environment), becomes a potent inhibitor of the protease. I believe all
these elements conspire against the protease to destroy it once it has
completed it's task. Indeed as the particle moves towards an ordered
icosahedral shape through polyprotein processing, the protease would be
predicted to be less likely to function.
So I would think the protease sees optimum conditions for activity for a
period, which deteriorates as it's function is realised before
inactivation and/or destruction. However, we obviously do not see a huge
sink of protease numbers, but rather a very discrete number and
quantifiable number of protease molecules - that perhaps, as you say -
many of our laws such as the law of mass transfer do not occur, but these
laws are also measured in large volumes compared to a virion {(if we
take your values of [E] = 1.0 nM in 1.0 mL, having 10^(-9) x 10^(-3) x 6
x 10^(+23) = 6 x 10^(+11) or 600,000,000,000 molecules in 1 x 10^(-6)m^3
compared to 100-120nM or volume of V[t] = 4/3 Pi r[t]^3, r[t] = 9.04 x
10^(-22)m^3 with 20 odd molecules)} I think it all equals about the same
thing, so perhaps it is irrelevant and the enzyme behaves the
same? Therefore features we see in our assays such as "rate constants" and
"equilibrium constants", still apply?
Len...
