[Cell-biology] Re: E. Coli ribosome diffusion in vivo?

dantimatter dantimatter at gmail.com
Sun Mar 5 15:21:15 EST 2006

from theo Odijk:

    Thank you for your query.
I've been rereading some of the literature
on the diffusion of small particles within the cytoplasm in bacteria
and otherwise.As far as I'm aware,nobody seems to have measured the
diffusion coefficient D of ribosomes in E.coli cytoplasm.Then the
next step is to theorize but unfortunately our
understanding of diffusion within living
cells is murky at present.

       Elowitz et al (J.Bact.181:197 (1999))
were able to monitor the diffusion of various
proteins in E.coli in vivo.If the Stokes-Einstein relation were to
hold, D would be inversely proportional to the protein size
i.e. inversely proportional to roughly the
protein mass to the power of one third.
This turns out not to be the case.Small
proteins do diffuse yet a 500 kDa large
protein appeared not to move at all.Hence,
it's difficult to judge how a 20 nm ribosome
particle will behave.

           Similar anomalies in the diffusion
of probes habe been witnessed in nonbacterial cytoplasm (see fig 2 in
A.S.Verkman, TIBS 27:27 (2002)).The
peculiar blocking of large probes could be
due to the fact (weak) physical networks
might form within the cytoplasm.Thus the
latter would behave like a viscoelastic fluid;
there could also be a fairly well-defined
correlation length which might
explain the remarkable downturn of the
curves in Verkman's review.Computer
simulations show that percolation clusters do occur in suspensions of
spheres (M.A.Miller and D.Frenkel,
J.Chem.Phys. 121:535 (2004)).I note that
this may happen even when the particles
are charged as in the case of proteins;
we may then define an effective attraction
(P.Prinsen and T.Odijk, J.Chem.Phys.
121:6525 (2004)).

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