Protein Folding

Frank Fuerst fant.1 at gmx.net
Wed Apr 12 03:26:59 EST 2000

John Kuszewski wrote:
> All the recent evidence is that folding happens quickly because
> of either [...folding funnels...] or the magic of enzymes 
> (ie., chaperonins).  

To my knowledge, chaperones do not act on folding kinetics in the
sense of the original posting, i.e. by helping the protein "solve" the
Levinthal paradox [1]. What they do is
a) prevent partially folded proteins from aggregation by binding them
and keeping them soluble
b) helping them out of kinetic traps, that means of kinetically
stable, but misfolded conformations, by partially unfolding them using
"mechanical" force driven by ATP.

Of course this changes the observed refolding kinetics - e.g. in the
case of firefly luciferase the refolding reaction in vitro takes
longer than overnight in a purified sample, but in the precense of
eucaryotic cell lysate (reticulozytes or wheat germ) it takes about 10
minutes. But this is not because the protein needs to try less
conformations, but rather because the protein gets stuck in a kinetic
trap and some unidentified chaperone helps it out (Herbst et al.,
Biochemistry _37_(18), 6586ff and references therein).

> No need for
> all that tedious mucking about in quantum mechanics.

Of course.

Bye, Frank

[1] Levinthal paradox: (over)simplified calculation that sampling all
possible conformations of a protein would take more time than the
lifetime of the universe.
Die Verwendung von mehreren Ausrufezeichen macht die Aussage nicht
ausrufender sondern ausufernder. [Michael Bauer in dnq]

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