X-Message-Number: 991
From: Thomas Donaldson
Newsgroups: sci.cryonics
Subject: Chaperonins (fwd)
Date: Wed, 15 Jul 1992 17:57:40 GMT
Keywords: protein folding, heat shock protein

[ To design molecular devices for repairing tissues of cryonically
  suspended patients, we will need to know how to design proteins
  that fold in the manner we want.  It turns out that protein folding
  is not as simple as once thought, and that proteins called
  "chaperonins" are important in assisting that folding.  This message
  from a recent issue of Periastron describes recent work on chaperonins.
  It is posted with permission of the author Thomas Donaldson
  <>.  (Note: The diagrams are missing because
  they could not easily be transferred to the email version.) - KQB ]

CHAPERONINS
by Thomas Donaldson
Periastron, P.O. Box 2365, Sunnyvale, CA 94087  USA

Our genes don't make proteins directly.  Instead they cause the creation
of a special template, mRNA (Messenger Ribonucleic Acid).  This mRNA then
passes out of the nucleus, moving to locations in the cell body where the
coded protein is needed.  At that location, the mRNA templates create the
new protein.

But the above gives a highly simplified account of just what happens.
Among the major simplifications one deserves a bit of special note: the
processes by which a protein, which starts out as a long chain of amino
acids strung together, can fold into its proper shape to take up action
as an enzyme or constituent of the cell.  (And even here I omit many
other questions: for instance, hemoglobin, just as many other
biochemicals, consists of two paired proteins, which somehow come
together around a heme molecule.  Just how does that pairing happen?).
Sufficient for the moment, however, to discuss protein folding and some
recent insights into it reported in NATURE (356(1992) 683-680) by the six
scientists involved, included Thomas Langer, Chi Lu, Harrison Echols,
John Flanagen, Manajit K Hayer, and F Ulrich Hartl.

Folding proteins?  At present a high consensus exists that the ultimate
shape of a protein depends solely on its sequence of amino acids.  If so,
then simply by knowing that sequence we could theoretically predict that
protein's final shape.  Yet when proteins actually form inside a cell,
other issues get in the way.  What can happen is not that the protein, in
pure isolation, folds automatically to its proper shape, but instead that
half-folded proteins aggregate together, or attach to others, in a way
that prevents them from completing their proper conformation.

It is for this reason that several different factors play a critical role
in guiding new proteins into their proper shape.  These factors have been
named chaperonins (from, as you must have guessed, the word chaperone).
In mammalian cells, two families of chaperonins play a large role: Hsp70
and Hsp60.  Apparently their original names came from the observation
that they would also help refold a protein that had lost its proper shape
due to heating: "Hsp" stands for "Heat Shock Protein".

But similar proteins, with similar roles, occur in nonmammalian cells.
As a step toward unravelling just what happens with our own Hsps, the
authors of this paper present a close study of just how the equivalent
proteins work in the bacteria E.  coli (a favorite subject for molecular
biologists).  These authors could distinguish 5 different proteins which
acted very much as do Hsp70s and Hsp60s in our own cells.  These have
been named DnaJ, DnaK, GrpE, GroEL, and GroES (I don't know the real
English origin of these names).

>From their experiments they report that no single one of these factors
will actually work to guide folding.  Instead, they act in sequence to
produce the final properly folded protein.  Their action requires energy,
and therefore the presence of ATP (a widespread energy molecule used in
all cells).  Magnesium ions also play a critical role.

To find out just how these molecules work, the authors used one subject
protein, rhodanese.  They chose this protein because it had a very marked
tendency, without any guidance, to aggregate into half-folded clumps.
The sequence of reactions they found went like this: first, DnaK would
bind to part of the rhodanese, even before it had left the ribosome where
it was forming.  At this stage, when the protein chain is nearly
complete, it folds into a halfway conformation.  DnaJ then links to the
combination of DnaK and protein chain.  DnaJ catalyzes a reaction in
which some of the DnaK is removed, and the protein folds up still more
(but still incompletely).  Then the GrpE molecule binds to this
combination, followed (with energy expenditure) by the release of both
DnaK and DnaJ, and the binding of GroEL and GroES to the subject
protein.  These two kinds of molecules guide the protein chain into its
final tightly folded state.  Another reaction releases both GroEL and
GroES.

Diagram XX accompanying this article comes, with minor changes, from the
NATURE article.  It gives a picture of how this sequence of reactions
happens.

To my mind, the action of chaperonins raises questions not only about
"accepted wisdom" but about possible methods of use when we try to
control such reactions ourselves.  Even now, no one proposes that
proteins, once formed, are not in their most energetically stable
conformation.  That's part of the idea that, if left to themselves, they
will automatically form into the "correct" shape.  Yet we know that there
are far too many proteins for every one to have been scrutinized.  In
some cases, or even many cases, chaperonins may plan an essential role in
guiding a protein into the proper shape.  This issue becomes especially
clear when we imagine what the energy curve for different conformations
of a complex protein can be: it can have several local minima (see
Diagram XX).

Presently, also, a good deal of effort has gone into finding ways to
compute the form of a folded protein from its amino acid sequence.  That
effort depends on the assumption that form comes solely from sequence.

Finally, and perhaps most important technologically, chaperonin reactions
tell us something which may turn out very important about our own use of
biochemistry to design molecular devices.  Of course we want every one of
our devices, at least in its quiescent state, to sit on a local minimum
of its energy curve.  But we do NOT have to limit ourselves to finding
and using special molecules which fall "naturally" into the shape we
desire.  We can also use reactions like those with chaperonins, and even
more complex, to guide our molecules into the forms we want.  So long as
their shapes remain stable under the conditions for which we design them,
they need not be the only shapes our designed molecules can adopt.

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