Very ‘sticky’ proteins – not too sticky after all?
Cell Communication and Signaling
Very 'sticky' proteins - not too sticky after all?
Stephan M Feller 0
Marc Lewitzky 0
0 Biological Systems Architecture Group, Weatherall Institute of Molecular Medicine, Department of Oncology, University of Oxford , Oxford OX3 9DS , UK
A considerable number of soluble proteins in cells that biochemists try to analyze are difficult to handle because they seem to behave like sponges that 'suck up' many other proteins. We argue here that this behavior is commonly an artifact introduced by the experimenting scientist and that we need to study proteins like animals in the wild: they will only reveal many of their secrets when carefully observed in their largely undisturbed, natural environment. Computational studies that attempt to realistically model cellular protein networks must also factor in the diverse protein habitats to be found in cells.
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Commentary
Most protein biochemists and cell biologists know sticky
proteins just too well. They are a pain to work with.
They hang on to chromatography and antibody capture
resins. When expressed in recombinant form, they form
monstrously sized aggregates and bind to a plethora of
irrelevant proteins from E. coli or other host cells. It
seems a fair guess that thousands of scientific papers are
fatally flawed by reporting supposedly specific but in
reality entirely nonspecific interactions of VSPs.
In some cases, the stickiness is artificially inflicted by
intentional protein modification, for example by the
addition of a tag onto the protein in a bad spot, or by
expressing inappropriate fragments that expose
hydrophobic core regions. But even when great care is taken
to avoid this, it appears that many proteins live their
lives as molecular glue balls. How can they function in
cells without disturbing the system? How can they not
get permanently stuck when intracellular protein
concentrations are often in excess of 200 mg/ml (a property
that leads to an extreme cuddling phenomenon known
as macromolecular crowding)? How can they seemingly
retain their stickiness for, in some cases, hundreds of
million years of evolution?
The simple answer could be: many of them may not
be so sticky after all when observed in their undisturbed
natural habitat. We need to appreciate much more how
different most experimental conditions that we routinely
use are compared to the normal environment of
proteins. In addition to a frequent lack of appropriate
protein modifications on recombinant proteins, which, if
present, could make proteins less sticky in vivo, possibly
the greatest determinant in cells that prevents
nonspecific stickiness is the intracellular compartmentalization of
naturally occurring proteins in space and time.
We propose that we must forever say Goodbye to the
belief that most intracellular proteins float about their
business like dumplings in a soup. This notion has been
cherished by biochemists for multiple decades, but it has
probably created a mental roadblock in many heads that
may prevent those biochemists from taking into account
new hypotheses which attempt to draw more holistic
pictures of molecular protein actions in cells [1].
Most intracellular proteins probably act similar to
sophisticated human beings, who move about freely for
short distances, but typically live in a defined village and
use appropriate transport infrastructure when traveling
to faraway places. They do not ever meet most of their
fellow countrymen and interact preferentially with those
they would like to meet, and they are usually protected
from the environment when travelling on major traffic
roads or highways.
The intracellular transport infrastructures, together
with the signaling protein networks that steer virtually
all biological processes, are key features of functional cell
architectures of which we have only rudimentary
knowledge so far.
We need to understand both, the molecular details of
the individual protein building blocks AND the
fundamental principles that shape cellular architectures to
finally come a bit closer to grasping how cells really
function. The newly emerging super-resolution imaging
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