protein folding puzzlement

Dr Engelbert Buxbaum engelbert_buxbaum at hotmail.com
Mon Nov 24 09:13:50 EST 2003

jacjentait wrote:

> I don't know if this is the correct forum but here goes ,
> Every molecular program i have seen has visuals that show molecules as beads
> or shapes floating in "space" .
> What is the "space" ?

Most protein structures come from X-ray crystallography. To oversimplify
a little, you could look at that molecule on the screen as a
representative for all the molecules in the crystal, a kind of "average
protein molecule". 

Thus the empty space around the structure is realy an artefact of the
way we generated the structure. In the crystal the protein molecule is
surrounded by the other proteins. It is also surounded by bound water
and ions, which are part of the structure. Often they are ignored, but
you can "switch them on" in visualistion programms like Protein Explorer
(free at www.umass.edu/microbio/chime/).

In the living cell, the protein is in a densley packed environment with
water, ions, metabolites and, of course, other proteins. Indeed, cells
have an entire array of molecular chaperones, specialised proteins
which, just  like their human counterpart, prevent inappropriate
interaction between densly packed proteins. 

A couple of years back there was a cartoon on this topic in TIBS,
showing how crowded the cytoplasm realy is at different scales. 

If you go down a further order of magnitude, into the atoms, they are
indeed mostly empty space, as the classical experiment of Rutherford

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