protein folding puzzlement

Frank Küster frank at kuesterei.ch
Thu Nov 13 11:27:20 EST 2003

"jacjentait" <jacjentait at xtra.co.nz> schrieb:

> 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" ?

For the protein structure as a whole, the "space" is of course water. Or
not so "of course", because that's only the case in computer
simulations. In in vitro-experiments it's buffer, and in vivo it's
buffered water with lots of small molecules and ions, crowded of other
macromolecules (proteins, RNA and the like).

In this sense, it is _very_ important for protein structure to consider
what surrounds it.

But if we look more closely at a protein structure and at its individual
atoms, it's a little different. From this point of view, also water is
just "beads or shapes" (quite round, in fact) in the same "space".

And this "space" is indeed nothing. Or should I say, the space is just
an artifact of our representation? All matter is made of atoms, and if
you look at a solid or liquid, there's only matter, nothing in
between. But if you look more closely at it with physical methods, you
notice that most of the mass of the atoms is in a very small space in
the middle of each atom, the nucleus. Around the nucleus go the
electrons. But they don't go round it like in a merry-go-round. It isn't
really possible to describe what they do in terms from our macroscopic
world: This is quantum mechanics. 

What comes out is that the electrons can be described by probabilities:
Most probably they are quite near to the nucleus, with a lower
probability they're somewhat farther - say, halfway to the nucleus of
the neighboring atom -, and with really low probability they are much
more far off: But it's not impossible.

Therefore, an atom or molecule doesn't have a fixed boundary like a ball
has. But in order to be able to visualize the shape, one takes the
volume within which the electrons can be expected to be with, say, 90%
probability. It's not necessarily a globular shape, but rather often for
atoms. This is where the round shapes come from in the programs and
pictures. And thus the space is just the volume where the electrons of
no atom are with more then 10% probability.

As this "space" is an artifact of visualization, one cannot say that it
is important for understanding molecular structures.

Bye, Frank
> Damn ... I thought I telepath'ed you not to let that out ... now I'll
Sorry, I'm not running stock Debian kernels, and I'm not running the
/dev/uri/geller patch.  My cutlery kept getting bent when I had it compiled,
so I got rid of it.                  [Matthew Palmer on debian-mentors]

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