protein folding puzzlement

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" ?

If , in a cell or cell organelle , I imagine a matrix or some medium that
all the molecules , h20 and structures "sit" in .
The strains of bonds between atoms , in molecules , must be mainly because
of the "space" and not the atoms actions .
Would the structure , physical actions , and gravities of this "space" not
be the main knowledge
to protein folding ?

william james tait .

"jacjentait" <[Only registered users see links. ].nz> schrieb:


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
--
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]

If I got this straight .

The "space" / vacuum / nothing is really where electrons are temporally not
..
and
The "space" is mostly electron repulsion at a very low probability .
The electrons are slower ( there more / higher probability ) at the atom and
faster (there less /extreme prob.) out further
near other atoms and repelling off those atom's electrons .

A block of varying density electron goo with atoms networked by denser
electron strings .

So
wouldn't protein folding depend on the weather of this low probability
interacting electron "space" ,
because these interactions could shield or expose a "start" in a gravity
towards a particular fold ?
Could the models model separately the low electron densities , a kind of
negative plot of the computation ? .

rethinking
I thought a lone molecule without an environment seems to me not real (
environment to me seems very important )
but
I then realised that the electrons are constantly moving so the whole
protein molecule is constantly dynamically moving anyway .
And therefore the major folding forces would come from this self shake .

Thank you for your neuron use .
william james tait .

maybe a desktop cray supercomputer is a good thing .

jacjentait wrote:



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 [Only registered users see links. ]).

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
showed.

>So wouldn't protein folding depend on the weather of this low




Also,






Well, under the theoretical 'low probablility' interacting 'space' scenerio,
there is a state of equilibrium that is attained by forces that pull in
various directions and there is a certain amount of stability achieved,
given that nothing changes and temperature, pressure, etc., remain constant.
However, in solution, the 'interactions' with the environment, eg., with
molecules of water, can't be avoided and aren't exactly 'low probability'.
--
Rolands G. Aravindan
[Only registered users see links. ]