"Clive Delmonte" <clived at ndirect.co.uk> said:
> Thank you for the molecular dynamics calculations.
Actually, they were just straight thermodynamics calculations.
The MD comes into play when I assert (without proof to back me
up because I don't have the references handy) that the standard
force field energies, which are derived from small chemistry
workd, give values reasonable close to that observed
experimentally. In this case, "reasonable" means well less than
that needed to allow your belief that a new, dominant DNA
conformation exists.
Thus, I cannot believe your model is feasible.
> If the true side-by-side model had been first on the scene, and
> then the double helix had come along, would it have been said that
> for 95% occupancy as a double helix, that the latter structure
> would have to be some 7 KJ/mol more stable and that that would
> be highly improbable ?
I cannot answer yes or no directly because your question
presupposes conditions I believe to be unlikely. Working in the
subjunctive case is tricky, but I'll try to respond that way.
If there had been a dominant side-by-side model, we would also
have to assume that the force field prediction and the experimental
results are close enough that few would be concerned about the
difference. I do not believe this could have happened, but suppose
for some bizarre reason no one ever thought to compare the two.
Then if someone proposed a double helix structure, that person
could use one of the standard force fields (Amber, CHARMm, MM3,
UMFF(?), etc.) to get an estimate of the energies of the two forms
and show that the double helix model gives a better theoretical
model, and yes, it would have to be at least 7kJ/mol better. Of
course, it would also have to be able to explain the other
experimental results, but my background is physics and I believe
in energetics arguments.
So a way to convince me is to construct a structural model,
solvate it along with the appropriate counter ions, equilibrate
the results, and compare the binding energies. Or just propose a
structure with chemically realistic parameters. But, I've seen
simulations of untwisting a double helix DNA to study how the
conformation changes, and I can promise that untwisting the DNA
is very energetically unfavorable.
> A true side-by-side model (attached)
I didn't find any structural model attached. There was a MS Word
document, but I do not have a program which can read that format.
There was also a repost of your Puzzle 6. If you have a 3D model could
you post it in PDB format? (The definition is available from
www.pdb.bnl.gov and I only need the ATOM records to view a structure.)
I can also do a file with lines of the form "atomname x y z" if you
have that.
> The central problem, at this stage, is not whether molecular
> dynamics seems to show one structure to be more or less stable than
> the other.
>> The central problem is how to explain the Puzzles.
I disagree.
I have explained the Puzzles by saying that your interpretation of
the experiments must be wrong.
The theoretical double helix model gives a predictive binding energy
close enough to experimental results such that a more dominate
conformation cannot exist without the presumption that the underlying
force field or experiments are wrong. Yet those measurements are
relatively easy to make and widely used so the likelihood of you being
correct is much lower than of you being incorrect.
You point out your problem 6. The central question is:
> The problem is evident: How and where would the torque arise inside a
> solid fibre that would permit one double helix to rotate so as to
> unwind one strand and rewind it onto an adjacent triple helix having
> a different diameter and rotating at a different angular velocity ?
This is also addressable by an energetics explanation. For the
environment of that fibre (which I assume was relatively dry compared
to standard DNA conditions) the triple-strand conformation was
energetically more favorable than the double-strand found in solution.
(I assume you draw a fibre from a solution; I have only the vaguest
understanding of fibre crystallography.)
There's an energy barrier between the 2- and 3- strand states, which
explains why it took several days for the transformation, and the
change in diffraction pattern means that the new state is much more
energetically favorable than the old one.
I don't know what you mean by "angular velocity" for this example.
Molecular motion is strongly affected by frictional forces and any
angular velocity contribution is quickly dampened. My assumption is
you are using the wrong term.
Also, you have an unwarranted belief that a "solid fibre" means
everything is fixed in place. Your intuition is likely based on your
macroscopic experience, which is invalid on the molecular scale.
Solids can diffuse through solids, albeit slowly, and the fibre
still has a large aqueous component which raises the diffusion rate.
(One of the big news stories last year in the semiconductor industry
was learning how to use copper and silicon together. The problem
is the copper would diffuse through the silicon and ruin the chip.
This is an example of solid-solid diffusion without any water on
a timescale which is physically and commercially relevant.)
> Inside the fibre, individual molecules would have a random axial
> translation so only very rarely would two adjacent double helices
> have the same axial starting point down the fibre, and they would be
> unlikely to be perfectly straight inside the fibre but would probably
> be entwined around neighbours.
Your statement neglects random thermal motions, which means the
molecules are *always* moving somewhat. Given the existance of a
dominant favorable energy state, eventually most of the system will
be in that state. This can be the source for the torque you require.
This can even be observed in macroscale experiments, with
sufficiently delicate instruments. Torsion balances are used to
measure the gravitational constant. When local variations in the
gravitational field are properly canceled, there is a very nice
rotational term which corresponds to the thermal motion of a
several hundred kg mass. This occurs even if the mass initially
had no rotational component. (It doesn't violate conservation
of momentum because you don't see change in the air molecules which
caused the rotation, nor the influence of those molecules on the
earth.)
I believe you do not know enough about thermodynamics/statisical
mechanics to understand why my argument is not only reasonable but
expected. Hence, you will not be able to construct an energetics
argument for why thermal effects are insufficient to explain your
Puzzle 6. Until you manage to do so, I again must argue that the
answer to your puzzles is that you do not understand the underlying
science enough to give a helpful, much less meaningful new
interpretations of the experiments you reference.
This level of thermodynamics understanding is available from
most any undergrad physics statistical mechanics book so should be
much easier to learn than the details of how xtal refinement software
works.
Andrew Dalke
dalke at acm.org
