VMD-L Mailing List

From: Andrew Dalke (dalke_at_dalkescientific.com)
Date: Wed Mar 05 2008 - 16:32:42 CST

On Mar 5, 2008, at 2:53 PM, Fei Chen wrote:
> I'm not sure whether it's apt to issue the problem here.
> I assume that there is some forces responsible for the structure or
> function of a protein.
> I want to find the main reason that result in the structure or
> function of a protein.
> I can compute the bond-force or non-bond force between two atoms in
> a protein, should some atoms' force be the most important for the
> structure or function of the protein? Are bond-force and non-bond
> force adequate? Or should I take other factors for account?

The answer is "yes to all".

You asked a question which is almost impossible to answer, because
there's a basic understanding that seems to be lacking in the question.

You need to get an understanding of chemistry first, or of physics.

The forces are that of quantum mechanics, although relativistic
quantum mechanics is mostly only needed for heavy/metallic atoms.

The approximation made for more organic systems is that nucleons are
point charges, electrons are "fast", and that the only force to worry
about is mediated by photons. That is, electricity and magnetism.

"bonds" are an approximation for how to think about the quantum
mechanics. They are useful, but incomplete. Molecular modeling also
talks about angle and dihedral forces, van der Waal forces, and
"normal" electrostatic forces. Some people talk about aromatics and
ring currents. All of these are aspects of the same electromagnetic
force.

The way that force is expressed differs for different molecules. All
molecules have a strong covalent component. That defines the primary
structure. But there's also additional structures caused by other
modes, like hydrogen bonds in alpha helices and beta sheets. There's
a force term caused by the change in entropy around polar proteins,
which has its own effect.

So the answer is "yes, there are other factors you'll need to take
into account." Knowing what those are pretty much describes the
field of structural biology.

                                Andrew
                                dalke_at_dalkescientific.com