

Physicists Discover Quantum Law Of Protein Folding - ryannielsen
http://www.technologyreview.com/blog/arxiv/26421/

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dalke
Read it again. The paper says that if you use a specific quantum mechanics
model then you get results with several free parameters. These parameters can
be tuned against 15 existing molecules and the equation gives some explanatory
power of why the folding is non-Arrhenius.

Several things must occur before you can say it's real: does it apply to other
molecules, what are the sources of the differences between prediction and
measurement, do molecules while folding really undergo some sort of non-
continuous motion and can it be detected and why hasn't it ever been seen
before, and do the matching corresponding Newtonian+statistical dynamics give
similar predictions?

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hagy
Exactly! This high level model doesn’t draw on any quantum specific phenomena
and is in many ways comparable to other stochastic dynamical models that have
been developed to explain the non-Arrhenius behavior of protein folding using
classical Langevin theory.

To argue for the inclusion of quantum theory in explaining protein dynamics is
to assert that proteins undergo classically forbidden conformational
transitions. The authors of the paper have provided no evidence for such
transitions nor even hypothesized about how such transitions could arise.
Their only argument against a classical description of protein folding is the
inability of molecular dynamics simulations to model the folding-kinetics of
some proteins. Seeing as molecular dynamics force fields only provide a rough
and approximate description of the forces between atoms within a protein it
should be no surprise these methods can’t accurately model the intricate
conformational transitions in protein folding.

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gus_massa
There are some extrange detals in the original paper.

For example the experimental points in the graphics do not have error bars.
The x axis is 1/temperature, so the error should be small. But in the y axis I
spect that the measures have a more visible error. Some of the graphics
("Protein A", "L9") have a very good theoretical fitting, so it is possible
that the experimental data have very small errors. But in others graphics
("Engrailed Homeo Domain", "Trpcage(WT)") the points are scattered around the
theoretical fitting, so perhaps the measures have a appreciable error or the
theoretical fitting has problems.

And in the lasts graphics the fitting is not very good. In particular in
"Villin Headpiece Subdomain" the fitting id horrble. I see that the
experimental point lie in something like an "U" but the fit is like a shallow
"^".

Another problem is that they have too many free parameters: "R" and "S" are
free. And "Tc" is free too (it is an experimental value, not deduced from the
model). But near the maximal point of the curve, everything is almost a
parabola, so with 3 free parameters it is possible to fit almost everything.
For example, for the first graphic ("Protein A") a possible fit using thee
parameters is

    
    
      ln(K_1)= -7.4161 * (1000/T - 3.1469)^2 + 12.418
    

They have a more difficult functional dependency, but with tree free
parameters it is not clear that they have the correct model.

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nickpinkston
There are other quantum-bio efficiencies being studied - such as this one for
best-path photosynthesis reaction chains:

<http://physicsworld.com/cws/article/news/41632>

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maxharris
Well I'll be damned! Wow!

It seems obvious now, but I really would never have thought that quantum
mechanics would matter here. I'm not sure that this simplifies anything. I
wonder what D.E. Shaw research is going to do about it if this pans out?
(They're the folks behind ANTON - see <http://www.deshawresearch.com/>)

~~~
nochiel
"Wow!...It seems obvious now..."

What a vigorous hand-wave! How, pray tell is it obvious?

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crayz
The idea that the mind is some sort of insanely complex, naturally evolved
quantum computer is becoming increasingly credible

~~~
Miky
No, it's not. There is extremely little to suggest that it uses quantum
effects for computation.

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vain
somebody hide this from deepak chopra before he claims it as validation to one
of his open ended theories!

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marckremers
Awesome site, thanks for the share.

