On Wednesday 13 May 2009 10:22:54 Patrick Loll wrote:
> Greg Petsko's group did something like this about a billion years ago
> (yet, strangely, I remember the paper, even though I'd be stumped if
> you asked me what I had for breakfast...)
>
> They covered the range from room temp down to very cold, using
> different cryoprotectants (importantly, they were not vitrifying
> their samples). I recall a plot of ADPs vs. temp that showed an
> essentially linear decrease down to some temp (maybe around 150 K or
> so?), after it plateaued, with no further reductions being seen at
> even very low temp. They rationalized this by saying (I think) that
> the decrease represented the dynamic disorder, which was damped at
> low temperatures, and the plateau represented the point where static
> disorder became the predominant contributor.
The problem with this and other older protein work is that it predates our
current capabilities to handle models of anisotropy in protein structures.
The interesting temperature-dependent effect manifests most significantly
as an evolution of anisotropy. It is not well captured by looking
only at isotropic B factors.
Ethan
> I remember thinking at the time that this made great intuitive sense.
> I have no idea if people still buy this.
>
> I can't put my finger on the reference, but if you start here you can
> probably find your way: Ringe D, Petsko GA. Study of protein dynamics
> by X-ray diffraction. Methods Enzymol. 1986;131:389-433.
>
> On 13 May 2009, at 12:30 PM, Jacob Keller wrote:
>
> >> The reason is that you've missed out one important term: the
> >> atomic displacement parameters (B-factors), which describe a
> >> combination of thermal motion and positional disorder between unit
> >> cells.
> >
> > A somewhat niggling point: isn't it true that the thermal motion is
> > insignificant at 100K? Does anybody know of a paper which
> > systematically measures B-factors as a function of temperature? The
> > asymptote of the resulting curve would represent all of the non-
> > thermal elements, right?
> >
> > JPK
>
> ------------------------------------------------------------------------
> ---------------
> Patrick J. Loll, Ph. D.
> Professor of Biochemistry & Molecular Biology
> Director, Biochemistry Graduate Program
> Drexel University College of Medicine
> Room 10-102 New College Building
> 245 N. 15th St., Mailstop 497
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>
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> pat.l...@drexelmed.edu
>
>
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
