From: Matt Newville
<newville@cars.uchicago.edu>
To: XAFS Analysis using Ifeffit
<ifeffit@millenia.cars.aps.anl.gov>
Sent: Tuesday, December 18, 2012 7:52
AM
Subject: Re: [Ifeffit]
Beryllium and EXAFS
Hi Gina,
On Mon, Dec 17, 2012
at 5:23 PM, Clayton, Gina <
ClaytonG@njhealth.org>
wrote:
> Hi there
>
> I am trying to find out more about
EXAFS. I am a protein crystallographer.
>
>
> I want to
identify the environment of a beryllium ion in the protein, I work with,
of which I have a crystal structure. EXAFS was recommended as a good
technique for identification of the beryllium site and species. The beryllium
is an acidic pocket of the protein surrounded by oxygens from the protein,
likely covalently bound. However I have had zero result finding a beam
line that can tune their setups to the Be edge at 111 eV. Also some EXAFS
users say that EXAFS technique would be good for working out the environment
of the Be but some say it would not . In particular I have been advised
that Be EXAFS would not be useful since the Be EXAFS signal
would have unacceptable interference from the carbon K-edge at 285 eV and the
oxygen K edge signal at 535 eV.
>
> Would EXAFS work or something
in a similar vein? Or, for instance, could the acidic pocket be
identified using EXAFS, by measuring the oxygens (instead of the Beryllium)
using the protein with and without beryllium?
>
>
> Thank
you so much for any advice.
>
> Gina
As you and as the
person who advised you suspect, you face a number
of
challenges:
1. The extremely low energy (111 eV). You
might be able to find a UV
source or x-ray beamline that can reach this
energy , but often such
work is done in vacuo, and so may not be suitable
for proteins. Using
electrons (from a TEM, say) might be possible too
-- these can
sometimes do C and N edges either directly or looking at
Electron
Energy Loss (send in an electron of high energy E1, and look
for
electrons of energy E1 - E, and scan the analyzer for the loss
energy
E through the absorption edge). Again, electron probes may not
be
what you want for your proteins.
2. The C K-edge will limit your
signal to "only" 175 eV. I would say
to not worry so much about this
limitation. You'll really be
measuring NEXAFS (near-edge X-ray
absorption ....) but that's OK.
People measure the B, C, N, and O K
edges, all facing the same
problem, especially for the O K edge: our planet
is more or less
covered with the stuff ;). These spectra tend to be
very rich and
sensitive to ligands.
3. Not much (zero?? I can almost
believe that!) literature on Be XAFS.
This is unfortunate because most
NEXAFS is measure and compare to
known spectra. I think that might
mean you have to spend effort to
building up a spectral library for Be in
organic phases.
I think trying to measure the O K edge with and without
Be is nearly
hopeless. All the X-ray spectroscopies average equally
over all the
atoms of the absorbing species. In addition all the
spectra are
grossly the same (a step function from 0 below the edge to 1
above the
edge). These make it difficult to see changes below about
1%. So I
think you would just have too high of an O::Be ratio
to see anything
useful.
One option to consider is using X-ray Raman
scattering
(http://en.wikipedia.org/wiki/X-ray_Raman_scattering).
Here, one hits
the sample with high-energy X-rays (say, 10 keV), which are
highly
penetrating for reasonably sized protein sample. One analyzes
an
energy loss (again, E1 - E, where here E1 is around 10 keV) to get
the
edge of interest. I'm familiar with (been involved with) studies
on
B, C, and O using this technique (all in solids, mostly at
high
pressure). See, for example, S. K. Lee, et al "Probing of
bonding
changes in B2O3 glasses at high pressure with inelastic
X-ray
scattering", Nature Materials 4, pp 851-854 (2005), and also
the work
of Simo Huotari. I'm not aware of anyone doing Be
K-edge this way,
but it should definitely be possible. For the work I've
been involved
with, Be would be challenging because there are other
excitations in
solids that appear around 100 eV. I believe that
effect would be far
suppressed in a protein, though I'm not
sure.
That's somewhat more exotic than straightfoward XAFS,, but it
might be
the best chance for measuring Be in a protein. I'm
not sure I know
any beamlines that do X-ray Raman on proteins, but I'd
suggest APS
beamline 20-ID or ESRF beamline as places to start.
The next
questions would be "how many Be atoms are in your
protein?", and "how
much material do you have?"....
Hope that
helps,
--Matt
Newville
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