I don't wish to vear away from Victor's thrust with starting this
thread and I would happily sign the petition you suggest.
But I feel I should respond to the assertions about 'problems of peer
review' at least with respect to Journals of my experience.
Some 'Editor handling of submissions'
Have you tried
csymmatch -pdbin-ref one.pdb -pdbin two.pdb
That will move chains to match asfar as possible, using sym ops and
allowedorigin shifts to generate the best fit.
Eleanor
On 11/18/2010 12:26 PM, Ian Tickle wrote:
OK now I understand. I couldn't find the script 'origin.com' you
Dear John,
I did not have the IUCr journals specifically in mind while making
these remarks.
Quite the contrary, I think due to you and other colleagues and
friends, they are
run competently and to the benefit of the community and of science at
large.
If I may though offer an opinion
Where do I find documentation for csymmatch ? Google is normally good
at finding program documentation (and sometimes code which is
infinitely better) but not in this case - I even tried spelling it
'csymatch' just in case!
I was just interested to know whether csymmatch tries all combinations
Regarding editorial decisions, I actually welcome editors making more rejection
decisions, i.e. reading the paper before sending it to referees, so I waste
less time, waiting as author, or as referee reading and commenting on papers
for which it would have been clear beforehand that they are
Hi all,
I have a crystallographical/biochemical problem, and maybe some of you guys can
help me out.
We have recently crystallized a protein:protein complex, whose Kd has been
measured being ca. 10 uM (both by fluorescence polarization and surface plasmon
resonance).
Despite the 'decent'
Dear Tassos,
Thankyou for sharing your own experiences as an Editor with Proteins,
and with PNAS, which I really appreciate, and in particular for your
suggestion of an anonymous Editor approach.This is interesting to me
not least as one of the three Appeals I rejected, to which I referred
below,
I can direct you to PDB entry 1EWY, where the average isotropic
temperature factor for the major component of the complex is ca. 47 A**2
and that for the smaller component is ca. 69 A**2. Similar values than
the ones you are reporting. I am assuming some sort of disorder, or if
you prefer,
Hi Sebastiano,
I have had some experience with protein:protein complexes with KD ~
10-1 uM, kinetic characterization and trying to purify a complex of
these proteins using SEC. While I would say that if you have reliable
evidence from SPR that you have a fast on (high Kon), then you must
(Apologies to those who have already seen this on the PyMol list)
Does anyone have experience of a working Mac Pro/Quadro FX 4800/120Hz
flat screen setup? I'm trying to put one together, and am getting
nowhere.
We have:
- Mac Pro (early 2010, MacPro 5,1) running 10.6.4
- Quadro FX 4800
A suggestion for purifying the complex: let's say there is a 5mL gap between
the complex and one of its (smaller)constituents A. You can pre-load the
column with, say, 5mL of A at 1uM, then inject the complex at 80-100uM, to
be injected right after the pre-load. This should provide
Dear Jacob,
The SEC is generally run to separate the complex from the unbound components.
If run the way your propose, the peak of unbound preinjected smaller component
coincides with the peak of the complex and the final stochiometry is not better
than by just mixing the components without
Well, mixing together has a much bigger pipetting error (to get, say,
500uM, you have to add 1000uM proteins A and B together, so with a
pipetting error of ~1% even (and concentrated protein solutions seem
to be tricky to pipette accurately), there would be an error of 10uM.
Also, there are the
Hi Sebastiano,
I don't see how the k-off would influence this, given the timescale of growing
crystals.
An explanation in terms of high Kd and relative lack of crystal contacts for
the component with higher temperature factors would sound more convincing to
me.
Mark
Quoting Vellieux
I should add that this procedure is really only advantageous for high
Koff complexes. If the complex does not dissociate appreciably in the
time required for SEC, I agree that there is no great benefit for
doing it my way. I have been working recently, however, on a high Koff
complex, so have been
The amount of small component one looses from the complex depends on the Koff
and the local concentrations during the SEC run, so I doubt if one could
estimate those losses with an error less than the 1% pipetting error you quote.
What I would do is to pipet dilute solutions, and concentrate
Well, if one of the components is a small peptide and the solutions
are dilute, it is hard to concentrate the complex, as the free peptide
will go through the concentrator! It's a tricky problem.
JPK
On Fri, Nov 19, 2010 at 9:38 AM, herman.schreu...@sanofi-aventis.com wrote:
The amount of
If the peptide is really small compared to the protein, I would just add excess
peptide and not worry about the stochiometry.
Best,
Herman
-Original Message-
From: Jacob Keller [mailto:j-kell...@fsm.northwestern.edu]
Sent: Friday, November 19, 2010 5:03 PM
To: Schreuder, Herman RD/DE
This doesn't directly address your question, but since the subject of analyzing
protein-protein interactions with gel filtration is raised on this bb
occasionally, I thought I would mention that there are cases in which
conventional gel filtration chromatography fails to provide evidence of a
Yes, this is where I heard of the technique, and my suggestion was a
modification of that, but my references were:
Hummel JP Dreyer WJ (1962) Measurement of protein-binding phenomena by gel
filtration. Biochim Biophys Acta 63:530-532.
Ratner D (1974) The interaction bacterial and phage
Sebastiano,
We observed similar phenomenon in our protein-protein complex. This
reference will give you details (Crystal Structure of an Electron Transfer
Complex between Aromatic Amine Dehydrogenase- Azurin from Alcaligenes
faecalis, Biochemistry, 45, 13500-13510, 2006).
Sukumar
Narayanasami
I took a look at his slides--looks pretty interesting, and I would
have liked to have heard the talk! I am not sure I would be ready to
advocate having no more journals, but I am interested in thinking
about the idea. Imagine just putting your data up on the website, and
you're finished! And then
On Fri, Nov 19, 2010 at 11:33 AM, Jacob Keller
j-kell...@fsm.northwestern.edu wrote:
I took a look at his slides--looks pretty interesting, and I would
have liked to have heard the talk! I am not sure I would be ready to
advocate having no more journals, but I am interested in thinking
about
I think you are right--it would have to be a centralized site, like
the openacademia.org proposed by Peter Mika. I think there should be
several levels in the site, which would correspond to level of
closeness to phenomena, somewhat like the progression from abstract
discussion results methods.
I don't think there is any relationship between rate constants and B
factors. Yes, there is the hand-wavy argument of disorder begets
disorder (and people almost always LITERALLY wave their hands when they
propose this), but you have to be much more careful than that when it
comes to
Maybe you should look at: Rotation barriers in crystals from atomic
displacement parameters Emily Maverick and Jack Dunitz (1987) Vol
62(2), 451-459.
They reported that the libration amplitude of one part of a crystalline
small molecule relative to another part is strongly correlated to bond
The journal was Molecular Physics (1987) Vol 62(2), 451-459.
(my brain librates when I type)
Daniel Anderson wrote:
Maybe you should look at: Rotation barriers in crystals from atomic
displacement parameters Emily Maverick and Jack Dunitz (1987) Vol
62(2), 451-459.
They reported that the
Hi All
does anyone know any software that can calculate and print out RMSD of
every residue (c alpha will be good) for homologous structures which has only
30-40 % sequence similarity? I looked on the web but all the software that I
found require the sequence to be the same for both
On Friday, November 19, 2010 02:55:54 pm Srivastava, Dhiraj (MU-Student) wrote:
Hi All
does anyone know any software that can calculate and print out RMSD of
every residue (c alpha will be good) for homologous structures which has only
30-40 % sequence similarity? I looked on the web
I looked on the web but all the software that I found require the sequence
to be the same for both structure.
most modern programs perform some kind of local-global alignment first
to define the corresponding residues and then compute the statistics.
BR
Dear Dhiraj;
Please try the following web site
http://www.cgl.ucsf.edu/home/meng/grpmt/structalign.html
Here you will find a number of option for structure base sequence
alignment no matter what is the similarity of your structures. Regarding
the RMSD of every residues you can find this option
Depending on the type of resin you should be able to use IMAC all the way up
to pH 11 or so (works for Ni-NTA, not sure about HIS-SELECT or other
resins). Obviously your buffer system changes (carbonate works well at 11).
Why not to elute the complex together with pure monomer and then try
On 10:51 Wed 17 Nov , Warren, Mark R wrote:
I am trying to compare the difference between two diffraction images
from a Mar detector before and after irradiation. At present I have
used the marcombine program to subtract the diffraction images, but I
don't have any statistical
I wish to thank everyone. I did try shifting to a higher pH and flushing 3l of
salt solution over the column which did not work. I tried 20ml 2M Urea on the
column and a stepwise shift to no urea that showed removal of the protein. I
will try binding studies to see if I did not denature the
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