Dear All,
I'm looking for a free program that I can use to measure the geometric
surface complementarity of protein-protein interfaces. I have created
inhibitor mutants that possess different binding affinities to their
cognate enzyme and it would be very helpful if I can quantify the shape
Dear CCP4 colleagues,
We have a protein that is composed of two domains
connected by a short peptide linker. We have some indirect evidence showing
that the two domains may somehow move against each other when exposed to
different pH. It is unlikely to have any obvious secondary structure
Daniel,
You'll probably have to monitor pH changes through size changes of your
protein, provided the structural changes will indeed cause size changes.
You said easy, so that probably rules out Small-Angle X-Ray Scattering
(SAXS), but that would be the highest-resolution method. You can try
Wouldn't a HSQC of 15N-labeled protein be a relatively easy yes/no
experiment? Maybe it would not be incredibly definitive?
Jacob
On Mon, Dec 6, 2010 at 11:10 AM, Mischa Machius mach...@med.unc.edu wrote:
Daniel,
You'll probably have to monitor pH changes through size changes of your
Hi
SAXS can be a right tool. However, how big is short peptide linker?
Check Nature paper by Askarieh G. and Hedhammar M. for non-His pH
sensor.
cheers
Alex
Am 06.12.2010 um 17:59 schrieb Daniel Jin jin_xiec...@yahoo.com:
Dear CCP4 colleagues,
We have a protein that is composed of
If there are backbone NMR assignments available then, definately a pH titration
using HSQCs would give site specific information. These are easy experiments
if someone can help you set them up.
The perturbations should map to the inter-domain interface.
If there are no assignments for the
Even without assignments, wouldn't a dramatic shift be seen in the
interacting residues? Also, I suggested the method because it is
pretty easy, probably doable in a week...
Jacob
On Mon, Dec 6, 2010 at 11:24 AM, Roopa Thapar rtha...@hwi.buffalo.edu wrote:
If there are backbone NMR assignments
I agree that the experiment is a good one and can easily be done, but without
assignments I think the interpretation could be ambiguous.
pH dependent chemical shift perturbations could occur far removed from the
linker (either due to a conformational change or the change in chemical
Dear colleagues,
I am analyzing a helical segment that looks a bit off from the
traditional alpha-helix. Does anyone knows a program for calculating
alpha helix translation per residue along the helical axis?
Thanks,
Young-Tae
Young-Tae Lee, Ph. D.
Research Associate
David Goodin lab
Well, I just got word that the protein is ~100kD anyway, so I think
the HSQC is out the window anyway!
Jacob
On Mon, Dec 6, 2010 at 12:16 PM, Roopa Thapar rtha...@hwi.buffalo.edu wrote:
I agree that the experiment is a good one and can easily be done, but without
assignments I think the
Dear Young-Tae,
The program Twister (Strelkov and Burkhard, 2002) can calculate this,
among other things. If you are interested I would gladly send you
the program.
Of course one should look into the reason for your helix having
an aberrant geometry. If it is just a slightly distorted a-helix
Dear Mohd, CCP4 contains a program SC which does the job.
sincerely
Mike Lawrence, PhD
Associate Professor and WEHI Fellow
Division of Structural Biology
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville
Victoria 3052, AUSTRALIA
Tel. 61-3-9345-2693
Fax
The venerable 600 series cryostream I use on our Raxis is getting too
flakey, and as they are no longer supported I cannot get it fixed. Should
anyone be thinking of sending one to the skip, I should be very pleased to
hear from you (directy).
Peter Moody
University of Leicester
Leicester UK
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