Thanks Edward! Actually Areaimol works well for my problem.
But now I have a new issue looking for some advice. I want to randomly
generate some points in the unit cell and make a quick judgment whether it
is outside of the solvent mask or not. It seems that Areaimol doesn't help
at this point, an
Dear all,
I'm refining a structure which has both N-linked and O-linked
glycosylation. I use Phenix to do the refinement. It works well for the
N-linked NAG. I defined the link as the following:
apply_cif_link {
data_link = "NAG-ASN"
residue_selection_1 = "chain A and resname NAG
Hi,
You can read the spectrophotometric absorption at 280 nm and 200nm in UV
range.
It should serve your purpose and provide a decent idea for the amount of
protein in the sample.
Provided that absorbance at 280nm is given by aromatic rings but at the same
time absorbance at 200nm is contributed by
Areaimol is good for determining the contact area from the difference you
mentioned. If you want to distinguish real clashes from comfortable
van-der-Waals
contacts, you can use pdbdist3:
http://sb20.lbl.gov/berry/for/pdbdist3.for
The two molecules have to be in separate pdb files. You
Hi,
I have 2 rigid and fixed proteins and want to quickly judge whether there
are some steric clashes. One quick way I am thinking is using CCP4
AREAIMOL to calculate the surfaces of each individual protein as well as
the heterodimer, and check whether the sum of the two individual surfaces
is lar
Hi Arpita
You can try QUANTI-iT
Protein assay kit from Invitrogen.
But still there is
nearly 20-50% discrepancy between this method and a Abosorbance at 280.
I also faced same
problem with a protein, then re-cloned by adding a Trp at the C-terminus.
Raj
E. Rajakumara
Postdoctoral Fellow Str
Hey, does Wikipedia lie? Also, the reference is to Lehninger's text,
although I did not verify it.
http://en.wikipedia.org/wiki/Heparin
On Sun, Apr 10, 2011 at 3:37 PM, Dima Klenchin
wrote:
>
>> heparin sulfate has the highest negative charge density of any known
>> biological molecule.
>
> Seem
heparin sulfate has the highest negative charge density of any known
biological molecule.
Seems to me that phytic acid (IP6, C6H6-(H2P04)6) and inositol
heptakisphosphate (IP7) should have higher charge per mass and per volume.
- Dima
Related fact I learned recently, perhaps of interest for fellow record-keepers:
heparin sulfate has the highest negative charge density of any known
biological molecule.
JPK
On Sat, Apr 9, 2011 at 9:38 PM, Raji Edayathumangalam wrote:
> Hi Alex,
>
> Most DNA-binding proteins has decent affinity
Hi Alex,
as you have a DNA binding protein does it have a high pI? If so, good old ion
exchange with an S-sepharose column should do it.
Cheers
James
Dr James Garnett
Division of Molecular Biosciences, Imperial College London,
Level 5, Biochemistry Building,
South Kensington,
LONDON SW7 2AZ,
U
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