329
> jinghuang at mednet dot ucla dot edu
> http://labs.pharmacology.ucla.edu/huanglab/
>
>
> From: Jacob Keller [j-kell...@fsm.northwestern.edu]
> Sent: Monday, September 05, 2011 12:18 PM
> To: Huang, Jing
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb]
y.ucla.edu/huanglab/
>
>
> From: Jacob Keller [j-kell...@fsm.northwestern.edu]
> Sent: Monday, September 05, 2011 12:18 PM
> To: Huang, Jing
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Trying to "digest" PISA result
UK
Subject: Re: [ccp4bb] Trying to "digest" PISA results
I did a similar assay years ago, but since the results were negative,
never published anything--it was seeing whether nucleotides bound to
my protein of interest by time courses of proteolysis +/- nucleotide.
One tricky part of the
at mednet dot ucla dot edu
> http://labs.pharmacology.ucla.edu/huanglab/
>
>
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller
> [j-kell...@fsm.northwestern.edu]
> Sent: Monday, September 05, 2011 10:10 AM
> To: CCP4BB@JI
b] Trying to "digest" PISA results
NMR...take that!
JPK
2011/9/5 Andreas Förster :
> AUC !
>
>
> Andreas
>
>
>
> On 05/09/2011 6:00, Jacob Keller wrote:
>>
>> mea culpa! How about FRET?
>>
>> JPK
>>
>> On Mon, Sep 5, 2011 at 11:
Free flow electrophoresis would be another option, by the way anybody on the
East Coast who has one of those instruments ? I'd be interested to get an email
directly.
Thanks,
Jürgen
On Sep 5, 2011, at 1:00 PM, Jacob Keller wrote:
mea culpa! How about FRET?
JPK
On Mon, Sep 5, 2011 at 11:39 A
NMR...take that!
JPK
2011/9/5 Andreas Förster :
> AUC !
>
>
> Andreas
>
>
>
> On 05/09/2011 6:00, Jacob Keller wrote:
>>
>> mea culpa! How about FRET?
>>
>> JPK
>>
>> On Mon, Sep 5, 2011 at 11:39 AM, Bosch, Juergen wrote:
>>>
>>> Hi Jacob,
>>> you forgot cross-linking to stabilize a weak complex
AUC !
Andreas
On 05/09/2011 6:00, Jacob Keller wrote:
mea culpa! How about FRET?
JPK
On Mon, Sep 5, 2011 at 11:39 AM, Bosch, Juergen wrote:
Hi Jacob,
you forgot cross-linking to stabilize a weak complex and verify that it
exists.
Jürgen
On Sep 5, 2011, at 11:45 AM, Jacob Keller wrote:
W
mea culpa! How about FRET?
JPK
On Mon, Sep 5, 2011 at 11:39 AM, Bosch, Juergen wrote:
> Hi Jacob,
> you forgot cross-linking to stabilize a weak complex and verify that it
> exists.
> Jürgen
> On Sep 5, 2011, at 11:45 AM, Jacob Keller wrote:
>
> Well, I guess I have always been curious what is t
Hi Jacob,
you forgot cross-linking to stabilize a weak complex and verify that it exists.
Jürgen
On Sep 5, 2011, at 11:45 AM, Jacob Keller wrote:
Well, I guess I have always been curious what is the gold standard
here--perhaps SEC, ITC, SPR, pulldowns? What if SEC shows a
polydisperse sample wi
Well, I guess I have always been curious what is the gold standard
here--perhaps SEC, ITC, SPR, pulldowns? What if SEC shows a
polydisperse sample with weak oligomerization, or SPR a very weak
binding constant? Do we then revert to a functional assay? Or what if
the functional assay does not show a
I get confused by these figures. As I understand it the "interface area" given
in Pisa is half the loss of accessible area on forming the complex: is that
right?
We're working on a complex with interface area ~500A^2, where the complex is
stable enough for gel filtration, and with a measured Kd
720 is not an impressive size for a stable interface, but it may do depending
on molecule size and exact chemistry of the interface (h-bonds, salt bridges,
disulphides, charges etc etc). Everything is subject to chemical environment
and concentration, as usual. For these entries, PISA gives diss
Like Jan, I find it very useful to sort out the clear cut cases.
Otherwise it is easy to get things wrong..
But isnt a buried surface area of 720 rather small for a stable
interface? If there is other confirming evidence like 2 diff space
groups then you feel more secure!!
On 09/01/2011 02:
This is regarding Ethan´s point, particularly:
>2) the protein has crystallized as a monomer even though it
>[sometimes] exists in solution as a dimer. The interface
>seen in the crystal is not the "real" dimer interface and
>thus the PISA score is correct.
I see the same exact interface i
I guess both of the mentioned possibilities occur and it is hard to judge
which one it is for a particular case.
PISA is extremely useful for clear-cut cases to judge them quick. In the
"borderline" ones it remains to be the task of the research teams to prove
what sort of oligomerisation state is
On Wednesday, 31 August 2011, Jan Dohnalek wrote:
> Wasn't the original question directed to our (growing) feeling that many
> times PISA says No obvious oligomerization pattern but we already have
> evidence of dimer formation etc..
> This should happen "occasionally" as the approach implied in th
Wasn't the original question directed to our (growing) feeling that many
times PISA says No obvious oligomerization pattern but we already have
evidence of dimer formation etc..
This should happen "occasionally" as the approach implied in the
calculations is statistical in a sense. We should not be
http://www.ebi.ac.uk/msd-srv/prot_int/pi_ilist_css.html
so it depends on how many 'stable assemblies' pisa can find i suppose.
more interfaces and especially if stable enough will make your
fraction go down. i would have been more surprised or worried if that
conservative mutation showed radically
I was playing around with PDBe PISA and came across the following:
For pdb entry 1OYA. The most promising interface has an area bury of around
720A^2 and DeltaG of -10.6Kcal/mol. sym_op(y,x,-z+1) and CSS of 0.039!
Assembly analysis says it has no strong indications that point to stable
quatern
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