Dear Fritz,
You are right. The recollection of that striking 2015 paper was somehow
too strong to be 100% faithful: these are two different modes of using the
ligand deposited on a solid support by drying a solution of it, to avoid the
DMSO problem.
Best wishes,
Gerard.
--
On
:)
Gerard,
"soaking"!
Thanks for the reference!
cheers
guenter
Dear Guenter,
The first description of the idea behind this technique that I am aware
of is that published almost 10 years ago by a French group under the name of
"'dry' co-crystallisation" in the following paper:
Dear Guenter,
The first description of the idea behind this technique that I am aware
of is that published almost 10 years ago by a French group under the name of
"'dry' co-crystallisation" in the following paper:
http://dx.doi.org/10.1107/S1399004715010342
Best wishe
Hi Amit,
like Artem wrote below, even despite poor solubility, soaks with dried
compounds work well (also in our hands).
We adapted it from the work of T. Barthel, J. Wollenhaupt and Manfred
Weiss. Also colleagues from industry report good results.
We add compound dissolved in DMSO to the crysta
Wednesday, October 2, 2024 at 2:51 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: [ccp4bb] Co-Crystallization with drug molecule
Hi everyone,
I am trying to crystallize a protein with a drug molecule. The protein
concentration
*Subject: *[ccp4bb] Co-Crystallization with drug molecule
Hi everyone,
I am trying to crystallize a protein with a drug molecule. The protein
concentration is 15.5 mg/ml, the drug stock concentration is 10 mM,
and the drug is dissolved in DMSO. I am adding the drug to a final
concentration of
ubject: [ccp4bb] Co-Crystallization with drug molecule
Hi everyone,
I am trying to crystallize a protein with a drug molecule. The protein
concentration is 15.5 mg/ml, the drug stock concentration is 10 mM, and the
drug is dissolved in DMSO. I am adding the drug to a final concentration of 1
mM in
, delete the e-mail and do not disclose its contents to
any person. Any unauthorized review, use, disclosure, copying or distribution
is strictly prohibited.
Von: CCP4 bulletin board Im Auftrag von Tom Peat
Gesendet: Mittwoch, 2. Oktober 2024 23:23
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Co-
K
Subject: Re: [ccp4bb] Co-Crystallization with drug molecule
Dear Amit
As David already pointed out, all proteins are different and it's hard to say
in advance what amount of DMSO may work (or not).
An additional concern is that DMSO can also interfere with ligand binding
(cases from m
Dear Amit
As David already pointed out, all proteins are different and it's hard to
say in advance what amount of DMSO may work (or not).
An additional concern is that DMSO can also interfere with ligand binding
(cases from my personal past history), especially if these
inhibitors/ligands are on
on behalf of amit gaur
Sent: Wednesday, October 2, 2024 2:51 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Co-Crystallization with drug molecule
Hi everyone,
I am trying to crystallize a protein with a drug molecule. The protein
concentration is 15.5 mg/ml, the drug stock concentration is
Hi everyone,
I am trying to crystallize a protein with a drug molecule. The protein
concentration is 15.5 mg/ml, the drug stock concentration is 10 mM, and the
drug is dissolved in DMSO. I am adding the drug to a final concentration of
1 mM in 100 ul of protein, and the DMSO volume is 10 ul for
Co
Thank you everyone for the detailed explanations/suggestions and sharing
your successful experience. It is very helpful.
Earlier I had thought that maybe with ΔTm, I could select the most
promising molecules. But now it is unlikely the case.
I should have also mentioned that the IC50 values for a
*Dear Saif*
*Hope you are doing well and safe!*
1) How much change in Tm (ΔTm) in a thermal shift assay is considered to be
significant ?
*As it has already been mentioned there is no specific cutoff for deltaTm
to be considered significant. DeltaTm depends on many factors, including
the type o
Hi Saif,
If your goal is to perform co-crystallization, I am completely agreed with
David's suggestions. Delta Tm does matter in the co-crystallization but
that's not always the case. I have some experience with protein complexes
where I successfully co-crystallized by using really high molar rat
Hello,
we had an interesting case in the lab many years ago... Using the
shift-assay, a student managed to identify conditions that markedly
stabilized the protein of interest. To cut a long story short, in the
end it turned out conditions were identified that gave monomers while
the biologic
ee MX representative
==
about.me/david_briggs
From: CCP4 bulletin board on behalf of Saif Mohd
Sent: 25 February 2021 14:55
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Co-crystallization and thermal shift assay
Hello everyone,
1) How much change in Tm (ΔTm
Hello everyone,
1) How much change in Tm (ΔTm) in a thermal shift assay is considered to be
significant ?
2) A negative ΔTm infers that the compound is making the protein unstable.
In such a case, will the co-crystallization be difficult or just impossible
or on the contrary it shouldn't matter
h more ligand.
Best,
Herman
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Roger Rowlett
Sent: Thursday, August 25, 2011 6:11 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Fwd: Re: [ccp4bb] co-crystalli
Successful complexation depends on the
concentration of protein, ligand, and the Kd of the protein-ligand
complex. For Kd>>[protein], you will probably require
[ligand] > 10 x Kd. As Kd approaches [protein], slightly
superstoichiometric quantities will be sufficient f
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Yvonne
TAN Yih Wan
Sent: Thursday, August 25, 2011 2:03 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] co-crystallization
Hi ,
I am co-crystallizing a protein with compound and would like to know how much
of compound to add
Yih Wan
Sent: Thursday, August 25, 2011 2:03 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] co-crystallization
Hi ,
I am co-crystallizing a protein with compound and would like to know how much
of compound to add to protein solution to start with. I know that the protein
binds compound in a 1 to 1
for me, I prefer to sock these compounds into your crystal. it will much more
easy than co-crystallizaiton. But each protein should be different.
Normally when I star to co-crystallization with small compound, I will set up
the complex with 1:1.2 molar ratio as first trial to see what should hap
Hi ,
I am co-crystallizing a protein with compound and would like to know how much
of compound to add to protein solution to start with. I know that the protein
binds compound in a 1 to 1 ratio but also noticed that the compound
precipitates out of solution when DMSO is diluted off. Where shoul
My Friends:
Thank you all, I'll consider your advice!
Best Wishes!
Rain Field
Hi -
You should not use literature as proof; every protein is different.
You would need to do site directed mutagenesis experiments,
to show which binding mode is relevant.
I am also not sure what 'completely different' means, if the ligands
are in different sites,
it could also be of interes
Thank you for your valuable advice.
My situation is this:
I got two completely different structures by soaking and co-crystallization.
I believe co-crystallization. But I don't know if I can find the literature
which I would cite as a proof.
Rain Field
Behalf Of Jürgen
Bosch
Sent: Saturday, May 15, 2010 6:42 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] co-crystallization VS crystal soaking
Hi Rain,
try both is my advice.
In some cases we (www.sgpp.org) were unsuccessful in soaking but successful
in co-crystallization. I assume your
Hi Rain,
try both is my advice.
In some cases we (www.sgpp.org) were unsuccessful in soaking but successful in
co-crystallization. I assume your question is directed towards ligands. If you
are in the comfortable situation of having your own structure at hand, check
out a) crystal lattice conta
Hi, friends:
Is there any published paper describing the case study of the difference
between co-crystallization and crystal soaking?
I mean has anybody observed different structures by these two methods?
Thank you!
Hi, friends:
Is there any published paper describing the case study of the difference
between co-crystallization and crystal soaking?
I mean has anybody observed different structures by these two methods?
Thank you!
Rain Fieldcn
2010-05-15
Just to be a pedantic pain - Km is not necessarily Kd. I
think that assumption only holds if the chemical step
following substrate binding is rate-limiting.
Phoebe
Original message
>Date: Mon, 1 Dec 2008 15:34:59 +0100
>From: mesters <[EMAIL PROTECTED]>
>Subject:
mesters wrote:
Yes!, there is:
the fraction of occupied protein with substance can be calculated: S /
(S + Km) with S being the concentration of the compound.
So, if S = Km, half of the sites are occupied (it follows from
Michaelis-Menten theory).
But- one warning (perhaps obvious but I th
you solve the structure.
- Original Message -
From: "Juergen Bosch" <[EMAIL PROTECTED]>
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, December 1, 2008 6:35:24 AM GMT -08:00 US/Canada Pacific
Subject: Re: [ccp4bb] co-crystallization
The Km changes with your reservoir, so predict
The Km changes with your reservoir, so predictions are limited. In
general if you have a low Km this is favourable but not a given that
your ligand will be found in the electron density map. As a starting
point try a molar ratio of >3 of the ligand to your protein and you
can go as high as
Yes!, there is:
the fraction of occupied protein with substance can be calculated: S /
(S + Km) with S being the concentration of the compound.
So, if S = Km, half of the sites are occupied (it follows from
Michaelis-Menten theory).
In order to saturate the enzyme for 90,90909 % with the co
Hello,everyone,
I have a question for cocrystallization, is there some relationship between Km
value and substrate concentration when making cocrystallization? How can I know
the substrate is enough for binding?
Thank you very much!
liuqing
___
) take place in a very
viscous environment (high PEG, high salt concentration)
George
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Joern
Krausze
Sent: Friday, November 28, 2008 4:40 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Co-crystallization
TECTED] On Behalf Of
Priya Mudgal
Sent: Thursday, November 27, 2008 11:09 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Co-crystallization
Dear All,
I am trying to co-crystallize a protein with substrate/substrate analogue
and for some reason it is not working. I have tried to co-crysta
May be you have to try different conditions
George
_
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Priya
Mudgal
Sent: Thursday, November 27, 2008 11:09 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Co-crystallization
Dear All,
I am trying to co-crystallize a prot
Dear All,
I am trying to co-crystallize a protein with substrate/substrate analogue
and for some reason it is not working. I have tried to co-crystallize with
upto 2 mM substrate and it does not bind. The protein precipitates out if I
go higher concentration. Soaking does not work either. Is th
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