] On Behalf Of James
Holton
Sent: Friday, November 19, 2010 9:20 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] relationship between B factors and Koff
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
,
Herman
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of James
Holton
Sent: Friday, November 19, 2010 9:20 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] relationship between B factors and Koff
I don't think there is any
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
...@onid.orst.edu
To: CCP4BB@JISCMAIL.AC.UK
Sent: Friday, November 19, 2010 7:32 AM
Subject: Re: [ccp4bb] relationship between B factors and Koff
Hi Sebastiano,
I have had some experience with protein:protein complexes with KD ~
10-1 uM, kinetic characterization and trying to purify a complex
.
Best, Herman
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jacob
Keller
Sent: Friday, November 19, 2010 3:01 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] relationship between B factors and Koff
A suggestion for purifying the complex
] On Behalf Of Jacob
Keller
Sent: Friday, November 19, 2010 3:01 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] relationship between B factors and Koff
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
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
Message -
From: Justin Hall hallj...@onid.orst.edu
To: CCP4BB@JISCMAIL.AC.UK
Sent: Friday, November 19, 2010 7:32 AM
Subject: Re: [ccp4bb] relationship between B factors and Koff
Hi Sebastiano,
I have had some experience with protein:protein complexes with KD ~
10-1 uM, kinetic
:57 PM
To: Schreuder, Herman RD/DE
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] relationship between B factors and Koff
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
To: Schreuder, Herman RD/DE
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] relationship between B factors and Koff
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
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] relationship between B factors and Koff
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
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
proteins with
immobilized Escherichia coli RNA polymerase. J Mol Biol 88(2):373-383.
JPK
- Original Message -
From: Tanner, John J. tanne...@missouri.edu
To: CCP4BB@JISCMAIL.AC.UK
Sent: Friday, November 19, 2010 11:25 AM
Subject: Re: [ccp4bb] relationship between B factors and Koff
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 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
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