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[ccp4bb]: SUMMARY - Examples of pH affecting ligand conformation wanted
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Dear CCP4 mailing listees,
Below is a summary of the replies I have received to date. Thanks to all who
responded !! (Since all the replies came from CCP4 mailing listees, I will
only send the summary to this mailing list.)
--Gerard
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Original question:
> Does anybody know of any published example of a case where pH affects the
> observed conformation of a cocrystallised ligand ? I.e., the same ligand in
> complex with the same protein assumes different conformations at different
> pH levels.
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From: Ingo P. Korndoerfer <ingo@wzw.tum.de>
possibly streptavidin ? i think there were some structures at nonphysiological
ph of 4.5 done, that were different from the structures at ph=8. would have to
look up the details, though. not sure whether ligand or protein conformation
were affected, either (sorry ... :-( ).
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From: "Bussiere, Dirksen" <Dirksen_Bussiere@chiron.com>
I have seen a fairly potent (low Ki, nanomolar) which bound differently at
different pH's. The difference was one complex was at pH 5.5-6.0; the other
at pH 7.5. Unfortunately, none of this was ever published, nor is it likely to
be published in the future.
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From: Markus Rudolph <Markus.Rudolph@bio.uni-goettingen.de>
not exactly a conformational change, but ALFx (x=3 or 4) is dependent on pH.
Published by Schlichting and Reinstein, NSB on UMP kinase. And as AlF3 is
planar and AlF4 tetragonal this might be of interest to you? Sorry if this is
not related to what you're after.
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From: Thomas Stout <tstout@exelixis.com>
The closest thing that comes to mind off the top of my head is:
J Biol Chem 1997 May 16;272(20):13220-8 Katz BA, Cass RT.
"In crystals of complexes of streptavidin with peptide ligands containing the
HPQ sequence the pKa of the peptide histidine is less than 3.0."
They don't show dramatic alternate modes of binding at differing pH's or
anything like that, but they did study the same protein-ligand complexes at a
number of differing pH's........
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From: Anthony Duff <A.Duff@staff.usyd.edu.au>
Probably this is not a suitable example, but... Rubisco and CABP. At the
wrong pH, lys201 does not carbamylate, Mg++ does not bind, and CABP binds in
an alternate, inhibitory manner.
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From: Doreen Dobritzsch <doreen@alfa.mbb.ki.se>
it's maybe not exactly what you are looking for, more a case of partially
flexible NADPH at one pH vs. defined NADPH conformation at another pH:
Dobritzsch et al. (2002) J. Biol. Chem. 277, pp. 13155-13166. "Crystal
Structure of the Productive Ternary Complex of Dihydropyrimidine Dehydrogenase
with NADPH and 5-Iodouracil"
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From: Leslie A. <andrew@mrc-lmb.cam.ac.uk>
This is not really pertinent to the question that you asked, but may (?) be of
interest anyway. AlF inhibited NTPases bind either AlF3 or AlF4 in a manner
that seems to depend on pH. There is one example (known to me) where the same
enzyme was crystallised at different pH's and indeed AlF3 was present in one
case and AlF4 in the other. If this is of interest I can find the reference
without too much trouble, just let me know.
--------------------------------------------------------------
From: Leo James <lcj@mrc-lmb.cam.ac.uk>
I dont know of any examples where ligands have been crystallised in different
pH dependent states, but this I think is an interesting related reference:
Hakasako M, Takahashi H, Shimba N, Shimada I, Arata Y. The pH-dependent
structural variation of complementarity-determining region H3 in the crystal
structures of the Fv fragment from an anti-dansyl monoclonal antibody. J Mol
Biol. 1999 Aug 6;291(1):117-34.
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From: I.Schlichting <ilme.schlichting@mpi-dortmund.mpg.de>
an example is:
Schlichting I. Reinstein J. pH influences fluoride coordination number of the
AlFx phosphoryl transfer transition state analog. [Journal Article] Nature
Structural Biology. 6(8):721-3, 1999 Aug. UI: 10426946
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From: Jens Kaiser <kaiser@biochem.mpg.de>
have a look at this one:
pH-dependent binding modes observed in trypsin crystals: Lessons for
structure-based drug design Stubbs MT, Reyda S, Dullweber F, Moller M, Klebe
G, Dorsch D, Mederski WWKR, Wurziger H CHEMBIOCHEM 3 (2-3): 246-249 MAR 1 2002
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From: Sue Cutfield <suemc@sanger.otago.ac.nz>
See Cutfield et al, Structure (1995), 3:1261-1271 (1EAG)
& Abad-Zapatero et al, Protein Science (1996), 5:640-652 (1ZAP)
We did the structure of a Candida albicans aspartic proteinase complexed with
an Abbott inhibitor at pH 4.5, then Abbott published the same, at pH 6.5.
There is a very clear conformational difference in a piperazine ring - good
density and not the disorder that I've seen with other less effective
inhibitors (unpublished!). We also had crystals at pH 6.5 but they were
inferior to those grown at the lower pH, closer to the optimal pH of activity.
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******************************************************************
Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:gerard@xray.bmc.uu.se
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