So who out there wants to start an all-D microbial culture by total
synthesis, a la the bacterium with the synthetic genome a while back?
Could it work, I wonder? I guess that would be a certain benchmark for
Man's conquest of nature.
JPK
ps maybe if there is a broadly-acting amino-acid isomerase or set of
isomerases of appropriate properties, this could be helpful for
getting the culture started--or even for preying on the L world?
On Wed, Feb 15, 2012 at 12:17 PM, David Schuller <[log in to unmask]> wrote:
> On 02/15/12 12:41, Jacob Keller wrote:
>
> Are there any all-D proteins out there, of known structure or
> otherwise? If so, do enantiomer-specific catalyses become inverted?
>
> JPK
>
> What do you mean by "Out There"? If you mean in the PDB, then yes. As of
> two weeks ago, there are ~ 14 racemic structures deposited; most in space
> group P -1, with one outlier in space group I -4 C 2. This includes RNA,
> DNA, and PNA, but 6 entries are actually protein. The longest is over 80
> residues.
>
> Theoretically, enantiomer-specific catalysis ought to be inverted, but most
> of the structures solved are not enzymes. kaliotoxin, plectasin, antifreeze
> protein, monellin, villin, and a designed peptide.
>
> On the other hand, if by "out there" you meant in nature outside of
> biochemistry and organic chemistry labs; then no, I am not aware of any
> all-D proteins. There are a few protein/peptides which include a small
> number of D-residues, which is marked up to nonribosomal synthesis.
>
> The first paper I managed to Google:
> http://jb.asm.org/content/185/24/7036.full
> Learning from Nature's Drug Factories: Nonribosomal Synthesis of Macrocyclic
> Peptides
> doi: 10.1128/JB.185.24.7036-7043.2003 J. Bacteriol. December 2003 vol. 185
> no. 24 7036-7043
>
> If racemic crystallization isn't exciting enough for you, look into
> quasi-racemic crystallization.
>
>
> On Wed, Feb 15, 2012 at 8:05 AM, David Schuller <[log in to unmask]> wrote:
>
> Wukovitz & Yeates (1995) Nature Struc. Biol. 2(12): 1062-1067
> predicts that the most probable space group for macromolecular
> crystallization is P -1 (P 1-bar). All you have to do to try it out is
> synthesize the all-D enantiomer of your protein and get it to fold properly.
>
>
> On 02/14/12 18:36, Prem Kaushal wrote:
>
>
> Hi
>
> We have a protein that crystallized in P21212 space group. We are looking
> for some different crystal forms. We tried few things did not work. Now we
> are thinking to mutate surface residues. Anybody aware of any software which
> can predict the mutations that might help in crystallizing protein in
> different space group, please inform me.
>
> Thanks in advance
>
> Prem
>
>
> --
> =======================================================================
> All Things Serve the Beam
> =======================================================================
> David J. Schuller
> modern man in a post-modern world
> MacCHESS, Cornell University
> [log in to unmask]
--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: [log in to unmask]
*******************************************
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