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 <[email protected]> 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 <[email protected]> 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 > [email protected] -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: [email protected] *******************************************
