Hi Jacob: After giving this a great deal of reflection ….. I realized that you would face the same paradox that God had to resolve six thousand years ago at the Dawn of Creation, i.e., He needed D-deoxyribose DNA to code for L-amino acid proteins, and vice versa. Likewise, you would probably be faced with a situation where you need L-deoxyribose DNA to code for D-amino acid proteins, so once again, you need a ribozyme self-replicase to escape the Irreducible Complexity(™). (The Central Dogma at least is achiral.)
At least it can be done six thousand years, which isn't unreasonable for a Ph.D. thesis project (especially when combined with an M.D.), and you, unlike Him, have access to a Sigma catalogue. All the best, Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA On Feb 15, 2012, at 10:28 AM, Jacob Keller wrote: > 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 <dj...@cornell.edu> 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 <dj...@cornell.edu> 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 >> schul...@cornell.edu > > > > -- > ******************************************* > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > email: j-kell...@northwestern.edu > *******************************************
